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- PDB-1aqe: CRYSTAL STRUCTURE OF THE Y73E MUTANT OF CYTOCHROME C OF CLASS III... -

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Basic information

Entry
Database: PDB / ID: 1aqe
TitleCRYSTAL STRUCTURE OF THE Y73E MUTANT OF CYTOCHROME C OF CLASS III (AMBLER) 26 KD
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT / OCTAHEME CYTOCHROME / POINT MUTANT
Function / homology
Function and homology information


anaerobic respiration / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Class III cytochrome C / Class III cytochrome C family / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c3, 26 kDa
Similarity search - Component
Biological speciesDesulfomicrobium norvegicum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCzjzek, M. / Haser, R.
Citation
Journal: Biochemistry / Year: 1998
Title: Structural and kinetic studies of the Y73E mutant of octaheme cytochrome c3 (Mr = 26 000) from Desulfovibrio desulfuricans Norway.
Authors: Aubert, C. / Giudici-Orticoni, M.T. / Czjzek, M. / Haser, R. / Bruschi, M. / Dolla, A.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: A Single Mutation in the Heme 4 Environment of Desulfovibrio Desulfuricans Norway Cytochrome C3 (Mr 26,000) Greatly Affects the Molecule Reactivity
Authors: Aubert, C. / Leroy, G. / Bruschi, M. / Wall, J.D. / Dolla, A.
#2: Journal: Structure / Year: 1996
Title: Crystal Structure of a Dimeric Octaheme Cytochrome C3 (Mr 26,000) from Desulfovibrio Desulfuricans Norway
Authors: Czjzek, M. / Guerlesquin, F. / Bruschi, M. / Haser, R.
History
DepositionJul 29, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 6, 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

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Assembly

Deposited unit
A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0696
Polymers12,5071
Non-polymers2,5625
Water1,838102
1
A: CYTOCHROME C3
hetero molecules

A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,13812
Polymers25,0142
Non-polymers5,12410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area11010 Å2
ΔGint-215 kcal/mol
Surface area12160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.620, 72.620, 60.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CYTOCHROME C3


Mass: 12506.900 Da / Num. of mol.: 1 / Mutation: Y73E
Source method: isolated from a genetically manipulated source
Details: MR 26000 / Source: (gene. exp.) Desulfomicrobium norvegicum (bacteria) / Strain: Norway 4
Description: SULFATE REDUCING BACTERIA, ALSO KNOWN AS DESULFOMICROBIUM BACULATUM
Plasmid: PJRD215 / Production host: Desulfovibrio desulfuricans (bacteria) / References: UniProt: P38554
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.53 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.6
Details: THE PROTEIN WAS CRYSTALLIZED FROM 2.4M AMMONIUM SULFATE, 100MM TRIS PH 7.6
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Czjzek, M., (1992) J. Mol. Biol., 228, 995.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.4 MTris-HCl1drop
313 %ethanol1reservoir
40.4 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 9880 / % possible obs: 95.7 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 20.97 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 4 % / Rmerge(I) obs: 0.35 / % possible all: 91.1
Reflection
*PLUS
Num. measured all: 53789

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CZJ

1czj


Resolution: 2.2→22 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.239 944 10 %RANDOM
Rwork0.175 ---
obs0.175 9868 95.85 %-
Displacement parametersBiso mean: 21.32 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 177 102 1138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.815
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.06
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.232
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
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.278 114 9.3 %
Rwork0.227 893 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.06
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.232

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