3RCY | pdb_00003rcy

CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing enzyme-like protein from Roseovarius sp. TM1035

PDB DOI: https://doi.org/10.2210/pdb3RCY/pdb

Classification: ISOMERASE
Organism(s): Roseovarius sp. TM1035
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-03-31 Released: 2011-05-18
Deposition Author(s): Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.181 (Depositor), 0.188 (DCC)
R-Value Work:
0.147 (Depositor), 0.154 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing enzyme-like protein from Roseovarius sp. TM1035

Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 380.56 kDa
Atom Count: 26,806
Modeled Residue Count: 3,166
Deposited Residue Count: 3,464
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 enzyme-like protein	A, B, C, D, E A, B, C, D, E, F, G, H	433	Roseovarius sp. TM1035	Mutation(s): 0 Gene Names: 149202287, RTM1035_13208

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIB Query on RIB Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth G] SDF format, chain M [auth A] SDF format, chain NA [auth H] SDF format, chain P [auth B] SDF format, chain PA [auth H] SDF format, chain Z [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain Z [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain Z [auth D]	CA [auth E] L [auth A] LA [auth G] M [auth A] NA [auth H] CA [auth E], L [auth A], LA [auth G], M [auth A], NA [auth H], P [auth B], PA [auth H], Z [auth D]	alpha-D-ribofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-AIHAYLRMSA-N		Interactions Focus chain CA [auth E] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain NA [auth H] Focus chain P [auth B] Focus chain PA [auth H] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain NA [auth H] Focus chain P [auth B] Focus chain PA [auth H] Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain J [auth A] SDF format, chain JA [auth G] SDF format, chain K [auth A] SDF format, chain KA [auth G] SDF format, chain MA [auth H] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain MA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain MA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	AA [auth E] DA [auth E] FA [auth F] GA [auth G] HA [auth G] AA [auth E], DA [auth E], FA [auth F], GA [auth G], HA [auth G], J [auth A], JA [auth G], K [auth A], KA [auth G], MA [auth H], O [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain J [auth A] Focus chain JA [auth G] Focus chain K [auth A] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain J [auth A] Focus chain JA [auth G] Focus chain K [auth A] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth G] SDF format, chain N [auth B] SDF format, chain OA [auth H] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D]	BA [auth E] EA [auth F] I [auth A] IA [auth G] N [auth B] BA [auth E], EA [auth F], I [auth A], IA [auth G], N [auth B], OA [auth H], S [auth C], V [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain EA [auth F] Focus chain I [auth A] Focus chain IA [auth G] Focus chain N [auth B] Focus chain OA [auth H] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth F] Focus chain I [auth A] Focus chain IA [auth G] Focus chain N [auth B] Focus chain OA [auth H] Focus chain S [auth C] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.181 (Depositor), 0.188 (DCC)
R-Value Work: 0.147 (Depositor), 0.154 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.978	α = 90
b = 162.143	β = 90
c = 141.954	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-05-18

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-05-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary