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- PDB-1a7v: CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS -

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Basic information

Entry
Database: PDB / ID: 1a7v
TitleCYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c'
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShibata, N. / Iba, S. / Misaki, S. / Meyer, T.E. / Bartsch, R.G. / Cusanovich, M.A. / Higuchi, Y. / Yasuoka, N.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Basis for monomer stabilization in Rhodopseudomonas palustris cytochrome c' derived from the crystal structure.
Authors: Shibata, N. / Iba, S. / Misaki, S. / Meyer, T.E. / Bartsch, R.G. / Cusanovich, M.A. / Morimoto, Y. / Higuchi, Y. / Yasuoka, N.
History
DepositionMar 18, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C'
B: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5374
Polymers26,3042
Non-polymers1,2332
Water3,513195
1
A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7692
Polymers13,1521
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7692
Polymers13,1521
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.000, 113.500, 34.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.997291, 0.046599, 0.056917), (-0.049179, -0.997784, -0.044807), (0.054703, -0.047485, 0.997373)
Vector: 58.0675, 79.9055, -0.0607)

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Components

#1: Protein CYTOCHROME C'


Mass: 13152.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: P00149
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
2100 mMMES1reservoir
330 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Jul 1, 1996
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 10513 / % possible obs: 89.1 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 2.1 / % possible all: 63
Reflection
*PLUS
Num. measured all: 39136
Reflection shell
*PLUS
% possible obs: 62.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CCY

2ccy


Resolution: 2.3→7 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.241 926 8.2 %RANDOM
Rwork0.194 ---
obs0.194 10028 83.5 %-
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 86 195 2123
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.31.5
X-RAY DIFFRACTIONx_mcangle_it6.32
X-RAY DIFFRACTIONx_scbond_it5.72
X-RAY DIFFRACTIONx_scangle_it8.22.5
Refine LS restraints NCSNCS model details: RESTRAINED / Rms dev Biso : 2 Å2 / Rms dev position: 0.1 Å / Weight Biso : 4.8 / Weight position: 100
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.274 82 6 %
Rwork0.243 618 -
obs--51.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor obs: 0.243

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