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- PDB-2vpw: Polysulfide reductase with bound menaquinone -

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Basic information

Entry
Database: PDB / ID: 2vpw
TitlePolysulfide reductase with bound menaquinone
Components
  • HYPOTHETICAL MEMBRANE SPANNING PROTEIN
  • NRFC PROTEIN
  • THIOSULFATE REDUCTASE
KeywordsOXIDOREDUCTASE / IRON / 4FE-4S / MOLYBDENUM / IRON-SULFUR / METAL-BINDING / MEMBRANE PROTEIN / RESPIRATORY ENZYME
Function / homology
Function and homology information


Oxidoreductases / molybdopterin cofactor binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / membrane / metal ion binding
Similarity search - Function
Formate dehydrogenase/DMSO reductase fold / Formate dehydrogenase/DMSO reductase domain / Formate dehydrogenase/DMSO reductase, / Formate dehydrogenase/DMSO reductase, / Polysulfide reductase / Polysulfide reductase / : / ADC-like domains / 4Fe-4S binding domain / : ...Formate dehydrogenase/DMSO reductase fold / Formate dehydrogenase/DMSO reductase domain / Formate dehydrogenase/DMSO reductase, / Formate dehydrogenase/DMSO reductase, / Polysulfide reductase / Polysulfide reductase / : / ADC-like domains / 4Fe-4S binding domain / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / 7Fe ferredoxin / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-Beta Plaits - #20 / Barwin-like endoglucanases - #20 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / N-terminal domain of TfIIb / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Single Sheet / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / Up-down Bundle / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MGD / MOLYBDENUM ATOM / MENAQUINONE-7 / IRON/SULFUR CLUSTER / Thiosulfate reductase / NrfC protein / Hypothetical membrane spanning protein
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsJormakka, M. / Yokoyama, K. / Yano, T. / Tamakoshi, M. / Akimoto, S. / Shimamura, T. / Curmi, P. / Iwata, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Molecular Mechanism of Energy Conservation in Polysulfide Respiration.
Authors: Jormakka, M. / Yokoyama, K. / Yano, T. / Tamakoshi, M. / Akimoto, S. / Shimamura, T. / Curmi, P. / Iwata, S.
History
DepositionMar 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOSULFATE REDUCTASE
B: NRFC PROTEIN
C: HYPOTHETICAL MEMBRANE SPANNING PROTEIN
E: THIOSULFATE REDUCTASE
F: NRFC PROTEIN
G: HYPOTHETICAL MEMBRANE SPANNING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,50324
Polymers271,5346
Non-polymers7,96918
Water23,1491285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20540 Å2
ΔGint-134.9 kcal/mol
Surface area96420 Å2
MethodPQS
Unit cell
Length a, b, c (Å)115.377, 163.580, 238.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 6 molecules AEBFCG

#1: Protein THIOSULFATE REDUCTASE / POLYSULFIDE REDUCTASE


Mass: 86737.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / References: UniProt: Q72LA4
#2: Protein NRFC PROTEIN


Mass: 21405.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / References: UniProt: Q72LA5
#3: Protein HYPOTHETICAL MEMBRANE SPANNING PROTEIN


Mass: 27623.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / References: UniProt: Q72LA6

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Non-polymers , 5 types, 1303 molecules

#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#6: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo
#7: Chemical ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H64O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1285 / 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: 3.98 Å3/Da / Density % sol: 68.86 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG400, 100MM MES PH 6.5, 200MM CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 79588 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.7
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.1 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3.1→39.82 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2719159.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1610 2 %RANDOM
Rwork0.271 ---
obs0.271 79365 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.108 Å2 / ksol: 0.350643 e/Å3
Displacement parametersBiso mean: 75.3 Å2
Baniso -1Baniso -2Baniso -3
1--18.36 Å20 Å20 Å2
2--17.29 Å20 Å2
3---1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.1→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18638 0 300 1285 20223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 260 2 %
Rwork0.332 12951 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PRO.PARPRO.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER.PARAM

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