2OFR | pdb_00002ofr

1.00 A Crystal Structure Of V36A/D129A/L130A Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 5.6

PDB DOI: https://doi.org/10.2210/pdb2OFR/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Rhodnius prolixus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-01-04 Released: 2008-01-08
Deposition Author(s): Amoia, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.148 (Depositor), 0.154 (DCC)
R-Value Work:
0.126 (Depositor), 0.133 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Ligand Protection and Nitric Oxide Interactions with Heme in Nitrophorin 4: Kinetic and Structural Analyses of a Loop Mutant

Amoia, A.M., Montfort, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 20.92 kDa
Atom Count: 2,076
Modeled Residue Count: 184
Deposited Residue Count: 184
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrophorin-4	A [auth X]	184	Rhodnius prolixus	Mutation(s): 3 EC: 1.7.6.1
UniProt
Find proteins for Q94734 (Rhodnius prolixus) Explore Q94734 Go to UniProtKB: Q94734
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q94734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
NO Query on NO Download:Ideal Coordinates CCD File SDF format, chain D [auth X] MOL2 format, chain D [auth X] mmCIF format, chain D [auth X]	D [auth X]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N		Interactions Focus chain D [auth X] Interactions & Density Focus chain D [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.148 (Depositor), 0.154 (DCC)
R-Value Work: 0.126 (Depositor), 0.133 (DCC)
R-Value Observed: 0.127 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.191	α = 90
b = 42.637	β = 94.12
c = 52.975	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-01-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-01-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary

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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.