4H83 | pdb_00004h83

Crystal structure of Mandelate racemase/muconate lactonizing enzyme (EFI target:502127)

PDB DOI: https://doi.org/10.2210/pdb4H83/pdb

Classification: ISOMERASE
Organism(s): marine actinobacterium PHSC20C1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-21 Released: 2012-10-10
Deposition Author(s): Kim, J., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.204 (Depositor), 0.210 (DCC)
R-Value Work:
0.147 (Depositor), 0.157 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Mandelate racemase/muconate lactonizing enzyme

Kim, J., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 261.44 kDa
Atom Count: 17,719
Modeled Residue Count: 2,155
Deposited Residue Count: 2,328
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	A, B, C, D, E A, B, C, D, E, F	388	marine actinobacterium PHSC20C1	Mutation(s): 0 Gene Names: A20C1_08358
UniProt
Find proteins for A0ACD6B9J9 (marine actinobacterium PHSC20C1) Explore A0ACD6B9J9 Go to UniProtKB: A0ACD6B9J9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9J9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth F] MOL2 format, chain P [auth F] mmCIF format, chain P [auth F]	P [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth F] Interactions & Density Focus chain P [auth F]
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain I [auth A] MOL2 format, chain R [auth F] MOL2 format, chain I [auth A] mmCIF format, chain R [auth F] mmCIF format, chain I [auth A]	I [auth A], R [auth F]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain R [auth F] Interactions & Density Focus chain I [auth A] Focus chain R [auth F]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] J [auth B] K [auth B] L [auth C] G [auth A], H [auth A], J [auth B], K [auth B], L [auth C], N [auth D], O [auth E], Q [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.204 (Depositor), 0.210 (DCC)
R-Value Work: 0.147 (Depositor), 0.157 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.983	α = 90
b = 102.95	β = 90
c = 234.431	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2012-11-14
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description