2AT3

1.00 A Crystal Structure Of L123V/L133V Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Imidazole at pH 5.6

PDB DOI: https://doi.org/10.2210/pdb2AT3/pdb

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

Deposited: 2005-08-24 Released: 2006-08-22
Deposition Author(s): Amoia, A.M., Montfort, W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.167
R-Value Work: 0.144
R-Value Observed: 0.145

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Heme distortion in nitrophorin 4: high resolution structures of mutated positions L123V and L133V and heme altered proteins

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

To be published.

Macromolecule Content

Total Structure Weight: 20.95 kDa
Atom Count: 2,122
Modelled Residue Count: 184
Deposited Residue Count: 184
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrophorin 4	A [auth X]	184	Rhodnius prolixus	Mutation(s): 2 EC: 1.7.6.1
UniProt
Find proteins for Q94734 (Rhodnius prolixus) Explore Q94734 Go to UniProtKB: Q94734
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q94734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM 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]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
IMD Query on IMD 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]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.167
R-Value Work: 0.144
R-Value Observed: 0.145
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.221	α = 90
b = 42.743	β = 94.09
c = 52.886	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
CrystalClear	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-08-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-22
Type: Initial release
Version 1.1: 2008-01-31
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-08-23
Changes: Data collection, Refinement description
Version 1.5: 2024-11-13
Changes: Structure summary

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.