5F1P | pdb_00005f1p

Crystal Structure of Dehydrogenase from Streptomyces platensis

PDB DOI: https://doi.org/10.2210/pdb5F1P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces platensis subsp. rosaceus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-11-30 Released: 2015-12-30
Deposition Author(s): Kim, Y., Li, H., Endres, M., Babnigg, G., Rudolf, J., Ma, M., Chang, C.-Y., Shen, B., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.242 (Depositor), 0.242 (DCC)
R-Value Work:
0.190 (Depositor), 0.191 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a Dehydrogenase, PtmO8, from Streptomyces platensis

Kim, Y., Li, H., Endres, M., Babnigg, G., Rudolf, J., Ma, M., Chang, C.-Y., Shen, B., Phillips Jr., G.N., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 54.37 kDa
Atom Count: 3,592
Modeled Residue Count: 484
Deposited Residue Count: 530
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PtmO8	A, B	265	Streptomyces platensis subsp. rosaceus	Mutation(s): 3
UniProt
Find proteins for A0A0A0UVL0 (Streptomyces platensis) Explore A0A0A0UVL0 Go to UniProtKB: A0A0A0UVL0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0A0UVL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.242 (Depositor), 0.242 (DCC)
R-Value Work: 0.190 (Depositor), 0.191 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.368	α = 90
b = 77.953	β = 105.47
c = 81.575	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-12-30

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2015-12-30
Type: Initial release
Version 1.1: 2017-02-22
Changes: Database references, Structure summary
Version 1.2: 2019-12-04
Changes: Author supporting evidence
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Structure summary