2J19 | pdb_00002j19

Ferrous Chloroperoxidase (high dose data set)

• PDB DOI: https://doi.org/10.2210/pdb2J19/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leptoxyphium fumago
• Mutation(s): No 


• Deposited: 2006-08-09 Released: 2006-12-18 
• Deposition Author(s): Beitlich, T., Kuhnel, K., Schulze-Briese, C., Shoeman, R.L., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Cryoradiolytic Reduction of Crystalline Heme Proteins: Analysis by Uv-Vis Spectroscopy and X-Ray Crystallography

Beitlich, T., Kuhnel, K., Schulze-Briese, C., Shoeman, R.L., Schlichting, I.

(2007) J Synchrotron Radiat 14: 11

• PubMed: 17211068 
• DOI: https://doi.org/10.1107/S0909049506049806
• Primary Citation Related Structures: 
  2J18, 2J19


• PubMed Abstract: 
  

  The X-ray crystallographic analysis of redox-active systems may be complicated by photoreduction. Although radiolytic reduction by the probing X-ray beam may be exploited to generate otherwise short-lived reaction intermediates of metalloproteins, it is generally an undesired feature. Here, the X-ray-induced reduction of the three heme proteins myoglobin, cytochrome P450cam and chloroperoxidase has been followed by on-line UV-Vis absorption spectroscopy. All three systems showed a very rapid reduction of the heme iron. In chloroperoxidase the change of the ionization state from ferric to ferrous heme is associated with a movement of the heme-coordinating water molecule. The influence of the energy of the incident X-ray photons and of the presence of scavengers on the apparent reduction rate of ferric myoglobin crystals was analyzed.

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Organizational Affiliation: 
• Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Jahnstrasse 29, 69120 Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 36.85 kDa 
• Atom Count: 2,943 
• Modeled Residue Count: 299 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHLOROPEROXIDASE	A	299	Leptoxyphium fumago	Mutation(s): 0  EC: 1.11.1.10
UniProt
Find proteins for P04963 (Leptoxyphium fumago) Explore P04963  Go to UniProtKB:  P04963
Glycosylation
Glycosylation Sites: 13

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	D	2		O-Glycosylation
Glycosylation Resources
GlyTouCan: G53402KW GlyCosmos: G53402KW GlyGen: G53402KW

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	F [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG	G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BR	Q [auth A], R [auth A], S [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
MN	E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111	D	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.73	α = 90
b = 150.46	β = 90
c = 100.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-18 
Deposition Author(s): Beitlich, T., Kuhnel, K., Schulze-Briese, C., Shoeman, R.L., Schlichting, I.

Revision History  

• Version 1.0: 2006-12-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-03-11
  Changes: Advisory, Data collection, Derived calculations, Other, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 3.2: 2024-10-23
  Changes: Structure summary