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- PDB-4cvi: Neutron Structure of Ferric Cytochrome c Peroxidase - Deuterium e... -

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Basic information

Entry
Database: PDB / ID: 4cvi
TitleNeutron Structure of Ferric Cytochrome c Peroxidase - Deuterium exchanged at room temperature
ComponentsCYTOCHROME C PEROXIDASE, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / HEME PEROXIDASE / REDOX / ELECTRON TRANSPORT / FERRIC / HEME / NEUTRON
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
DEUTERATED WATER / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.1 Å
AuthorsCasadei, C.M. / Gumiero, A. / Blakeley, M.P. / Ostermann, A. / Raven, E.L. / Moody, P.C.E.
CitationJournal: Science / Year: 2014
Title: Neutron Cryo-Crystallography Captures the Protonation State of Ferryl Heme in a Peroxidase
Authors: Casadei, C.M. / Gumiero, A. / Metcalfe, C.L. / Murphy, E.J. / Basran, J. / Concilio, M.G. / Teixeira, S.C.M. / Schrader, T.E. / Fielding, A.J. / Ostermann, A. / Blakeley, M.P. / Raven, E.L. / Moody, P.C.E.
History
DepositionMar 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Jan 25, 2017Group: Data collection
Revision 2.0Jun 28, 2017Group: Atomic model / Refinement description / Category: atom_site / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _software.name
Revision 2.1Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.2Sep 13, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 2.3Jun 6, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline

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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)34,2462
Polymers33,6291
Non-polymers6161
Water3,567198
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.700, 76.800, 107.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME C PEROXIDASE, MITOCHONDRIAL / / CCP / CYTOCHROME C PEROXIDASE


Mass: 33629.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Organ: MITOCHONDRION / Plasmid: PLEICS03 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D6VXC7, UniProt: P00431*PLUS, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.27 %
Crystal growpH: 6 / Details: PH 6.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12901
22901
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
SEALED TUBEXenocs GeniX 3D Cu HF11.54181.5418
NUCLEAR REACTORILL LADI III23.2-4.23.2-4.2
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATEOct 1, 2013
2IMAGE PLATEAug 1, 2013
Radiation
IDMonochromatorMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1XENOCS MULTILAYERMx-ray1
2MULTILAYER NI-TIneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
23.21
34.21
Reflection

Entry-ID: 4CVI

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(F)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)Observed criterion F maxObserved criterion F minObserved criterion I maxObserved criterion I minScaling rejects
2.1-14.82430794.73.50.061114.6
2.4-39.71269573.8003.80.15127.600000
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.152.40.2434.6197.3
2.4-2.532.40.1944.4248

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
LAUEGENdata reduction
SCALAdata scaling
PHENIXphasing
PHENIXphasing
PHENIXphasing
Refinement

Baniso 12: 0 Å2 / Baniso 13: 0 Å2 / % reflection Rfree: 10 % / Diffraction-ID: 1 / Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBaniso 11 (Å2)Baniso 22 (Å2)Baniso 23 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection obs (%)SU MLσ(F)Phase errorBsol (Å2)ksol (e/Å3)
2.1-14.77X-RAY DIFFRACTION2.17785.98210-8.15990.17660.13370.138124302430794.90.171.3716.6235.2710.408
2.407-39.84NEUTRON DIFFRACTION-2.53529.999-0-7.46380.24330.17590.182612701269573.760.321.5822.441.4360.472
Refinement stepCycle: LAST / Resolution: 2.1→14.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 43 198 2598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125325
X-RAY DIFFRACTIONf_angle_d1.3499106
X-RAY DIFFRACTIONf_dihedral_angle_d17.6591373
X-RAY DIFFRACTIONf_chiral_restr0.089329
X-RAY DIFFRACTIONf_plane_restr0.008915
NEUTRON DIFFRACTIONf_bond_d0.0125325
NEUTRON DIFFRACTIONf_angle_d1.3499106
NEUTRON DIFFRACTIONf_dihedral_angle_d17.6591373
NEUTRON DIFFRACTIONf_chiral_restr0.089329
NEUTRON DIFFRACTIONf_plane_restr0.008915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14270.19011460.1581310X-RAY DIFFRACTION98
2.1427-2.18920.21951420.16381285X-RAY DIFFRACTION97
2.1892-2.23990.2011440.15391299X-RAY DIFFRACTION98
2.2399-2.29580.20881460.15011309X-RAY DIFFRACTION98
2.2958-2.35760.18931450.14151301X-RAY DIFFRACTION98
2.3576-2.42670.22731430.14671293X-RAY DIFFRACTION97
2.4267-2.50460.18661440.14891294X-RAY DIFFRACTION97
2.5046-2.59370.19031460.13751312X-RAY DIFFRACTION97
2.5937-2.69690.19441430.141289X-RAY DIFFRACTION96
2.6969-2.81890.22271440.14681294X-RAY DIFFRACTION96
2.8189-2.96640.18491430.14651279X-RAY DIFFRACTION96
2.9664-3.15050.18551440.13591296X-RAY DIFFRACTION95
3.1505-3.39110.20121430.12811293X-RAY DIFFRACTION94
3.3911-3.72730.14621430.12141279X-RAY DIFFRACTION94
3.7273-4.25540.14861410.10181278X-RAY DIFFRACTION92
4.2554-5.31940.12751390.11141259X-RAY DIFFRACTION91
5.3194-14.77020.16831340.15121207X-RAY DIFFRACTION82
2.4069-2.50320.3492840.2964768NEUTRON DIFFRACTION46
2.5032-2.61710.32581020.2694906NEUTRON DIFFRACTION54
2.6171-2.75510.31761120.22491015NEUTRON DIFFRACTION60
2.7551-2.92760.28191290.18671156NEUTRON DIFFRACTION69
2.9276-3.15360.23011410.17581279NEUTRON DIFFRACTION75
3.1536-3.47080.21521620.16491432NEUTRON DIFFRACTION83
3.4708-3.97260.22541710.14841553NEUTRON DIFFRACTION90
3.9726-5.00350.22311810.14341631NEUTRON DIFFRACTION94
5.0035-39.84510.22881880.17591685NEUTRON DIFFRACTION91

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