3S4T | pdb_00003s4t

Crystal structure of putative amidohydrolase-2 (EFI-target 500288)from Polaromonas sp. JS666

PDB DOI: https://doi.org/10.2210/pdb3S4T/pdb

Classification: HYDROLASE
Organism(s): Polaromonas sp. JS666
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-05-20 Released: 2011-08-24
Deposition Author(s): Ramagopal, U.A., Toro, R., Girlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.207 (Depositor), 0.220 (DCC)
R-Value Work:
0.175 (Depositor), 0.190 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of putative amidohydrolase-2 (EFI-target 500288)from Polaromonas sp. JS666

Ramagopal, U.A., Toro, R., Girlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 330.86 kDa
Atom Count: 23,306
Modeled Residue Count: 2,606
Deposited Residue Count: 2,784
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase 2	A, B, C, D, E A, B, C, D, E, F, G, H	348	Polaromonas sp. JS666	Mutation(s): 0 Gene Names: Bpro_2061 EC: 4.1.1.103
UniProt
Find proteins for Q12BV1 (Polaromonas sp. (strain JS666 / ATCC BAA-500)) Explore Q12BV1 Go to UniProtKB: Q12BV1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12BV1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain XA [auth G] SDF format, chain WA [auth G] SDF format, chain RA [auth F] SDF format, chain QA [auth F] SDF format, chain Q [auth B] SDF format, chain I [auth A] SDF format, chain DA [auth D] MOL2 format, chain XA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain RA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain XA [auth G] mmCIF format, chain WA [auth G] mmCIF format, chain RA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth D]	DA [auth D] I [auth A] Q [auth B] QA [auth F] RA [auth F] DA [auth D], I [auth A], Q [auth B], QA [auth F], RA [auth F], WA [auth G], XA [auth G]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain I [auth A] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain WA [auth G] Focus chain XA [auth G] Interactions & Density Focus chain DA [auth D] Focus chain I [auth A] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain WA [auth G] Focus chain XA [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain ZA [auth G] SDF format, chain Z [auth C] SDF format, chain YA [auth G] SDF format, chain Y [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain SA [auth F] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain NA [auth E] SDF format, chain MA [auth E] SDF format, chain M [auth A] SDF format, chain LB [auth H] SDF format, chain LA [auth E] SDF format, chain L [auth A] SDF format, chain KB [auth H] SDF format, chain KA [auth E] SDF format, chain K [auth A] SDF format, chain JB [auth H] SDF format, chain J [auth A] SDF format, chain IB [auth H] SDF format, chain HB [auth H] SDF format, chain HA [auth D] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain DB [auth G] SDF format, chain CB [auth G] SDF format, chain BB [auth G] SDF format, chain AB [auth G] MOL2 format, chain ZA [auth G] MOL2 format, chain Z [auth C] MOL2 format, chain YA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain NA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth H] MOL2 format, chain LA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth H] MOL2 format, chain KA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth H] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth H] MOL2 format, chain HB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth G] MOL2 format, chain CB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain AB [auth G] mmCIF format, chain ZA [auth G] mmCIF format, chain Z [auth C] mmCIF format, chain YA [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain NA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth H] mmCIF format, chain LA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth H] mmCIF format, chain KA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth H] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth H] mmCIF format, chain HB [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth G] mmCIF format, chain CB [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain AB [auth G]	AB [auth G] BB [auth G] CB [auth G] DB [auth G] EA [auth D] AB [auth G], BB [auth G], CB [auth G], DB [auth G], EA [auth D], FA [auth D], GA [auth D], HA [auth D], HB [auth H], IB [auth H], J [auth A], JB [auth H], K [auth A], KA [auth E], KB [auth H], L [auth A], LA [auth E], LB [auth H], M [auth A], MA [auth E], NA [auth E], R [auth B], S [auth B], SA [auth F], T [auth B], U [auth B], Y [auth C], YA [auth G], Z [auth C], ZA [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth G] Focus chain BB [auth G] Focus chain CB [auth G] Focus chain DB [auth G] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IB [auth H] Focus chain J [auth A] Focus chain JB [auth H] Focus chain K [auth A] Focus chain KA [auth E] Focus chain KB [auth H] Focus chain L [auth A] Focus chain LA [auth E] Focus chain LB [auth H] Focus chain M [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain Z [auth C] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain BB [auth G] Focus chain CB [auth G] Focus chain DB [auth G] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IB [auth H] Focus chain J [auth A] Focus chain JB [auth H] Focus chain K [auth A] Focus chain KA [auth E] Focus chain KB [auth H] Focus chain L [auth A] Focus chain LA [auth E] Focus chain LB [auth H] Focus chain M [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain Z [auth C] Focus chain ZA [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain VA [auth F] SDF format, chain JA [auth D] SDF format, chain CA [auth C] MOL2 format, chain VA [auth F] MOL2 format, chain JA [auth D] MOL2 format, chain CA [auth C] mmCIF format, chain VA [auth F] mmCIF format, chain JA [auth D] mmCIF format, chain CA [auth C]	CA [auth C], JA [auth D], VA [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain JA [auth D] Focus chain VA [auth F] Interactions & Density Focus chain CA [auth C] Focus chain JA [auth D] Focus chain VA [auth F]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain UA [auth F] SDF format, chain TA [auth F] SDF format, chain PA [auth E] SDF format, chain P [auth A] SDF format, chain OA [auth E] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MB [auth H] SDF format, chain IA [auth D] SDF format, chain GB [auth G] SDF format, chain FB [auth G] SDF format, chain EB [auth G] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain PA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain GB [auth G] MOL2 format, chain FB [auth G] MOL2 format, chain EB [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain TA [auth F] mmCIF format, chain PA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth H] mmCIF format, chain IA [auth D] mmCIF format, chain GB [auth G] mmCIF format, chain FB [auth G] mmCIF format, chain EB [auth G] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] EB [auth G] FB [auth G] GB [auth G] AA [auth C], BA [auth C], EB [auth G], FB [auth G], GB [auth G], IA [auth D], MB [auth H], N [auth A], O [auth A], OA [auth E], P [auth A], PA [auth E], TA [auth F], UA [auth F], V [auth B], W [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EB [auth G] Focus chain FB [auth G] Focus chain GB [auth G] Focus chain IA [auth D] Focus chain MB [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EB [auth G] Focus chain FB [auth G] Focus chain GB [auth G] Focus chain IA [auth D] Focus chain MB [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain V [auth B] Focus chain W [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.207 (Depositor), 0.220 (DCC)
R-Value Work: 0.175 (Depositor), 0.190 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.024	α = 90
b = 151.241	β = 91.96
c = 143.41	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-24

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2011-08-24
Type: Initial release
Version 1.1: 2018-01-31
Changes: Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-10-09
Changes: Structure summary