2RDX | pdb_00002rdx

Crystal structure of mandelate racemase/muconate lactonizing enzyme from Roseovarius nubinhibens ISM

PDB DOI: https://doi.org/10.2210/pdb2RDX/pdb
Entry: 2RDX supersedes: 2QYE

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Roseovarius nubinhibens ISM
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-09-25 Released: 2007-10-09
Deposition Author(s): Patskovsky, Y., Bonanno, J., Sauder, J.M., Ozyurt, S., Gilmore, M., Lau, C., Maletic, M., Gheyi, T., Wasserman, S.R., Koss, J., Gerlt, J.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.256 (Depositor), 0.255 (DCC)
R-Value Work:
0.194 (Depositor), 0.197 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of mandelate racemase/muconate lactonizing enzyme from Roseovarius nubinhibens ISM.

Patskovsky, Y., Bonanno, J.B., Sauder, J.M., Gilmore, M., Ozyurt, S., Lau, C., Maletic, M., Gheyi, T., Wasserman, S.R., Koss, J., Gerlt, J.A., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 334.09 kDa
Atom Count: 23,975
Modeled Residue Count: 2,943
Deposited Residue Count: 3,032
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, putative	A, B, C, D, E A, B, C, D, E, F, G, H	379	Roseovarius nubinhibens ISM	Mutation(s): 0 Gene Names: ISM_14070
UniProt
Find proteins for A3SNF8 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM)) Explore A3SNF8 Go to UniProtKB: A3SNF8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3SNF8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth H] SDF format, chain U [auth G] SDF format, chain S [auth F] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain W [auth H] MOL2 format, chain U [auth G] MOL2 format, chain S [auth F] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain W [auth H] mmCIF format, chain U [auth G] mmCIF format, chain S [auth F] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] N [auth C] P [auth D] S [auth F] J [auth A], K [auth A], N [auth C], P [auth D], S [auth F], U [auth G], W [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain V [auth H] SDF format, chain T [auth G] SDF format, chain R [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain V [auth H] MOL2 format, chain T [auth G] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain V [auth H] mmCIF format, chain T [auth G] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A] L [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], L [auth B], M [auth C], O [auth D], Q [auth E], R [auth F], T [auth G], V [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain V [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain V [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.256 (Depositor), 0.255 (DCC)
R-Value Work: 0.194 (Depositor), 0.197 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.415	α = 90
b = 169.219	β = 90
c = 223.476	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-10-09

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

This entry supersedes: 2QYE

Revision History (Full details and data files)

Version 1.0: 2007-10-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references