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- PDB-1duw: STRUCTURE OF NONAHEME CYTOCHROME C -

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Basic information

Entry
Database: PDB / ID: 1duw
TitleSTRUCTURE OF NONAHEME CYTOCHROME C
ComponentsNONAHEME CYTOCHROME C
KeywordsELECTRON TRANSPORT / heme / cytochrome c / hydrogenase / hmc operon
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
: / Class III cytochrome C / Class III cytochrome C family / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
HEME C / Nonaheme cytochrome c
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 Å
AuthorsUmhau, S. / Fritz, G. / Diederichs, K. / Breed, J. / Kroneck, P.M. / Welte, W.
CitationJournal: Biochemistry / Year: 2001
Title: Three-dimensional structure of the nonaheme cytochrome c from Desulfovibrio desulfuricans Essex in the Fe(III) state at 1.89 A resolution.
Authors: Umhau, S. / Fritz, G. / Diederichs, K. / Breed, J. / Welte, W. / Kroneck, P.M.
History
DepositionJan 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _diffrn_source.pdbx_synchrotron_site / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NONAHEME CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,38611
Polymers31,7271
Non-polymers5,65910
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NONAHEME CYTOCHROME C
hetero molecules

A: NONAHEME CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,77222
Polymers63,4552
Non-polymers11,31720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area25230 Å2
ΔGint-437 kcal/mol
Surface area27160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.400, 55.400, 236.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NONAHEME CYTOCHROME C


Mass: 31727.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DESUFOVIBRIO DESULFURICANS STRAIN: ESSEX6 COLLECTION: ATCC 29577
Source: (natural) Desulfovibrio desulfuricans (bacteria) / Strain: ESSEX6 / References: UniProt: Q9XCU0
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Isopropanol, HEPES pH 7.5, , VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Details: drop consists of equal amounts of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
215 %(w/v)PEG60001reservoirprecipitant
3100 mMHEPES-NaOH1reservoirprecipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.83
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 101894 / Num. obs: 27269 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.7
Reflection shellResolution: 1.89→1.98 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.187 / Num. unique all: 3249 / % possible all: 80.6
Reflection
*PLUS
Highest resolution: 1.89 Å / Lowest resolution: 30 Å / Num. measured all: 101894
Reflection shell
*PLUS
% possible obs: 80.6 % / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
SOLVEphasing
SHELXL-97refinement
MAR345data collection
XDSdata scaling
RefinementResolution: 1.89→30 Å / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2126 -RANDOM
Rwork0.183 ---
all0.191 28326 --
obs0.183 25623 7.5 %-
Refinement stepCycle: LAST / Resolution: 1.89→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 393 423 3001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d2.38
X-RAY DIFFRACTIONs_bond_d0.01
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.204 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.38

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