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- PDB-3h4n: PpcD, A cytochrome c7 from Geobacter sulfurreducens -

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Basic information

Entry
Database: PDB / ID: 3h4n
TitlePpcD, A cytochrome c7 from Geobacter sulfurreducens
ComponentsCytochrome c7
KeywordsELECTRON TRANSPORT / Cytochrome c7 / Multiheme cytochrome / 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: 2010
Title: Structural characterization of a family of cytochromes c(7) involved in Fe(III) respiration by Geobacter sulfurreducens.
Authors: Pokkuluri, P.R. / Londer, Y.Y. / Yang, X. / Duke, N.E. / Erickson, J. / Orshonsky, V. / Johnson, G. / Schiffer, M.
History
DepositionApr 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 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 c7
B: Cytochrome c7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1698
Polymers15,4702
Non-polymers3,6996
Water3,513195
1
A: Cytochrome c7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5844
Polymers7,7351
Non-polymers1,8493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5844
Polymers7,7351
Non-polymers1,8493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.400, 55.900, 94.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTwo molecules per asymmetric unit; Monomer in solution based on size exclusion column chromatography and dynamic light scattering

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Components

#1: Protein Cytochrome c7 / Cytochrome c3


Mass: 7734.983 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: cyd-4, GSU1024 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB7123 / References: UniProt: Q74ED8
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Crystal obtained from Index screen-95 (30% PEG monomethylether 2000, 0.1 M potassium thiocyanate), 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: 1.74041, 1.73818, 1.78832, 1.69077, 1.0332
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 25, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.740411
21.738181
31.788321
41.690771
51.03321
ReflectionResolution: 1.34→50 Å / Num. all: 60576 / Num. obs: 60576 / % possible obs: 97 % / Redundancy: 4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 42.1
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 3 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 8.4 / Num. unique all: 4902 / % possible all: 79

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→36.04 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.697 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17256 3111 9.8 %RANDOM
Rwork0.14939 ---
obs0.15171 28548 98.86 %-
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: 8.874 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.35→36.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 258 195 1458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221419
X-RAY DIFFRACTIONr_bond_other_d0.0020.021159
X-RAY DIFFRACTIONr_angle_refined_deg1.4132.511973
X-RAY DIFFRACTIONr_angle_other_deg0.86532748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2325136
X-RAY DIFFRACTIONr_chiral_restr0.0810.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021457
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02178
X-RAY DIFFRACTIONr_nbd_refined0.4280.2380
X-RAY DIFFRACTIONr_nbd_other0.2440.21355
X-RAY DIFFRACTIONr_nbtor_other0.0830.2637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.227
X-RAY DIFFRACTIONr_mcbond_it0.8911.5679
X-RAY DIFFRACTIONr_mcangle_it1.46221089
X-RAY DIFFRACTIONr_scbond_it1.6963740
X-RAY DIFFRACTIONr_scangle_it2.3624.5883
X-RAY DIFFRACTIONr_rigid_bond_restr0.9821419
X-RAY DIFFRACTIONr_sphericity_free2.5722195
X-RAY DIFFRACTIONr_sphericity_bonded1.41321358
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.157 163
Rwork0.132 1630
obs-1630
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)
11.3495-0.2371-0.40050.55710.23460.57310.0046-0.060.01160.0193-0.00950.00230.00080.02960.00480.0183-0.0053-0.00450.00160.00210.0111.28713.41816.7204
21.22890.1301-0.12560.585-0.15620.2710.03530.10420.0324-0.014-0.01890.0007-0.004-0.041-0.01640.01520.0080.00390.01830.0060.00234.42145.307431.354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 75
2X-RAY DIFFRACTION2B4 - 75

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