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- PDB-2c1u: CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PAR... -

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Basic information

Entry
Database: PDB / ID: 2c1u
TitleCRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS - OXIDISED FORM
ComponentsDI-HAEM CYTOCHROME C PEROXIDASE
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / HEME / PERIPLASMIC / PEROXIDASE
Function / homologyCytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Orthogonal Bundle / Mainly Alpha / HEME C
Function and homology information
Biological speciesPARACOCCUS PANTOTROPHUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsEchalier, A. / Fulop, V.
CitationJournal: Structure / Year: 2006
Title: Activation and Catalysis of the Di-Heme Cytochrome C Peroxidase from Paracoccus Pantotrophus
Authors: Echalier, A. / Goodhew, C.F. / Pettigrew, G.W. / Fulop, V.
History
DepositionSep 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DI-HAEM CYTOCHROME C PEROXIDASE
B: DI-HAEM CYTOCHROME C PEROXIDASE
C: DI-HAEM CYTOCHROME C PEROXIDASE
D: DI-HAEM CYTOCHROME C PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,41416
Polymers145,3064
Non-polymers5,10812
Water15,006833
1
A: DI-HAEM CYTOCHROME C PEROXIDASE
B: DI-HAEM CYTOCHROME C PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2078
Polymers72,6532
Non-polymers2,5546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DI-HAEM CYTOCHROME C PEROXIDASE
D: DI-HAEM CYTOCHROME C PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2078
Polymers72,6532
Non-polymers2,5546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.800, 51.100, 167.900
Angle α, β, γ (deg.)90.00, 98.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DI-HAEM CYTOCHROME C PEROXIDASE


Mass: 36326.523 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS PANTOTROPHUS (bacteria) / References: cytochrome-c peroxidase
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 833 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growpH: 8.2
Details: ECHALER ET AL., (2004). ACTA CRYST. D60, 331-333., pH 8.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 85916 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.7 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E7B

1e7b


Resolution: 1.95→29.88 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.164 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2569 3 %RANDOM
Rwork0.169 ---
obs0.17 83347 88.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.894 Å20 Å2-1.951 Å2
2---2.618 Å20 Å2
3---0.167 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9835 0 348 833 11016
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 182
Rwork0.239 5872
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9871-0.9669-0.04751.7175-0.13960.5522-0.01980.071-0.17980.00850.01680.18350.1478-0.11840.003-0.0638-0.0380.07610.0765-0.0114-0.025730.847-14.82421.655
21.3643-0.00180.11391.4809-0.04512.91080.0080.03330.17530.13380.07340.2166-0.2607-0.3159-0.0814-0.1310.05740.11490.07580.0319-0.060216.6598.79321.36
31.0262-1.1285-0.05472.34380.22220.54130.00850.04890.1683-0.05320.0431-0.2173-0.10880.1088-0.0515-0.0902-0.04270.06450.086-0.0016-0.048153.8353.44120.775
41.8356-0.46430.44311.6827-0.51343.28930.12770.2834-0.0952-0.0484-0.0224-0.25380.35620.3827-0.1053-0.14930.06390.03410.1139-0.0543-0.058667.906-20.23319.936
51.09881.0083-0.02351.86030.24560.5101-0.0217-0.0158-0.1876-0.05840.0622-0.210.11360.1254-0.0405-0.0820.03360.09020.0826-0.0128-0.026633.577-3.22560.796
61.69290.04410.53950.94840.00512.99580.01340.12830.1837-0.10790.0807-0.1822-0.34360.2873-0.0941-0.1099-0.05940.14110.0823-0.0184-0.039847.80920.33459.482
71.26421.1385-0.08622.3267-0.14490.6969-0.0014-0.03490.2375-0.02480.02660.2518-0.0495-0.0668-0.0252-0.0960.02950.06470.0684-0.0066-0.039710.88315.16864.048
81.86570.69530.58311.94591.193.13310.1304-0.2566-0.0780.1234-0.1310.30670.29-0.35840.0006-0.1306-0.07120.04970.08660.0278-0.0739-3.086-8.50565.994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 179
2X-RAY DIFFRACTION1A317 - 338
3X-RAY DIFFRACTION1A401
4X-RAY DIFFRACTION2A4 - 21
5X-RAY DIFFRACTION2A180 - 316
6X-RAY DIFFRACTION2A402
7X-RAY DIFFRACTION3B22 - 179
8X-RAY DIFFRACTION3B317 - 338
9X-RAY DIFFRACTION3B401
10X-RAY DIFFRACTION4B4 - 21
11X-RAY DIFFRACTION4B180 - 316
12X-RAY DIFFRACTION4B402
13X-RAY DIFFRACTION5C22 - 179
14X-RAY DIFFRACTION5C317 - 338
15X-RAY DIFFRACTION5C401
16X-RAY DIFFRACTION6C4 - 21
17X-RAY DIFFRACTION6C180 - 316
18X-RAY DIFFRACTION6C402
19X-RAY DIFFRACTION7D22 - 179
20X-RAY DIFFRACTION7D317 - 338
21X-RAY DIFFRACTION7D401
22X-RAY DIFFRACTION8D4 - 21
23X-RAY DIFFRACTION8D180 - 316
24X-RAY DIFFRACTION8D402

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