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- PDB-3bxu: PpcB, A Cytochrome c7 from Geobacter sulfurreducens -

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Basic information

Entry
Database: PDB / ID: 3bxu
TitlePpcB, A Cytochrome c7 from Geobacter sulfurreducens
ComponentsCytochrome c3
KeywordsELECTRON TRANSPORT / Multiheme cytochromes / cytochrome c7 Geobacter sulfurreducens
Function / homology
Function and homology information


sulfur utilization / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c7-like / Cytochrome c7 and related cytochrome c / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsPokkuluri, P.R. / Schiffer, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Structural insights into the modulation of the redox properties of two Geobacter sulfurreducens homologous triheme cytochromes.
Authors: Morgado, L. / Bruix, M. / Orshonsky, V. / Londer, Y.Y. / Duke, N.E. / Yang, X. / Pokkuluri, P.R. / Schiffer, M. / Salgueiro, C.A.
History
DepositionJan 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c3
B: Cytochrome c3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2659
Polymers15,4702
Non-polymers3,7957
Water3,621201
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-152.7 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.200, 47.500, 88.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological unit of PpcB is unknown. It appears to be a dimer in the crystal with a buried surface area of 1190 square angstrom calculated with the program SURFACE (CCP4).

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Components

#1: Protein Cytochrome c3


Mass: 7735.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: cyd-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q74G83
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 45% Jeffamine ED-2001 0.2 M ammonium iodide, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.73766, 1.73859, 1.78875
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 18, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.737661
21.738591
31.788751
ReflectionResolution: 1.35→50 Å / Num. obs: 58322 / % possible obs: 93 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 22.4
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3851 / % possible all: 62

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→19.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.931 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The number of unique measured reflections is too large because the Bijvoet pairs are treated as separate reflections with the scale anomalous option in HKL2000. The following side chain ...Details: The number of unique measured reflections is too large because the Bijvoet pairs are treated as separate reflections with the scale anomalous option in HKL2000. The following side chain atoms are in weak density and are probably disordered. On Chain A, Asp2: OD1; Lys9: CD, CE, NZ; Lys18: CD, CE, NZ; Lys19: CD, CE, NZ; Lys33: CD, CE, NZ; Lys49: CD, CE, NZ; Lys52: NZ; Glu56: CD, OE1, OE2; Lys60: CD, CE, NZ; Lys70: CG, CD, CE, NZ; Lys71: CB, CG, CD, CE, NZ; on Chain B, Lys9: CG, CD, CE, NZ; Lsy18: NZ; Lys33: CE, NZ; Lys37: CE, NZ; Met58: SD, CE; Lys60: CG, CD, CE, NZ. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18575 3006 9.9 %RANDOM
Rwork0.16168 ---
obs0.16411 27324 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.746 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 263 201 1540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221406
X-RAY DIFFRACTIONr_bond_other_d0.0020.021109
X-RAY DIFFRACTIONr_angle_refined_deg1.6482.5081963
X-RAY DIFFRACTIONr_angle_other_deg1.87732609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015142
X-RAY DIFFRACTIONr_chiral_restr0.1010.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021478
X-RAY DIFFRACTIONr_gen_planes_other0.0290.02190
X-RAY DIFFRACTIONr_nbd_refined0.4040.2410
X-RAY DIFFRACTIONr_nbd_other0.240.21368
X-RAY DIFFRACTIONr_nbtor_other0.0920.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2140
X-RAY DIFFRACTIONr_metal_ion_refined0.0160.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.241
X-RAY DIFFRACTIONr_mcbond_it0.9441.5704
X-RAY DIFFRACTIONr_mcangle_it1.49121123
X-RAY DIFFRACTIONr_scbond_it1.9683702
X-RAY DIFFRACTIONr_scangle_it2.7064.5838
X-RAY DIFFRACTIONr_rigid_bond_restr1.06721406
X-RAY DIFFRACTIONr_sphericity_free3.1172201
X-RAY DIFFRACTIONr_sphericity_bonded1.74121341
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 124
Rwork0.219 1286
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0909-0.34440.0261.0526-0.42311.09-0.01760.0079-0.0056-0.03060.0776-0.00350.0108-0.0715-0.060.02140.003-0.00170.0055-0.00310.00987.3736-0.914711.8341
21.7063-0.4625-0.41480.6039-0.0181.4389-0.0083-0.0176-0.01090.01440.0321-0.01380.0274-0.0276-0.02380.023-0.011-0.00440.0060.00570.0179-7.7491-0.6995-10.1498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA - F1 - 741
2X-RAY DIFFRACTION2BB - I1 - 741

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