2GGE | pdb_00002gge

Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme from Bacillus Subtilis complexed with MG++ at 1.8 A

PDB DOI: https://doi.org/10.2210/pdb2GGE/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2006-03-23 Released: 2006-04-18
Deposition Author(s): Malashkevich, V.N., Sauder, J.M., Schwinn, K.D., Emtage, S., Thompson, D.A., Rutter, M.E., Dickey, M., Groshong, C., Bain, K.T., Adams, J.M., Reyes, C., Rooney, I., Powell, A., Boice, A., Gheyi, T., Ozyurt, S., Atwell, S., Wasserman, S.R., Burley, S.K., Sali, A., Babbitt, P., Pieper, U., Gerlt, J.A., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.253 (Depositor), 0.252 (DCC)
R-Value Work:
0.189 (Depositor), 0.188 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme from Bacillus Subtilis complexed with MG++ at 1.8 A

Malashkevich, V.N., Sauder, J.M., Schwinn, K.D., Emtage, S., Thompson, D.A., Rutter, M.E., Dickey, M., Groshong, C., Bain, K.T., Adams, J.M., Reyes, C., Rooney, I., Powell, A., Boice, A., Gheyi, T., Ozyurt, S., Atwell, S., Wasserman, S.R., Burley, S.K., Sali, A., Babbitt, P., Pieper, U., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 347.51 kDa
Atom Count: 25,632
Modeled Residue Count: 2,991
Deposited Residue Count: 3,056
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
yitF	A, B, C, D, E A, B, C, D, E, F, G, H	382	Bacillus subtilis	Mutation(s): 0 Gene Names: YITF EC: 5
UniProt
Find proteins for O06741 (Bacillus subtilis (strain 168)) Explore O06741 Go to UniProtKB: O06741
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O06741
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.253 (Depositor), 0.252 (DCC)
R-Value Work: 0.189 (Depositor), 0.188 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.417	α = 90
b = 110.654	β = 105.77
c = 129.308	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
CCP4	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-04-18

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2006-04-18
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-11-14
Changes: Data collection, Structure summary
Version 1.5: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2023-08-30
Changes: Data collection, Database references, Refinement description