1A2F

PROBING THE STRENGTH AND CHARACTER OF AN ASP-HIS-X HYDROGEN BOND BY INTRODUCING BURIED CHARGES

PDB DOI: https://doi.org/10.2210/pdb1A2F/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 1998-01-02 Released: 1998-11-25
Deposition Author(s): Cao, Y., Goodin, D.B., Mcree, D.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Work: 0.184
R-Value Observed: 0.184

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Probing the Strength and Character of an Asp-His-X Hydrogen Bond by Introducing Buried Charges

Cao, Y., Musah, R.A., Goodin, D.B., Mcree, D.E.

To be published.

Macromolecule Content

Total Structure Weight: 33.84 kDa
Atom Count: 2,501
Modelled Residue Count: 291
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C PEROXIDASE	A	291	Saccharomyces cerevisiae	Mutation(s): 3 Gene Names: CCP EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00431 Go to UniProtKB: P00431
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00431
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: 2.10 Å
R-Value Work: 0.184
R-Value Observed: 0.184
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.8	α = 90
b = 73.5	β = 90
c = 44.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
XTALVIEW	refinement
X-PLOR	refinement
XENGEN	data reduction
XENGEN	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1998-11-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1998-11-25
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2022-12-21
Changes: Database references, Derived calculations
Version 1.4: 2023-08-09
Changes: Refinement description
Version 1.5: 2024-05-22
Changes: Data collection

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.