2AT6 | pdb_00002at6

1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) Deuteroporphyrin IX Complexed With Water at pH 5.6

PDB DOI: https://doi.org/10.2210/pdb2AT6/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Rhodnius prolixus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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: 1.22 Å
R-Value Free:
0.167 (Depositor), 0.168 (DCC)
R-Value Work:
0.133 (Depositor), 0.136 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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: 20.86 kDa
Atom Count: 2,125
Modeled Residue Count: 184
Deposited Residue Count: 184
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrophorin 4	A [auth X]	184	Rhodnius prolixus	Mutation(s): 0 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDE Query on FDE 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]	FE(III) DEUTEROPORPHYRIN IX C₃₀ H₂₈ Fe N₄ O₄ QQYZTXBVPVYDJC-RWRCOHKGSA-L		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free: 0.167 (Depositor), 0.168 (DCC)
R-Value Work: 0.133 (Depositor), 0.136 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.288	α = 90
b = 42.699	β = 94.35
c = 52.979	γ = 90

Software Package:

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

Structure Validation

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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: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-13
Changes: Data collection, 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.