4IHC | pdb_00004ihc

Crystal structure of probable mannonate dehydratase Dd703_0947 (target EFI-502222) from Dickeya dadantii Ech703

PDB DOI: https://doi.org/10.2210/pdb4IHC/pdb

Classification: ISOMERASE
Organism(s): Musicola paradisiaca Ech703
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-12-18 Released: 2013-01-16
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N.F., Stead, M., Love, J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.228 (Depositor), 0.228 (DCC)
R-Value Work:
0.173 (Depositor)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of mannonate dehydratase Dd703_0947 from Dickeya dadantii Ech703

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N.F., Stead, M., Love, J., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 395.76 kDa
Atom Count: 26,763
Modeled Residue Count: 3,162
Deposited Residue Count: 3,520
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A, B, C, D, E A, B, C, D, E, F, G, H	440	Musicola paradisiaca Ech703	Mutation(s): 0 Gene Names: Dd703_0947 EC: 4.2.1 (UniProt), 4.2.1.8 (UniProt), 4.2.1.39 (UniProt)
UniProt
Find proteins for C6CBG9 (Musicola paradisiaca (strain Ech703)) Explore C6CBG9 Go to UniProtKB: C6CBG9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6CBG9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain NB [auth H] SDF format, chain SA [auth E] SDF format, chain V [auth B] SDF format, chain YA [auth F] SDF format, chain U [auth B] SDF format, chain TA [auth E] SDF format, chain T [auth B] SDF format, chain RA [auth E] SDF format, chain OB [auth H] SDF format, chain N [auth A] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KA [auth D] SDF format, chain IA [auth D] SDF format, chain DA [auth C] SDF format, chain CB [auth F] SDF format, chain AA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain NB [auth H] MOL2 format, chain SA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain OB [auth H] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain AA [auth C] mmCIF format, chain AB [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain NB [auth H] mmCIF format, chain SA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain OB [auth H] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain AA [auth C]	AA [auth C] AB [auth F] BA [auth C] CB [auth F] DA [auth C] AA [auth C], AB [auth F], BA [auth C], CB [auth F], DA [auth C], IA [auth D], KA [auth D], L [auth A], LA [auth D], N [auth A], NB [auth H], OB [auth H], RA [auth E], SA [auth E], T [auth B], TA [auth E], U [auth B], V [auth B], YA [auth F]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain IA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain N [auth A] Focus chain NB [auth H] Focus chain OB [auth H] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain YA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain IA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain N [auth A] Focus chain NB [auth H] Focus chain OB [auth H] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain YA [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain J [auth A] SDF format, chain JB [auth H] SDF format, chain LB [auth H] SDF format, chain X [auth C] SDF format, chain VA [auth F] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain NA [auth E] SDF format, chain M [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain EB [auth G] SDF format, chain CA [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth H] MOL2 format, chain LB [auth H] MOL2 format, chain X [auth C] MOL2 format, chain VA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain EB [auth G] MOL2 format, chain CA [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth H] mmCIF format, chain LB [auth H] mmCIF format, chain X [auth C] mmCIF format, chain VA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain EB [auth G] mmCIF format, chain CA [auth C]	BB [auth F] CA [auth C] EB [auth G] FA [auth D] GA [auth D] BB [auth F], CA [auth C], EB [auth G], FA [auth D], GA [auth D], J [auth A], JB [auth H], LB [auth H], M [auth A], NA [auth E], P [auth B], R [auth B], VA [auth F], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain CA [auth C] Focus chain EB [auth G] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain JB [auth H] Focus chain LB [auth H] Focus chain M [auth A] Focus chain NA [auth E] Focus chain P [auth B] Focus chain R [auth B] Focus chain VA [auth F] Focus chain X [auth C] Interactions & Density Focus chain BB [auth F] Focus chain CA [auth C] Focus chain EB [auth G] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain JB [auth H] Focus chain LB [auth H] Focus chain M [auth A] Focus chain NA [auth E] Focus chain P [auth B] Focus chain R [auth B] Focus chain VA [auth F] Focus chain X [auth C]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain ZA [auth F] SDF format, chain Y [auth C] SDF format, chain WA [auth F] SDF format, chain S [auth B] SDF format, chain QA [auth E] SDF format, chain MB [auth H] SDF format, chain K [auth A] SDF format, chain JA [auth D] SDF format, chain HB [auth G] MOL2 format, chain ZA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain WA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain MB [auth H] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain HB [auth G] mmCIF format, chain ZA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain WA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain MB [auth H] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain HB [auth G]	HB [auth G] JA [auth D] K [auth A] MB [auth H] QA [auth E] HB [auth G], JA [auth D], K [auth A], MB [auth H], QA [auth E], S [auth B], WA [auth F], Y [auth C], ZA [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain HB [auth G] Focus chain JA [auth D] Focus chain K [auth A] Focus chain MB [auth H] Focus chain QA [auth E] Focus chain S [auth B] Focus chain WA [auth F] Focus chain Y [auth C] Focus chain ZA [auth F] Interactions & Density Focus chain HB [auth G] Focus chain JA [auth D] Focus chain K [auth A] Focus chain MB [auth H] Focus chain QA [auth E] Focus chain S [auth B] Focus chain WA [auth F] Focus chain Y [auth C] Focus chain ZA [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain KB [auth H] SDF format, chain Z [auth C] SDF format, chain XA [auth F] SDF format, chain Q [auth B] SDF format, chain PA [auth E] SDF format, chain OA [auth E] SDF format, chain HA [auth D] SDF format, chain GB [auth G] SDF format, chain FB [auth G] MOL2 format, chain KB [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain XA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain HA [auth D] MOL2 format, chain GB [auth G] MOL2 format, chain FB [auth G] mmCIF format, chain KB [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain XA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain OA [auth E] mmCIF format, chain HA [auth D] mmCIF format, chain GB [auth G] mmCIF format, chain FB [auth G]	FB [auth G] GB [auth G] HA [auth D] KB [auth H] OA [auth E] FB [auth G], GB [auth G], HA [auth D], KB [auth H], OA [auth E], PA [auth E], Q [auth B], XA [auth F], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FB [auth G] Focus chain GB [auth G] Focus chain HA [auth D] Focus chain KB [auth H] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain XA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain FB [auth G] Focus chain GB [auth G] Focus chain HA [auth D] Focus chain KB [auth H] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain XA [auth F] Focus chain Z [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain UA [auth F] SDF format, chain O [auth B] SDF format, chain MA [auth E] SDF format, chain IB [auth H] SDF format, chain I [auth A] SDF format, chain EA [auth D] SDF format, chain DB [auth G] MOL2 format, chain W [auth C] MOL2 format, chain UA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain MA [auth E] MOL2 format, chain IB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth G] mmCIF format, chain W [auth C] mmCIF format, chain UA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain MA [auth E] mmCIF format, chain IB [auth H] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth G]	DB [auth G] EA [auth D] I [auth A] IB [auth H] MA [auth E] DB [auth G], EA [auth D], I [auth A], IB [auth H], MA [auth E], O [auth B], UA [auth F], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DB [auth G] Focus chain EA [auth D] Focus chain I [auth A] Focus chain IB [auth H] Focus chain MA [auth E] Focus chain O [auth B] Focus chain UA [auth F] Focus chain W [auth C] Interactions & Density Focus chain DB [auth G] Focus chain EA [auth D] Focus chain I [auth A] Focus chain IB [auth H] Focus chain MA [auth E] Focus chain O [auth B] Focus chain UA [auth F] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.228 (Depositor), 0.228 (DCC)
R-Value Work: 0.173 (Depositor)
R-Value Observed: 0.175 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.331	α = 90
b = 224.347	β = 97.96
c = 87.076	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-01-16

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-01-16
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description