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- PDB-1b7v: Structure of the C-553 cytochrome from Bacillus pasteruii to 1.7 ... -

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Basic information

Entry
Database: PDB / ID: 1b7v
TitleStructure of the C-553 cytochrome from Bacillus pasteruii to 1.7 A resolution
ComponentsPROTEIN (CYTOCHROME C-553)
KeywordsELECTRON TRANSFER / CYTOCHROME
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 / MAD / Resolution: 1.7 Å
AuthorsGonzalez, A. / Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, 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: 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.
#2: 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.
History
DepositionJan 22, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2013Group: Data collection / Database references / Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _diffrn_source.pdbx_synchrotron_site / _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: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 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: PROTEIN (CYTOCHROME C-553)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7342
Polymers7,1161
Non-polymers6191
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.090, 39.160, 43.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein PROTEIN (CYTOCHROME C-553)


Mass: 7115.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) Sporosarcina pasteurii (bacteria) / Cellular location: MEMBRANE-BOUND / Strain: 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.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTER LYS: THE FIRST 21 RESIDUES WERE NOT VISIBLE, PROTEIN PRESUMEDLY CLEAVED AT RESIDUE VAL 22

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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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8MG/ML OF CYTOCHROME, 20MM TRIS.HCL, PH 8.0 AT 20 DEGREES C, HANGING DROPS IN HAMPTON RESEARCH 24-WELL LINBRO PLATES, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutionsName: TRIS.HCL
Crystal
*PLUS
Density % sol: 41 %
Crystal grow
*PLUS
Temperature: 20 K
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG BW7A11.741
SYNCHROTRONEMBL/DESY, HAMBURG BW7A21.735
SYNCHROTRONEMBL/DESY, HAMBURG BW7A31
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7411
21.7351
311
ReflectionResolution: 1.7→20 Å / Num. obs: 7404 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.04 / Net I/σ(I): 8.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.101 / % possible all: 97.1
Reflection
*PLUS
Redundancy: 3.52 % / Num. measured all: 26088 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 97.1 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / SU B: 1.94 / SU ML: 0.06 / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.206 343 5 %RANDOM
Rwork0.174 ---
obs0.174 7404 99.5 %-
all-7404 --
Displacement parametersBiso mean: 10.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms496 0 43 128 667
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0270.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5933
X-RAY DIFFRACTIONp_mcangle_it2.0545
X-RAY DIFFRACTIONp_scbond_it3.8116
X-RAY DIFFRACTIONp_scangle_it5.248
X-RAY DIFFRACTIONp_plane_restr0.0248
X-RAY DIFFRACTIONp_chiral_restr0.071
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.3770.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.47
X-RAY DIFFRACTIONp_staggered_tor12.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor15.220
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 10.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_mcbond_it3
X-RAY DIFFRACTIONp_scbond_it6
X-RAY DIFFRACTIONp_mcangle_it5
X-RAY DIFFRACTIONp_scangle_it8

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