4L1Y | pdb_00004l1y

Crystal structure of Cimex nitrophorin A21V mutant

PDB DOI: https://doi.org/10.2210/pdb4L1Y/pdb

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

Deposited: 2013-06-04 Released: 2014-09-17
Deposition Author(s): Badgandi, H.B., Weichsel, A., Montfort, W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.259 (Depositor), 0.261 (DCC)
R-Value Work:
0.220 (Depositor), 0.225 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Proximal Cysteine Protonation in Cimex Nitrophorin is key to efficient NO transport and release.

Badgandi, H.B., Hazzard, J.T., Weichsel, A., Tollin, G., Montfort, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 32.25 kDa
Atom Count: 2,496
Modeled Residue Count: 280
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Salivary nitrophorin	A	280	Cimex lectularius	Mutation(s): 1
UniProt
Find proteins for O76745 (Cimex lectularius) Explore O76745 Go to UniProtKB: O76745
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O76745
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.259 (Depositor), 0.261 (DCC)
R-Value Work: 0.220 (Depositor), 0.225 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.959	α = 90
b = 42.228	β = 94.84
c = 65.579	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
REFMAC	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, 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.