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- PDB-1jdl: Structure of cytochrome c2 from Rhodospirillum Centenum -

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Basic information

Entry
Database: PDB / ID: 1jdl
TitleStructure of cytochrome c2 from Rhodospirillum Centenum
ComponentsCYTOCHROME C2, ISO-2
KeywordsELECTRON TRANSPORT / ALPHA HELIX
Function / homology
Function and homology information


photosynthesis / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c2 iso-2
Similarity search - Component
Biological speciesRhodospirillum centenum (bacteria)
MethodX-RAY DIFFRACTION / SAD, MIR,MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCamara-Artigas, A. / Williams, J.C. / Allen, J.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of cytochrome c2 from Rhodospirillum centenum.
Authors: Camara-Artigas, A. / Williams, J.C. / Allen, J.P.
#1: Journal: Biochemistry / Year: 1994
Title: Interaction Between Cytochrome c2 and Reaction Centers from Purple Bacteria
Authors: Wang, S. / Li, X. / Williams, J.C. / Allen, J.P. / Mathis, P.
#2: Journal: Biochemistry / Year: 1994
Title: Relationship Between Rate and Free Energy Difference for Electron Transfer from Cytochrome c2 to the Reaction Center in Rhodobacter sphaeroides.
Authors: Lin, X. / Williams, J.C. / Allen, J.P. / Mathis, P.
History
DepositionJun 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 16, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 C2, ISO-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6692
Polymers13,0531
Non-polymers6161
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.700, 59.900, 65.400
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 C2, ISO-2 / C552


Mass: 13052.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodospirillum centenum (bacteria) / References: UniProt: P81154
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.139 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 6000, potassium phosphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 277 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
210 %PEG60001reservoir
30.1 Mphosphate1reservoirpH7

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
21
31
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU200HB11.5418
ROTATING ANODERIGAKU RU20021.5418
ROTATING ANODERIGAKU RU20031.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS IIC1IMAGE PLATEOct 10, 1999
RIGAKU RAXIS IIC2IMAGE PLATEOct 12, 1999
RIGAKU RAXIS IIC3IMAGE PLATEOct 15, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 13248 / Num. obs: 13248 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 16.9 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 2986
Reflection shellResolution: 1.7→20 Å / Redundancy: 10 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 149 / Num. unique all: 1169 / % possible all: 88.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 223519 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / % possible obs: 88.4 % / Num. unique obs: 1169

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD, MIR,MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2c2c

2c2c


Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1079 8.4 %random
Rwork0.19 ---
all-13248 --
obs-12801 95.4 %-
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0.05 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 43 87 1022
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d1.47
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.7-1.760.2626810.2661X-RAY DIFFRACTION90788.4
1.76-1.830.25391220.2391X-RAY DIFFRACTION103997.9
1.83-1.910.18121390.1955X-RAY DIFFRACTION1117100
1.91-2.020.22011350.2002X-RAY DIFFRACTION1154100
2.02-2.140.18861240.1957X-RAY DIFFRACTION1174100
2.14-2.310.21041320.2093X-RAY DIFFRACTION1196100
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 8.4 % / Rfactor obs: 0.192 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.47
LS refinement shell
*PLUS
Rfactor Rfree: 0.289 / Rfactor obs: 0.249

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