3MI5

Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

PDB DOI: https://doi.org/10.2210/pdb3MI5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-04-09 Released: 2011-04-27
Deposition Author(s): Purpero, V.M., Lipscomb, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.185
R-Value Work: 0.151
R-Value Observed: 0.153

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

Purpero, V.M., Lipscomb, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 302.66 kDa
Atom Count: 24,211
Modelled Residue Count: 2,628
Deposited Residue Count: 2,628
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocatechuate 3,4-dioxygenase alpha chain	A C [auth B] E [auth C] G [auth D] I [auth E] A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	200	Pseudomonas putida	Mutation(s): 0 Gene Names: pcaG EC: 1.13.11.3
UniProt
Find proteins for P00436 (Pseudomonas putida) Explore P00436 Go to UniProtKB: P00436
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00436
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocatechuate 3,4-dioxygenase beta chain	B [auth M] D [auth N] F [auth O] H [auth P] J [auth Q] B [auth M], D [auth N], F [auth O], H [auth P], J [auth Q], L [auth R]	238	Pseudomonas putida	Mutation(s): 2 Gene Names: pcaH EC: 1.13.11.3
UniProt
Find proteins for P00437 (Pseudomonas putida) Explore P00437 Go to UniProtKB: P00437
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00437
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAQ Query on CAQ Download Ideal Coordinates CCD File SDF format, chain CC [auth P] SDF format, chain DA [auth M] SDF format, chain HD [auth R] SDF format, chain IB [auth O] SDF format, chain KA [auth B] SDF format, chain KC [auth E] SDF format, chain RC [auth Q] SDF format, chain S [auth A] SDF format, chain SA [auth N] SDF format, chain TB [auth D] SDF format, chain ZA [auth C] SDF format, chain ZC [auth F] MOL2 format, chain CC [auth P] MOL2 format, chain DA [auth M] MOL2 format, chain HD [auth R] MOL2 format, chain IB [auth O] MOL2 format, chain KA [auth B] MOL2 format, chain KC [auth E] MOL2 format, chain RC [auth Q] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth N] MOL2 format, chain TB [auth D] MOL2 format, chain ZA [auth C] MOL2 format, chain ZC [auth F]	CC [auth P] DA [auth M] HD [auth R] IB [auth O] KA [auth B] CC [auth P], DA [auth M], HD [auth R], IB [auth O], KA [auth B], KC [auth E], RC [auth Q], S [auth A], SA [auth N], TB [auth D], ZA [auth C], ZC [auth F]	CATECHOL C₆ H₆ O₂ YCIMNLLNPGFGHC-UHFFFAOYSA-N		Interactions Focus chain CC [auth P] Focus chain DA [auth M] Focus chain HD [auth R] Focus chain IB [auth O] Focus chain KA [auth B] Focus chain KC [auth E] Focus chain RC [auth Q] Focus chain S [auth A] Focus chain SA [auth N] Focus chain TB [auth D] Focus chain ZA [auth C] Focus chain ZC [auth F] Interactions & Density Focus chain CC [auth P] Focus chain DA [auth M] Focus chain HD [auth R] Focus chain IB [auth O] Focus chain KA [auth B] Focus chain KC [auth E] Focus chain RC [auth Q] Focus chain S [auth A] Focus chain SA [auth N] Focus chain TB [auth D] Focus chain ZA [auth C] Focus chain ZC [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BC [auth P] SDF format, chain CB [auth O] SDF format, chain EC [auth E] SDF format, chain FA [auth B] SDF format, chain GD [auth R] SDF format, chain M [auth A] SDF format, chain MB [auth D] SDF format, chain NA [auth N] SDF format, chain NC [auth Q] SDF format, chain QC [auth Q] SDF format, chain UA [auth C] SDF format, chain UC [auth F] MOL2 format, chain BC [auth P] MOL2 format, chain CB [auth O] MOL2 format, chain EC [auth E] MOL2 format, chain FA [auth B] MOL2 format, chain GD [auth R] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain NA [auth N] MOL2 format, chain NC [auth Q] MOL2 format, chain QC [auth Q] MOL2 format, chain UA [auth C] MOL2 format, chain UC [auth F]	BC [auth P] CB [auth O] EC [auth E] FA [auth B] GD [auth R] BC [auth P], CB [auth O], EC [auth E], FA [auth B], GD [auth R], M [auth A], MB [auth D], NA [auth N], NC [auth Q], QC [auth Q], UA [auth C], UC [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BC [auth P] Focus chain CB [auth O] Focus chain EC [auth E] Focus chain FA [auth B] Focus chain GD [auth R] Focus chain M [auth A] Focus chain MB [auth D] Focus chain NA [auth N] Focus chain NC [auth Q] Focus chain QC [auth Q] Focus chain UA [auth C] Focus chain UC [auth F] Interactions & Density Focus chain BC [auth P] Focus chain CB [auth O] Focus chain EC [auth E] Focus chain FA [auth B] Focus chain GD [auth R] Focus chain M [auth A] Focus chain MB [auth D] Focus chain NA [auth N] Focus chain NC [auth Q] Focus chain QC [auth Q] Focus chain UA [auth C] Focus chain UC [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain PC [auth Q] SDF format, chain WC [auth F] SDF format, chain XB [auth P] SDF format, chain XC [auth F] SDF format, chain AA [auth M] SDF format, chain AB [auth C] SDF format, chain CD [auth R] SDF format, chain DB [auth O] SDF format, chain EB [auth O] SDF format, chain ED [auth R] SDF format, chain FC [auth E] SDF format, chain FD [auth R] SDF format, chain GB [auth O] SDF format, chain GC [auth E] SDF format, chain HA [auth B] SDF format, chain HB [auth O] SDF format, chain IC [auth E] SDF format, chain JA [auth B] SDF format, chain JC [auth E] SDF format, chain LA [auth B] SDF format, chain O [auth A] SDF format, chain OB [auth D] SDF format, chain OC [auth Q] SDF format, chain P [auth A] SDF format, chain PA [auth N] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth N] SDF format, chain RB [auth D] SDF format, chain SC [auth Q] SDF format, chain T [auth A] SDF format, chain V [auth M] SDF format, chain VA [auth C] SDF format, chain VC [auth F] SDF format, chain W [auth M] SDF format, chain WA [auth C] SDF format, chain WB [auth P] SDF format, chain XA [auth C] SDF format, chain Z [auth M] SDF format, chain ZB [auth P] MOL2 format, chain PC [auth Q] MOL2 format, chain WC [auth F] MOL2 format, chain XB [auth P] MOL2 format, chain XC [auth F] MOL2 format, chain AA [auth M] MOL2 format, chain AB [auth C] MOL2 format, chain CD [auth R] MOL2 format, chain DB [auth O] MOL2 format, chain EB [auth O] MOL2 format, chain ED [auth R] MOL2 format, chain FC [auth E] MOL2 format, chain FD [auth R] MOL2 format, chain GB [auth O] MOL2 format, chain GC [auth E] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth O] MOL2 format, chain IC [auth E] MOL2 format, chain JA [auth B] MOL2 format, chain JC [auth E] MOL2 format, chain LA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth D] MOL2 format, chain OC [auth Q] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth N] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth N] MOL2 format, chain RB [auth D] MOL2 format, chain SC [auth Q] MOL2 format, chain T [auth A] MOL2 format, chain V [auth M] MOL2 format, chain VA [auth C] MOL2 format, chain VC [auth F] MOL2 format, chain W [auth M] MOL2 format, chain WA [auth C] MOL2 format, chain WB [auth P] MOL2 format, chain XA [auth C] MOL2 format, chain Z [auth M] MOL2 format, chain ZB [auth P]	AA [auth M] AB [auth C] CD [auth R] DB [auth O] EB [auth O] AA [auth M], AB [auth C], CD [auth R], DB [auth O], EB [auth O], ED [auth R], FC [auth E], FD [auth R], GB [auth O], GC [auth E], HA [auth B], HB [auth O], IC [auth E], JA [auth B], JC [auth E], LA [auth B], O [auth A], OB [auth D], OC [auth Q], P [auth A], PA [auth N], PB [auth D], PC [auth Q], Q [auth A], QB [auth D], R [auth A], RA [auth N], RB [auth D], SC [auth Q], T [auth A], V [auth M], VA [auth C], VC [auth F], W [auth M], WA [auth C], WB [auth P], WC [auth F], XA [auth C], XB [auth P], XC [auth F], Z [auth M], ZB [auth P]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain AB [auth C] Focus chain CD [auth R] Focus chain DB [auth O] Focus chain EB [auth O] Focus chain ED [auth R] Focus chain FC [auth E] Focus chain FD [auth R] Focus chain GB [auth O] Focus chain GC [auth E] Focus chain HA [auth B] Focus chain HB [auth O] Focus chain IC [auth E] Focus chain JA [auth B] Focus chain JC [auth E] Focus chain LA [auth B] Focus chain O [auth A] Focus chain OB [auth D] Focus chain OC [auth Q] Focus chain P [auth A] Focus chain PA [auth N] Focus chain PB [auth D] Focus chain PC [auth Q] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth N] Focus chain RB [auth D] Focus chain SC [auth Q] Focus chain T [auth A] Focus chain V [auth M] Focus chain VA [auth C] Focus chain VC [auth F] Focus chain W [auth M] Focus chain WA [auth C] Focus chain WB [auth P] Focus chain WC [auth F] Focus chain XA [auth C] Focus chain XB [auth P] Focus chain XC [auth F] Focus chain Z [auth M] Focus chain ZB [auth P] Interactions & Density Focus chain AA [auth M] Focus chain AB [auth C] Focus chain CD [auth R] Focus chain DB [auth O] Focus chain EB [auth O] Focus chain ED [auth R] Focus chain FC [auth E] Focus chain FD [auth R] Focus chain GB [auth O] Focus chain GC [auth E] Focus chain HA [auth B] Focus chain HB [auth O] Focus chain IC [auth E] Focus chain JA [auth B] Focus chain JC [auth E] Focus chain LA [auth B] Focus chain O [auth A] Focus chain OB [auth D] Focus chain OC [auth Q] Focus chain P [auth A] Focus chain PA [auth N] Focus chain PB [auth D] Focus chain PC [auth Q] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth N] Focus chain RB [auth D] Focus chain SC [auth Q] Focus chain T [auth A] Focus chain V [auth M] Focus chain VA [auth C] Focus chain VC [auth F] Focus chain W [auth M] Focus chain WA [auth C] Focus chain WB [auth P] Focus chain WC [auth F] Focus chain XA [auth C] Focus chain XB [auth P] Focus chain XC [auth F] Focus chain Z [auth M] Focus chain ZB [auth P]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain VB [auth P] SDF format, chain Y [auth M] SDF format, chain AC [auth P] SDF format, chain AD [auth F] SDF format, chain BA [auth M] SDF format, chain DC [auth P] SDF format, chain DD [auth R] SDF format, chain EA [auth M] SDF format, chain FB [auth O] SDF format, chain GA [auth B] SDF format, chain HC [auth E] SDF format, chain IA [auth B] SDF format, chain JB [auth O] SDF format, chain JD [auth R] SDF format, chain LB [auth O] SDF format, chain LC [auth E] SDF format, chain N [auth A] SDF format, chain NB [auth D] SDF format, chain OA [auth N] SDF format, chain QA [auth N] SDF format, chain SB [auth D] SDF format, chain X [auth M] SDF format, chain YA [auth C] SDF format, chain YB [auth P] SDF format, chain YC [auth F] MOL2 format, chain VB [auth P] MOL2 format, chain Y [auth M] MOL2 format, chain AC [auth P] MOL2 format, chain AD [auth F] MOL2 format, chain BA [auth M] MOL2 format, chain DC [auth P] MOL2 format, chain DD [auth R] MOL2 format, chain EA [auth M] MOL2 format, chain FB [auth O] MOL2 format, chain GA [auth B] MOL2 format, chain HC [auth E] MOL2 format, chain IA [auth B] MOL2 format, chain JB [auth O] MOL2 format, chain JD [auth R] MOL2 format, chain LB [auth O] MOL2 format, chain LC [auth E] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain OA [auth N] MOL2 format, chain QA [auth N] MOL2 format, chain SB [auth D] MOL2 format, chain X [auth M] MOL2 format, chain YA [auth C] MOL2 format, chain YB [auth P] MOL2 format, chain YC [auth F]	AC [auth P] AD [auth F] BA [auth M] DC [auth P] DD [auth R] AC [auth P], AD [auth F], BA [auth M], DC [auth P], DD [auth R], EA [auth M], FB [auth O], GA [auth B], HC [auth E], IA [auth B], JB [auth O], JD [auth R], LB [auth O], LC [auth E], N [auth A], NB [auth D], OA [auth N], QA [auth N], SB [auth D], VB [auth P], X [auth M], Y [auth M], YA [auth C], YB [auth P], YC [auth F]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain AC [auth P] Focus chain AD [auth F] Focus chain BA [auth M] Focus chain DC [auth P] Focus chain DD [auth R] Focus chain EA [auth M] Focus chain FB [auth O] Focus chain GA [auth B] Focus chain HC [auth E] Focus chain IA [auth B] Focus chain JB [auth O] Focus chain JD [auth R] Focus chain LB [auth O] Focus chain LC [auth E] Focus chain N [auth A] Focus chain NB [auth D] Focus chain OA [auth N] Focus chain QA [auth N] Focus chain SB [auth D] Focus chain VB [auth P] Focus chain X [auth M] Focus chain Y [auth M] Focus chain YA [auth C] Focus chain YB [auth P] Focus chain YC [auth F] Interactions & Density Focus chain AC [auth P] Focus chain AD [auth F] Focus chain BA [auth M] Focus chain DC [auth P] Focus chain DD [auth R] Focus chain EA [auth M] Focus chain FB [auth O] Focus chain GA [auth B] Focus chain HC [auth E] Focus chain IA [auth B] Focus chain JB [auth O] Focus chain JD [auth R] Focus chain LB [auth O] Focus chain LC [auth E] Focus chain N [auth A] Focus chain NB [auth D] Focus chain OA [auth N] Focus chain QA [auth N] Focus chain SB [auth D] Focus chain VB [auth P] Focus chain X [auth M] Focus chain Y [auth M] Focus chain YA [auth C] Focus chain YB [auth P] Focus chain YC [auth F]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain BB [auth O] SDF format, chain BD [auth R] SDF format, chain MA [auth N] SDF format, chain MC [auth Q] SDF format, chain U [auth M] SDF format, chain UB [auth P] MOL2 format, chain BB [auth O] MOL2 format, chain BD [auth R] MOL2 format, chain MA [auth N] MOL2 format, chain MC [auth Q] MOL2 format, chain U [auth M] MOL2 format, chain UB [auth P]	BB [auth O] BD [auth R] MA [auth N] MC [auth Q] U [auth M] BB [auth O], BD [auth R], MA [auth N], MC [auth Q], U [auth M], UB [auth P]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain BB [auth O] Focus chain BD [auth R] Focus chain MA [auth N] Focus chain MC [auth Q] Focus chain U [auth M] Focus chain UB [auth P] Interactions & Density Focus chain BB [auth O] Focus chain BD [auth R] Focus chain MA [auth N] Focus chain MC [auth Q] Focus chain U [auth M] Focus chain UB [auth P]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth M] SDF format, chain ID [auth R] SDF format, chain KB [auth O] SDF format, chain TA [auth N] SDF format, chain TC [auth Q] MOL2 format, chain CA [auth M] MOL2 format, chain ID [auth R] MOL2 format, chain KB [auth O] MOL2 format, chain TA [auth N] MOL2 format, chain TC [auth Q]	CA [auth M], ID [auth R], KB [auth O], TA [auth N], TC [auth Q]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth M] Focus chain ID [auth R] Focus chain KB [auth O] Focus chain TA [auth N] Focus chain TC [auth Q] Interactions & Density Focus chain CA [auth M] Focus chain ID [auth R] Focus chain KB [auth O] Focus chain TA [auth N] Focus chain TC [auth Q]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.185
R-Value Work: 0.151
R-Value Observed: 0.153
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.543	α = 90
b = 167.995	β = 132.4
c = 128.342	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-04-27

Deposition Author(s):

Purpero, V.M.

Lipscomb, J.D.

Revision History (Full details and data files)

Version 1.0: 2011-04-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Advisory, Refinement description
Version 1.3: 2021-10-06
Changes: Advisory, Database references, Derived calculations
Version 1.4: 2024-02-21
Changes: Data collection