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- PDB-4xv8: CcP gateless cavity -

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Basic information

Entry
Database: PDB / ID: 4xv8
TitleCcP gateless cavity
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
BENZAMIDINE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 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)110580 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 18, 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
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0273
Polymers33,2901
Non-polymers7372
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.460, 76.950, 107.710
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: 33290.062 Da / Num. of mol.: 1 / Fragment: unp residues 71-361 / Mutation: P190G, W191G
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.: 1
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 3.18 Å3/Da / Density % sol: 61.33 %
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: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2011
RadiationMonochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionNumber: 257569 / Rmerge(I) obs: 0.053 / Χ2: 1.01 / D res high: 1.57 Å / Num. obs: 60219 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
4.967.02130210.031
4.054.96163410.029
3.514.05192010.031
3.143.51216910.035
2.873.14239010.038
2.652.87258710.042
2.482.65279010.048
2.342.48292310.054
2.222.34314110.061
2.122.22326610.071
2.032.12341410.087
1.952.03355610.106
1.881.95370510.139
1.811.88380210.174
1.761.81393110.225
1.71.76408610.285
1.651.7416010.367
1.611.65430310.434
1.571.61440010.555
ReflectionResolution: 1.57→39.76 Å / Num. obs: 60219 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 17.76 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.9
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
xia20.3.3.3data reduction
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→39.76 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 11.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.14 3040 5.05 %Random selection
Rwork0.108 ---
obs0.11 60160 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.52 Å2
Refinement stepCycle: LAST / Resolution: 1.57→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 52 295 2675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172653
X-RAY DIFFRACTIONf_angle_d1.5923631
X-RAY DIFFRACTIONf_dihedral_angle_d15.167987
X-RAY DIFFRACTIONf_chiral_restr0.108351
X-RAY DIFFRACTIONf_plane_restr0.01490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.59450.19751500.16962540X-RAY DIFFRACTION100
1.5945-1.62070.21611400.16382555X-RAY DIFFRACTION100
1.6207-1.64860.19281410.14932552X-RAY DIFFRACTION100
1.6486-1.67860.19541540.15482589X-RAY DIFFRACTION100
1.6786-1.71090.17721320.14592602X-RAY DIFFRACTION100
1.7109-1.74580.12931340.13062540X-RAY DIFFRACTION100
1.7458-1.78380.16141340.12462582X-RAY DIFFRACTION100
1.7838-1.82530.15321220.11232585X-RAY DIFFRACTION100
1.8253-1.87090.15811530.10022564X-RAY DIFFRACTION100
1.8709-1.92150.12121420.09692606X-RAY DIFFRACTION100
1.9215-1.9780.12281520.09382564X-RAY DIFFRACTION100
1.978-2.04190.14551430.09362563X-RAY DIFFRACTION100
2.0419-2.11490.13191310.09812584X-RAY DIFFRACTION100
2.1149-2.19950.14071360.09322604X-RAY DIFFRACTION100
2.1995-2.29960.12881140.0972623X-RAY DIFFRACTION100
2.2996-2.42090.12911470.1022580X-RAY DIFFRACTION100
2.4209-2.57250.13221370.11192636X-RAY DIFFRACTION99
2.5725-2.77110.14771420.11392584X-RAY DIFFRACTION99
2.7711-3.04990.14151390.11122620X-RAY DIFFRACTION99
3.0499-3.49090.13091200.10782658X-RAY DIFFRACTION99
3.4909-4.39730.11481360.09192639X-RAY DIFFRACTION98
4.3973-39.76850.14671410.11122750X-RAY DIFFRACTION97

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