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- PDB-1gws: hexadecaheme high molecular weight cytochrome Hmc from Desulfovib... -

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Basic information

Entry
Database: PDB / ID: 1gws
Titlehexadecaheme high molecular weight cytochrome Hmc from Desulfovibrio vulgaris Hildenborough
ComponentsHIGH-MOLECULAR-WEIGHT CYTOCHROME C
KeywordsELECTRON TRANSPORT / MULTIHEME CYTOCHROME / SULFATE REDUCING BACTERIA / PERIPLASMIC / HEME
Function / homology
Function and homology information


periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
High-molecular-weight cytochrome c / 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 / High-molecular-weight cytochrome c
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCzjzek, M. / Haser, R. / Bruschi, M.
CitationJournal: Structure / Year: 2002
Title: The Crystal Structure of the Hexadaca-Heme Cytochrome Hmc and a Structural Model of its Complex with Cytochrome C3
Authors: Czjzek, M. / Elantak, L. / Zamboni, V. / Morelli, X. / Dolla, A. / Guerlesquin, F. / Bruschi, M.
History
DepositionMar 25, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Sep 25, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / exptl_crystal_grow / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _pdbx_nonpoly_scheme.entity_id / _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 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_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: HIGH-MOLECULAR-WEIGHT CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,90917
Polymers59,0131
Non-polymers9,89616
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)108.386, 108.386, 102.809
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein HIGH-MOLECULAR-WEIGHT CYTOCHROME C / CYTOCHROME CC3


Mass: 59012.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 12 COVALENTLY LINKED HEMES / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: P24092
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.727 Å3/Da / Density % sol: 54.8 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% JEFFAMINE M-600, MES PH 6.5, 50 MM CSCL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %Jeffamine M-6001reservoir
250 mMcesium chloride1reservoir
3100 mMMES1reservoirpH6.5
46 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.73891
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2001 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73891 Å / Relative weight: 1
ReflectionResolution: 2.5→27 Å / Num. obs: 23044 / % possible obs: 97.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 1.9 / % possible all: 84.6
Reflection
*PLUS
Highest resolution: 2.42 Å / Lowest resolution: 27 Å / % possible obs: 99.4 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 99.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
DENZOdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→33.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.016 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ALA A 144, NO DENSITY PRESENT FOR SIDE CHAIN, THE RESIDUE WAS THERFORE MODELED AS ALA ALA A 512, NO DENSITY PRESENT FOR SIDE CHAIN, THE RESIDUE WAS THERFORE MODELED AS ALA
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1281 4.8 %RANDOM
Rwork0.201 ---
obs-25316 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 36.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å2-1.55 Å20 Å2
2---3.11 Å20 Å2
3---4.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 688 151 4632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0224676
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6752.3946534
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3223502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.39815744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1710.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023639
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.40.32532
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.5382
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1550.521
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6760.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2491.52510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.25124014
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.49332166
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9144.52520
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 94
Rwork0.235 1845
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)
11.91490.38610.05490.70320.10621.55220.15340.02090.03620.02020.00510.0363-0.02460.1126-0.15850.26650.01410.00050.2868-0.01760.00114.91966.412-3.835
22.7684-0.297-1.0640.8272-0.10730.81070.09260.1049-0.04660.0298-0.06820.0963-0.0296-0.1023-0.02440.24660.02360.02090.27790.0030.0175-21.0969.895-1.936
3-0.091-0.1872-0.03260.9431-0.06250.3821-0.05370.0250.03210.0840.0302-0.07270.02580.04130.02350.24680.0219-0.01050.31660.00830.0488-32.50994.5128.791
41.15240.7502-0.49062.2275-1.12550.6915-0.00270.15280.18570.02140.01120.085-0.0432-0.0399-0.00850.24190.0096-0.04420.33750.03950.0167-31.75121.066-6.083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 114
2X-RAY DIFFRACTION1A601 - 603
3X-RAY DIFFRACTION2A115 - 222
4X-RAY DIFFRACTION2A604 - 607
5X-RAY DIFFRACTION3A260 - 357
6X-RAY DIFFRACTION3A608 - 612
7X-RAY DIFFRACTION4A410 - 512
8X-RAY DIFFRACTION4A613 - 616
Software
*PLUS
Name: REFMAC / Version: '5.0.36 18/01/2001' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.42 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.462 Å / Rfactor Rfree: 0.324 / Rfactor Rwork: 0.235 / Num. reflection Rwork: 1845 / Total num. of bins used: 20

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