3C76 | pdb_00003c76

1.07 A crystal structure of L133V mutant of nitrophorin 4 from Rhodnius prolixus complexed with ammonia at PH 7.5

PDB DOI: https://doi.org/10.2210/pdb3C76/pdb
Entry: 3C76 supersedes: 2ASZ

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

Deposited: 2008-02-06 Released: 2008-03-04
Deposition Author(s): Amoia, A.M., Montfort, W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.07 Å
R-Value Free:
0.165 (Depositor), 0.170 (DCC)
R-Value Work:
0.139 (Depositor), 0.150 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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: 20.91 kDa
Atom Count: 2,060
Modeled 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): 1 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 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]
NH3 Query on NH3 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]	AMMONIA H₃ N QGZKDVFQNNGYKY-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.07 Å
R-Value Free: 0.165 (Depositor), 0.170 (DCC)
R-Value Work: 0.139 (Depositor), 0.150 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.32	α = 90
b = 42.847	β = 94.26
c = 52.871	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data scaling
d*TREK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-03-04

Deposition Author(s):

This entry supersedes: 2ASZ

Revision History (Full details and data files)

Version 1.0: 2008-03-04
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: 2024-10-09
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.