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- PDB-6qvm: Undecaheme cytochrome from S-layer of Carboxydothermus ferrireducens -

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Basic information

Entry
Database: PDB / ID: 6qvm
TitleUndecaheme cytochrome from S-layer of Carboxydothermus ferrireducens
ComponentsMultiheme cytochrome cf
KeywordsOXIDOREDUCTASE / multiheme cytochrome / s-layer binding domain / O-glycosylation / extremophile / cytochrome c / cytochrome f
Function / homologyHEME C / PHOSPHATE ION
Function and homology information
Biological speciesCarboxydothermus ferrireducens DSM 11255 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsOsipov, E.M. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Gavrilov, S.F. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-24-00172 Russian Federation
CitationJournal: Structure / Year: 2023
Title: Extracellular Fe(III) reductase structure reveals a modular organization enabling S-layer insertion and electron transfer to insoluble substrates
Authors: Tikhonova, T.V. / Osipov, E.M. / Dergousova, N.I. / Boyko, K.M. / Elizarov, I.M. / Gavrilov, S.N. / Khrenova, M.G. / Robb, F.T. / Solovieva, A.Y. / Bonch-Osmolovskaya, E.A. / Popov, V.O.
History
DepositionMar 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 8, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.pdbx_database_id_DOI ..._chem_comp.pdbx_synonyms / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multiheme cytochrome cf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,75020
Polymers74,0291
Non-polymers8,72119
Water4,630257
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15010 Å2
ΔGint-219 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.679, 193.980, 170.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1050-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Multiheme cytochrome cf


Mass: 74028.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Carboxydothermus ferrireducens DSM 11255 (bacteria)
Plasmid details: Grown on magnetite

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GalpNAc]{[(3+1)][b-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2- ...2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGalpNAcb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2112h-1b_1-5_2*NCC/3=O]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GalpNAc]{[(3+1)][b-D-GalpNAc]{[(3+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 273 molecules

#4: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 4.35 Å3/Da / Density % sol: 71.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 8 % PEG 8000, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.90000, 1.73950
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.73951
ReflectionResolution: 2.5→97 Å / Num. obs: 45039 / % possible obs: 99.82 % / Redundancy: 12 % / CC1/2: 0.998 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4370 / CC1/2: 0.889 / Rpim(I) all: 0.256 / Rrim(I) all: 0.923 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDSdata reduction
iMOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→66.433 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 21.46
Details: Maximum-likelihood refinement with Hendrikson-Lattman coefficients
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 4286 4.98 %RANDOM
Rwork0.1776 ---
obs0.1792 44941 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→66.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4948 0 597 257 5802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135801
X-RAY DIFFRACTIONf_angle_d0.9797988
X-RAY DIFFRACTIONf_dihedral_angle_d17.9673154
X-RAY DIFFRACTIONf_chiral_restr0.046790
X-RAY DIFFRACTIONf_plane_restr0.005977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.37421170.27232740X-RAY DIFFRACTION100
2.5284-2.55820.28051290.2552745X-RAY DIFFRACTION100
2.5582-2.58940.28251430.23892746X-RAY DIFFRACTION100
2.5894-2.62220.31111290.23422744X-RAY DIFFRACTION100
2.6222-2.65670.26951400.23492695X-RAY DIFFRACTION100
2.6567-2.69310.29821360.22752737X-RAY DIFFRACTION99
2.6931-2.73150.25441490.22332681X-RAY DIFFRACTION100
2.7315-2.77230.25621500.22142742X-RAY DIFFRACTION100
2.7723-2.81560.26421730.20742730X-RAY DIFFRACTION100
2.8156-2.86180.21571490.20862712X-RAY DIFFRACTION100
2.8618-2.91110.2041820.20772672X-RAY DIFFRACTION100
2.9111-2.96410.2471630.20522689X-RAY DIFFRACTION100
2.9641-3.02110.2371730.19962722X-RAY DIFFRACTION100
3.0211-3.08280.23561450.19462745X-RAY DIFFRACTION100
3.0828-3.14980.23221460.18792693X-RAY DIFFRACTION100
3.1498-3.22310.22151150.19822776X-RAY DIFFRACTION100
3.2231-3.30370.20811620.18972678X-RAY DIFFRACTION100
3.3037-3.3930.23181290.19022772X-RAY DIFFRACTION99
3.393-3.49280.19611510.19222708X-RAY DIFFRACTION100
3.4928-3.60550.24751490.19672746X-RAY DIFFRACTION100
3.6055-3.73440.24031110.18822755X-RAY DIFFRACTION100
3.7344-3.88390.22511540.17092716X-RAY DIFFRACTION100
3.8839-4.06060.22271100.15222741X-RAY DIFFRACTION100
4.0606-4.27470.15621330.14512741X-RAY DIFFRACTION100
4.2747-4.54250.18411450.13822735X-RAY DIFFRACTION100
4.5425-4.89310.14071650.13512695X-RAY DIFFRACTION100
4.8931-5.38530.2031410.14082732X-RAY DIFFRACTION100
5.3853-6.16410.17771440.15182729X-RAY DIFFRACTION100
6.1641-7.76420.16171050.14592759X-RAY DIFFRACTION99
7.7642-66.4560.16141480.1632710X-RAY DIFFRACTION99
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)
10.1439-0.0435-0.05410.15050.09140.3530.0498-0.0234-0.02790.1766-0.10860.0589-0.532-0.0621-0.03930.49970.0901-0.00530.1624-0.03390.235428.625886.730760.6258
20.0413-0.0140.06350.0450.01690.0220.13620.0925-0.1072-0.2707-0.0041-0.32030.1053-0.164300.499-0.09310.04630.3153-0.10330.481822.195511.653264.2691
30.0323-0.0026-0.01730.02820.01260.0169-0.04690.0762-0.02160.09090.11880.05740.054-0.114300.1984-0.02590.04560.2880.0050.193310.217838.577978.0418
40.1612-0.03840.23750.3063-0.25930.45310.01850.0457-0.00950.0996-0.049-0.0023-0.07770.07190.00280.1083-0.0231-0.0070.1771-0.00720.132940.207756.461562.4933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 414 through 658 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 413 )

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