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- PDB-256b: IMPROVEMENT OF THE 2.5 ANGSTROMS RESOLUTION MODEL OF CYTOCHROME B... -

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Basic information

Entry
Database: PDB / ID: 256b
TitleIMPROVEMENT OF THE 2.5 ANGSTROMS RESOLUTION MODEL OF CYTOCHROME B562 BY REDETERMINING THE PRIMARY STRUCTURE AND USING MOLECULAR GRAPHICS
ComponentsCYTOCHROME B562
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsHamada, K. / Bethge, P.H. / Mathews, F.S.
Citation
Journal: J.Mol.Biol. / Year: 1981
Title: Improvement of the 2.5 A resolution model of cytochrome b562 by redetermining the primary structure and using molecular graphics.
Authors: Lederer, F. / Glatigny, A. / Bethge, P.H. / Bellamy, H.D. / Matthew, F.S.
#1: Journal: J.Biol.Chem. / Year: 1979
Title: The Structure of Cytochrome B562 from Escherichia Coli at 2.5 Angstroms Resolution
Authors: Mathews, F.S. / Bethge, P.H. / Czerwinski, E.W.
#2: Journal: J.Mol.Biol. / Year: 1974
Title: Location of the Iron Atom and the Non-Crystallographic Symmetry Elements in Cytochrome B562
Authors: Czerwinski, E.W. / Mathews, F.S.
History
DepositionJan 16, 1990Processing site: BNL
SupersessionJan 15, 1991ID: 156B
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 27, 2014Group: Derived calculations
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME B562
B: CYTOCHROME B562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2168
Polymers23,5982
Non-polymers1,6176
Water2,972165
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A: CYTOCHROME B562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6084
Polymers11,7991
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME B562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6084
Polymers11,7991
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.710, 50.480, 32.730
Angle α, β, γ (deg.)102.76, 86.55, 106.70
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0924, 0.21325, -0.97262), (0.22896, -0.94607, -0.22918), (-0.96904, -0.24387, 0.0386))

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Components

#1: Protein CYTOCHROME B562


Mass: 11799.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion / Details: Lederer, F., (1981) J. Mol. Biol., 148, 427.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.0 Mphosphate1drop
20.1 M1reserviorLiCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.4→6 Å / Rfactor obs: 0.164
Refinement stepCycle: LAST / Resolution: 1.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 106 165 1923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.033
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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