1CCL | pdb_00001ccl

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

PDB DOI: https://doi.org/10.2210/pdb1CCL/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: 2.00 Å
R-Value Work:
0.184 (Depositor), 0.502 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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: 33.82 kDa
Atom Count: 2,498
Modeled Residue Count: 291
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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: 2.00 Å
R-Value Work: 0.184 (Depositor), 0.502 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.4	α = 90
b = 73.2	β = 90
c = 44.5	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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Ligand Structure Quality Assessment

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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

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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.