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- PDB-3dp5: Crystal structure of Geobacter sulfurreducens OmcF with N-termina... -

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Basic information

Entry
Database: PDB / ID: 3dp5
TitleCrystal structure of Geobacter sulfurreducens OmcF with N-terminal Strep-tag II
ComponentsCytochrome c family protein
KeywordsELECTRON TRANSPORT / c-type cytochrome / Fe SAD phasing / dissimilatory metal reduction / Geobacter sulfurreducens
Function / homology
Function and homology information


plasma membrane-derived thylakoid lumen / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c6 / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Lipoprotein cytochrome c, 1 heme-binding site
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.86 Å
AuthorsLukat, P. / Hoffmann, M. / Einsle, O.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2008
Title: Crystal packing of the c(6)-type cytochrome OmcF from Geobacter sulfurreducens is mediated by an N-terminal Strep-tag II
Authors: Lukat, P. / Hoffmann, M. / Einsle, O.
History
DepositionJul 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_atom_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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 c family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0663
Polymers10,3521
Non-polymers7152
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.475, 40.125, 42.085
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cytochrome c family protein / OmcF


Mass: 10351.609 Da / Num. of mol.: 1 / Fragment: UNP residues 26-104, OmcF
Source method: isolated from a genetically manipulated source
Details: Coexpression with the CCM-system on pEC86 plasmid / Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA / Gene: GSU2432 / Plasmid details: Modified with N-terminal Strep-tag II / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q74AE4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4-1.8M ammonium sulfate, 2% PEG400, 100mM HEPES/NaOH, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 2007 / Details: mirrors
RadiationMonochromator: Osmic Blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→33.08 Å / Num. obs: 8066 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 21.78 % / Biso Wilson estimate: 21.934 Å2 / Rsym value: 0.105 / Net I/σ(I): 23.5
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 16.04 % / Rmerge(I) obs: 0.4952 / Mean I/σ(I) obs: 6.06 / Num. unique all: 394 / Rsym value: 0.4952 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→33.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.128 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.153 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20987 371 4.6 %RANDOM
Rwork0.17045 ---
obs0.17236 7669 99.68 %-
all-7684 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.934 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.86→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms739 0 48 120 907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022815
X-RAY DIFFRACTIONr_angle_refined_deg1.7762.1171125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.0045100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60222.42433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13915105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.24157
X-RAY DIFFRACTIONr_chiral_restr0.1330.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02661
X-RAY DIFFRACTIONr_nbd_refined0.2640.2406
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2547
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.237
X-RAY DIFFRACTIONr_mcbond_it0.9831.5513
X-RAY DIFFRACTIONr_mcangle_it1.422795
X-RAY DIFFRACTIONr_scbond_it2.2833349
X-RAY DIFFRACTIONr_scangle_it3.3894.5328
LS refinement shellResolution: 1.857→1.906 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 25 -
Rwork0.26 536 -
obs-327 96.56 %

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