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- PDB-4xva: Crystal structure of wild type cytochrome c peroxidase -

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Basic information

Entry
Database: PDB / ID: 4xva
TitleCrystal structure of wild type cytochrome c peroxidase
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Model system / flexibility / thermodynamics / cryptic site / transient protein sites / ligand binding
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BENZIMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.66 Å
AuthorsFischer, M. / Fraser, J.S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM59957 United States
National Institutes of Health/Office of the DirectorOD009180 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110580 United States
National Science Foundation (NSF, United States)STC-1231306 United States
Citation
Journal: Chembiochem / Year: 2015
Title: One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.
Authors: Fischer, M. / Shoichet, B.K. / Fraser, J.S.
#1: Journal: Nat Chem / Year: 2014
Title: Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.
Authors: Fischer, M. / Coleman, R.G. / Fraser, J.S. / Shoichet, B.K.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c peroxidase, mitochondrial
C: Cytochrome c peroxidase, mitochondrial
E: Cytochrome c peroxidase, mitochondrial
G: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,70111
Polymers133,8814
Non-polymers2,8207
Water5,098283
1
A: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2053
Polymers33,4701
Non-polymers7352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2053
Polymers33,4701
Non-polymers7352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2053
Polymers33,4701
Non-polymers7352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0872
Polymers33,4701
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.110, 104.760, 185.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological assembly is a monomer

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Components

#1: Protein
Cytochrome c peroxidase, mitochondrial / / CCP


Mass: 33470.137 Da / Num. of mol.: 4 / Fragment: unp residues 69-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CCP1, CCP, CPO, YKR066C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-BZI / BENZIMIDAZOLE / Benzimidazole


Mass: 118.136 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Compound soaked into crystal grown in equal volume of 500mM MES buffer and 25% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2012
RadiationMonochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11591
21.115871
ReflectionResolution: 2.66→92.63 Å / Num. obs: 47484 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 52.99 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.3
Reflection shellResolution: 2.66→2.73 Å / Redundancy: 4 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
xia20.3.3.3data reduction
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→92.63 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 2426 5.11 %
Rwork0.233 --
obs0.235 47483 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.96 Å2
Refinement stepCycle: LAST / Resolution: 2.66→92.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9453 0 199 283 9935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0169973
X-RAY DIFFRACTIONf_angle_d1.39413569
X-RAY DIFFRACTIONf_dihedral_angle_d14.7223602
X-RAY DIFFRACTIONf_chiral_restr0.1031325
X-RAY DIFFRACTIONf_plane_restr0.0081778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.662-2.71640.36911570.32372527X-RAY DIFFRACTION97
2.7164-2.77540.40571320.31232611X-RAY DIFFRACTION100
2.7754-2.840.3741540.29482614X-RAY DIFFRACTION100
2.84-2.9110.35631330.27942649X-RAY DIFFRACTION100
2.911-2.98970.28491210.26342648X-RAY DIFFRACTION100
2.9897-3.07770.27261520.25592590X-RAY DIFFRACTION100
3.0777-3.17710.28381460.26062639X-RAY DIFFRACTION100
3.1771-3.29060.33571250.2592623X-RAY DIFFRACTION100
3.2906-3.42240.33741500.25042624X-RAY DIFFRACTION100
3.4224-3.57810.29231400.23952629X-RAY DIFFRACTION100
3.5781-3.76680.2611330.21612674X-RAY DIFFRACTION100
3.7668-4.00280.25451430.20162652X-RAY DIFFRACTION100
4.0028-4.31180.23761720.20372616X-RAY DIFFRACTION100
4.3118-4.74570.23531310.1942686X-RAY DIFFRACTION100
4.7457-5.43240.24541460.19952685X-RAY DIFFRACTION100
5.4324-6.84390.23821410.23622733X-RAY DIFFRACTION100
6.8439-92.68110.28271500.23882857X-RAY DIFFRACTION99

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