3P3B | pdb_00003p3b

CRYSTAL STRUCTURE OF Galacturonate DEHYDRATASE FROM GEOBACILLUS SP. COMPLEXED WITH D-TARTRATE

PDB DOI: https://doi.org/10.2210/pdb3P3B/pdb

Classification: LYASE
Organism(s): Paenibacillus sp. Y412MC10
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-10-04 Released: 2011-06-29
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., 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: 1.65 Å
R-Value Free:
0.252 (Depositor), 0.247 (DCC)
R-Value Work:
0.216 (Depositor), 0.214 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

CRYSTAL STRUCTURE OF Galacturonate DEHYDRATASE FROM GEOBACILLUS SP. COMPLEXED WITH D-TARTRATE.

Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., Gerlt, J.A., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 88.24 kDa
Atom Count: 6,208
Modeled Residue Count: 741
Deposited Residue Count: 784
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	392	Paenibacillus sp. Y412MC10	Mutation(s): 0 Gene Names: GYMC10_3367

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAR Query on TAR Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.252 (Depositor), 0.247 (DCC)
R-Value Work: 0.216 (Depositor), 0.214 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.859	α = 90
b = 66.051	β = 95.48
c = 75.664	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-06-29

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2011-06-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-12-14
Changes: Database references, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references