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- PDB-1etp: CRYSTAL STRUCTURE OF CYTOCHROME C4 FROM PSEUDOMONAS STUTZERI -

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Basic information

Entry
Database: PDB / ID: 1etp
TitleCRYSTAL STRUCTURE OF CYTOCHROME C4 FROM PSEUDOMONAS STUTZERI
ComponentsCYTOCHROME C4
KeywordsELECTRON TRANSPORT / CYTOCHROME C4 / DIHEME PROTEIN / PSEUDOMONAS STUTZERI
Function / homology
Function and homology information


periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c4-like / : / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c4
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsKadziola, A. / Larsen, S.
Citation
Journal: Structure / Year: 1997
Title: Crystal structure of the dihaem cytochrome c4 from Pseudomonas stutzeri determined at 2.2A resolution.
Authors: Kadziola, A. / Larsen, S.
#1: Journal: Eur.J.Biochem. / Year: 1995
Title: Electron Transfer and Spectral Alpha-Band Properties of the Di-Heme Protein Cytochrome C4 from Pseudomonas Stutzeri
Authors: Conrad, L.S. / Karlsson, J.J. / Ulstrup, J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Crystallization and Preliminary Crystallographic Investigations of Cytochrome C4 from Pseudomonas Stutzeri
Authors: Kadziola, A. / Larsen, S. / Christensen, H.M. / Karlsson, J.-J. / Ulstrup, J.
#3: Journal: Gene / Year: 1994
Title: Cloning and Characterisation of the Gene Encoding Cytochrome C4 from Pseudomonas Stutzeri
Authors: Christensen, H.E.
History
DepositionJan 23, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C4
B: CYTOCHROME C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8666
Polymers39,4002
Non-polymers2,4664
Water2,486138
1
A: CYTOCHROME C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9333
Polymers19,7001
Non-polymers1,2332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9333
Polymers19,7001
Non-polymers1,2332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.490, 58.580, 63.510
Angle α, β, γ (deg.)90.00, 96.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.798002, 0.444533, -0.40692), (-0.557893, -0.800268, 0.219832), (-0.227923, 0.402444, 0.886617)
Vector: 20.5437, 22.6585, -32.0602)

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Components

#1: Protein CYTOCHROME C4


Mass: 19700.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas stutzeri (bacteria) / References: UniProt: Q52369
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES HIS 18 AND MET 66 FORM HEME IRON LIGAND BONDS TO THE N-TERMINAL HEME WHILE HIS 123 AND MET ...RESIDUES HIS 18 AND MET 66 FORM HEME IRON LIGAND BONDS TO THE N-TERMINAL HEME WHILE HIS 123 AND MET 167 FORM HEME IRON LIGAND BONDS TO THE C-TERMINAL HEME.
Has protein modificationY
Nonpolymer detailsTHE DEPOSITOR INDICATED THAT THE CHARGE ON THE HEME GROUP IS 2+ OR 3+.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 39 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Kadziola, A., (1995) Acta Crystallogr.,Sect.D, 51, 1071.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22.5 mMTris1drop
30.05 M1dropNaCl
40.1 Mammonium acetate1drop
515 %PEG40001drop
60.05 Msodium citrate1drop
70.2 Mammonium acetate1reservoir
830 %PEG40001reservoir
90.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 274 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 12, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→58.7 Å / Num. obs: 18020 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.033 / Net I/σ(I): 13.5
Reflection
*PLUS
Rmerge(I) obs: 0.033

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→8 Å / σ(F): 0
Details: RAMACHANDRAN PLOT ONE RESIDUE IN EACH MOLECULE (LISTED BELOW) ARE FOUND IN THE 'FORBIDDEN' REGION OF THE RAMACHANDRAN PLOT. BOTH RESIDUES ARE SITUATED IN REGIONS WITH WELL DEFINED ELECTRON ...Details: RAMACHANDRAN PLOT ONE RESIDUE IN EACH MOLECULE (LISTED BELOW) ARE FOUND IN THE 'FORBIDDEN' REGION OF THE RAMACHANDRAN PLOT. BOTH RESIDUES ARE SITUATED IN REGIONS WITH WELL DEFINED ELECTRON DENSITY. PHI PSI OMEGA 1 ALA A 124 65.95 149.82 -180.00 2 ALA B 124 76.18 151.83 -179.44
RfactorNum. reflection% reflection
Rfree0.267 -10 %
Rwork0.201 --
obs0.201 17609 97.3 %
Displacement parametersBiso mean: 22.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 172 138 3066
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46

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