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- PDB-3u99: The experimental X-ray structure of the new diheme cytochrome typ... -

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Basic information

Entry
Database: PDB / ID: 3u99
TitleThe experimental X-ray structure of the new diheme cytochrome type c from Shewanella baltica OS155 sb-DHC
ComponentsDiheme cytochrome c
KeywordsELECTRON TRANSPORT / Cytochrome c fold / Electron transfer protein / diheme protein / bacterium Shewanella Baltica OS155
Function / homologyDihaem cytochrome c / Dihaem cytochrome c / metal ion binding / HEME C / Diheme cytochrome c
Function and homology information
Biological speciesShewanella baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.146 Å
AuthorsDe March, M. / Di Rocco, G. / Geremia, S.
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 2015
Title: High-resolution crystal structure of the recombinant diheme cytochrome c from Shewanella baltica (OS155).
Authors: De March, M. / Di Rocco, G. / Hickey, N. / Geremia, S.
#1: Journal: J.Biol.Inorg.Chem. / Year: 2011
Title: Cloning, expression, and physicochemical characterization of a new diheme cytochrome c from Shewanella baltica OS155.
Authors: Di Rocco, G. / Battistuzzi, G. / Bortolotti, C.A. / Borsari, M. / Ferrari, E. / Monari, S. / Sola, M.
#2: Journal: Biochemistry / Year: 2006
Title: Structural and functional studies on DHC, the diheme cytochrome c from Rhodobacter sphaeroides, and its interaction with SHP, the sphaeroides heme protein.
Authors: Gibson, H.R. / Mowat, C.G. / Miles, C.S. / Li, B.R. / Leys, D. / Reid, G.A. / Chapman, S.K.
#3: Journal: Biochemistry / Year: 2005
Title: Structural and biochemical characterization of DHC2, a novel diheme cytochrome c from Geobacter sulfurreducens.
Authors: Heitmann, D. / Einsle, O.
#4: Journal: Biochemistry / Year: 2002
Title: The 1.25 A resolution structure of the diheme NapB subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement.
Authors: Brige, A. / Leys, D. / Meyer, T.E. / Cusanovich, M.A. / Van Beeumen, J.J.
History
DepositionOct 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id / _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: Diheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6253
Polymers16,3881
Non-polymers1,2372
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.810, 42.970, 81.070
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 Diheme cytochrome c


Mass: 16388.250 Da / Num. of mol.: 1 / Fragment: UNP Residues 40-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella baltica (bacteria) / Strain: OS155 / ATCC BAA-1091 / Gene: Sbal_0241 / Production host: Escherichia coli (E. coli) / References: UniProt: A3CZ62
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Tris pH 6.5, PEG3350, Ammonium Sulphate, Dithionite, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.08→17.97 Å / Num. all: 58315 / Num. obs: 58150 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.107
Reflection shellResolution: 1.08→2.45 Å / % possible all: 96.9

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FW5

1fw5


Resolution: 1.146→10.8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1536 2379 RANDOM
Rwork0.1067 --
all0.1383 45277 -
obs0.1067 26836 -
Refinement stepCycle: LAST / Resolution: 1.146→10.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 86 250 1313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04

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