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- PDB-1c75: 0.97 A "AB INITIO" CRYSTAL STRUCTURE OF CYTOCHROME C-553 FROM BAC... -

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Entry
Database: PDB / ID: 1c75
Title0.97 A "AB INITIO" CRYSTAL STRUCTURE OF CYTOCHROME C-553 FROM BACILLUS PASTEURII
ComponentsCYTOCHROME C-553
KeywordsELECTRON TRANSPORT / C-553 / HEME / CYTOCHROME / BACILLUS PASTEURII / AB INITIO / ATOMIC RESOLUTION
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Cytochrome c, Bacillus subtilis c550-related / : / Cytochrome C oxidase, cbb3-type, subunit III / 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
HEME C / Cytochrome c-553
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.97 Å
AuthorsBenini, S. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S.
Citation
Journal: Biochemistry / Year: 2000
Title: Crystal structure of oxidized Bacillus pasteurii cytochrome c553 at 0.97-A resolution.
Authors: Benini, S. / Gonzalez, A. / Rypniewski, W.R. / Wilson, K.S. / Van Beeumen, J.J. / Ciurli, S.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1999
Title: Cytochrome C-553 from the Alkalophilic Bacterium Bacillus Pasteurii Has the Primary Structure Characteristics of a Lipoprotein
Authors: Vandenberghe, I.H.M. / Guisez, Y. / Ciurli, S. / Benini, S. / Van-Beeumen, J.J.
#2: Journal: J.Biol.Inorg.Chem. / Year: 1998
Title: Modulation of Bacillus Pasteurii Cytochrome C553 Reduction Potential by Structural and Solution Parameters
Authors: Benini, S. / Borsari, M. / Ciurli, S. / Dikiy, A. / Lamborghini, M.
#3: Journal: Proteins / Year: 1997
Title: Crystals of Cytochrome C-553 from Bacillus Pasteurii Show Diffraction to 0.97 A Resolution
Authors: Benini, S. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S.
History
DepositionFeb 9, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionMar 22, 2000ID: 1B7C
Revision 1.0Mar 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / software / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _software.name ..._diffrn_source.pdbx_synchrotron_site / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
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.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 27, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: 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 C-553
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7342
Polymers7,1161
Non-polymers6191
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.144, 39.422, 44.021
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-553


Mass: 7115.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN (DSM) / Source: (natural) Sporosarcina pasteurii (bacteria) / Cellular location: CYTOPLASM / Strain: DSM 33 / References: UniProt: P82599
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.08 Å3/Da / Density % sol: 38 % / Description: THE STRUCTURE WAS SOLVED "AB INITIO"
Crystal growpH: 5
Details: 3.2 M AMMONIUM SULPHATE IN 100 MM SODIUM CITRATE BUFFER PH 5.0
Crystal
*PLUS
Density % sol: 41 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
220 mMTris-HCl1drop
3100 mMsodium acetate1reservoir
43.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.885
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 23, 1996 / Details: SEGMENTED MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 0.97→20 Å / Num. obs: 38959 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.46 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 17.16
Reflection shellResolution: 0.97→0.99 Å / Redundancy: 2.72 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.18 / Rsym value: 0.242 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 5.47 % / Num. measured all: 212694 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS

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Processing

Software
NameVersionClassification
SHELXL-97refinement
REFMACARP (CCP4)refinement
SCALEPACKdata scaling
ARP/wARPmodel building
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 0.97→20 Å / Num. parameters: 6286 / Num. restraintsaints: 7877 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
all0.1162 38898 -
obs0.1162 -99.9 %
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201
Refine analyzeNum. disordered residues: 14 / Occupancy sum hydrogen: 486 / Occupancy sum non hydrogen: 661.12
Refinement stepCycle: LAST / Resolution: 0.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms497 0 43 125 665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0.02
X-RAY DIFFRACTIONs_from_restr_planes0.034
X-RAY DIFFRACTIONs_zero_chiral_vol0.117
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.064
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.117
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_plane_restr0.034
X-RAY DIFFRACTIONs_chiral_restr0.117

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