6NI8 | pdb_00006ni8

Pseudomonas fluorescens isocyanide hydratase rotating anode 298K

PDB DOI: https://doi.org/10.2210/pdb6NI8/pdb

Classification: LYASE
Organism(s): Pseudomonas protegens Pf-5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-26 Released: 2020-01-08
Deposition Author(s): Wilson, M.A., Dasgupta, M., van den Bedem, H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.150 (Depositor), 0.149 (DCC)
R-Value Work:
0.110 (Depositor), 0.110 (DCC)
R-Value Observed:
0.112 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6NI8

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

Literature

Cysteine modification can gate non-equilibrium conformational dynamics during enzyme catalysis

Dasgupta, M., Budday, D., Madzelan, P., Seravalli, J., Hayes, B., Sierra, R.G., Applegate, G., Tiwari, V., Berkowitz, D.B., Thompson, M., Fraser, J.S., Wall, M.E., van den Bedem, H., Wilson, M.A.

(2019) bioRxiv

DOI: https://doi.org/10.1101/524751

Macromolecule Content

Total Structure Weight: 48.36 kDa
Atom Count: 4,158
Modeled Residue Count: 456
Deposited Residue Count: 462
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isonitrile hydratase InhA	A, B	231	Pseudomonas protegens Pf-5	Mutation(s): 0 Gene Names: inhA, PFL_4109 EC: 4.2.1.103
UniProt
Find proteins for Q4K977 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4K977 Go to UniProtKB: Q4K977
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4K977
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.150 (Depositor), 0.149 (DCC)
R-Value Work: 0.110 (Depositor), 0.110 (DCC)
R-Value Observed: 0.112 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.195	α = 90
b = 58.13	β = 112.81
c = 69.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-08

Deposition Author(s):

van den Bedem, H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM123159

Revision History (Full details and data files)

Version 1.0: 2020-01-08
Type: Initial release
Version 1.1: 2020-07-22
Changes: Database references
Version 1.2: 2023-10-11
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.