3MQT

Crystal structure of a mandelate racemase/muconate lactonizing enzyme from Shewanella pealeana

PDB DOI: https://doi.org/10.2210/pdb3MQT/pdb

Classification: ISOMERASE
Organism(s): Shewanella pealeana ATCC 700345
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-04-28 Released: 2010-05-12
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.213
R-Value Work: 0.185
R-Value Observed: 0.186

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal STRUCTURE OF A MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME FROM SHEWANELLA PEALEANA

Agarwal, R., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 1,068.04 kDa
Atom Count: 72,942
Modelled Residue Count: 9,063
Deposited Residue Count: 9,456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	394	Shewanella pealeana ATCC 700345	Mutation(s): 0 Gene Names: Spea_3246
UniProt
Find proteins for A8H7M5 (Shewanella pealeana (strain ATCC 700345 / ANG-SQ1)) Explore A8H7M5 Go to UniProtKB: A8H7M5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8H7M5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth F] SDF format, chain CA [auth G] SDF format, chain DA [auth H] SDF format, chain EA [auth K] SDF format, chain FA [auth L] SDF format, chain GA [auth U] SDF format, chain HA [auth V] SDF format, chain IA [auth W] SDF format, chain JA [auth X] SDF format, chain Y [auth A] SDF format, chain Z [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain GA [auth U] MOL2 format, chain HA [auth V] MOL2 format, chain IA [auth W] MOL2 format, chain JA [auth X] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain EA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain GA [auth U] mmCIF format, chain HA [auth V] mmCIF format, chain IA [auth W] mmCIF format, chain JA [auth X] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth D]	AA [auth E] BA [auth F] CA [auth G] DA [auth H] EA [auth K] AA [auth E], BA [auth F], CA [auth G], DA [auth H], EA [auth K], FA [auth L], GA [auth U], HA [auth V], IA [auth W], JA [auth X], Y [auth A], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth U] Focus chain HA [auth V] Focus chain IA [auth W] Focus chain JA [auth X] Focus chain Y [auth A] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth U] Focus chain HA [auth V] Focus chain IA [auth W] Focus chain JA [auth X] Focus chain Y [auth A] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.213
R-Value Work: 0.185
R-Value Observed: 0.186
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.164	α = 98.47
b = 146.142	β = 96.8
c = 158.71	γ = 105.04

Software Package:

Software Name	Purpose
CBASS	data collection
CCP4	model building
MOLREP	phasing
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Agarwal, R.

Burley, S.K.

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description