6A39 | pdb_00006a39

The crystal structure of Mandelate oxidase Y128F with C4a-Malic acid-monooxide-FMN adduct

PDB DOI: https://doi.org/10.2210/pdb6A39/pdb

Classification: FLAVOPROTEIN
Organism(s): Amycolatopsis orientalis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-06-15 Released: 2019-06-19
Deposition Author(s): Li, T.L., Lin, K.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.235 (Depositor), 0.243 (DCC)
R-Value Work:
0.190 (Depositor), 0.199 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of Mandelate oxidase mutant Y128F with C4a-Malic acid-monooxide-FMN adduct

Li, T.L., Lin, K.H.

To be published.

Macromolecule Content

Total Structure Weight: 40.63 kDa
Atom Count: 2,769
Modeled Residue Count: 330
Deposited Residue Count: 377
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxymandelate oxidase	A	377	Amycolatopsis orientalis	Mutation(s): 1 Gene Names: hmo EC: 1.1.3.46
UniProt
Find proteins for O52792 (Amycolatopsis orientalis) Explore O52792 Go to UniProtKB: O52792
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O52792
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B8C Query on B8C Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(~{E})-2-[[(4~{a}~{S})-7,8-dimethyl-2,4-bis(oxidanylidene)-10-[(2~{S},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl]-5~{H}-benzo[g]pteridin-4~{a}-yl]oxy]-3-oxidanyl-but-2-enedioic acid C₂₁ H₂₅ N₄ O₁₅ P CYUZEIATLQOYCB-IVDAFHBWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.235 (Depositor), 0.243 (DCC)
R-Value Work: 0.190 (Depositor), 0.199 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.44	α = 90
b = 138.44	β = 90
c = 109.144	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.