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- PDB-4ydd: Crystal structure of the perchlorate reductase PcrAB from Azospir... -

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Basic information

Entry
Database: PDB / ID: 4ydd
TitleCrystal structure of the perchlorate reductase PcrAB from Azospira suillum PS
Components(DMSO reductase family type II enzyme, ...) x 2
KeywordsOXIDOREDUCTASE / electron-shuttling protein
Function / homology
Function and homology information


oxidoreductase complex / anaerobic respiration / cellular respiration / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / oxidoreductase activity / metal ion binding
Similarity search - Function
DMSO reductase family, type II, iron-sulphur subunit / DMSO reductase family, type II, molybdopterin subunit / Nitrate reductase alpha subunit-like, MopB domain / 4Fe-4S dicluster domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase ...DMSO reductase family, type II, iron-sulphur subunit / DMSO reductase family, type II, molybdopterin subunit / Nitrate reductase alpha subunit-like, MopB domain / 4Fe-4S dicluster domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
FE3-S4 CLUSTER / Chem-MD1 / Chem-MGD / MOLYBDENUM ATOM / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / DMSO reductase family type II enzyme, iron-sulfur subunit / DMSO reductase family type II enzyme, molybdopterin subunit
Similarity search - Component
Biological speciesDechlorosoma suillum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsTsai, C.-L. / Youngblut, M.D. / Tainer, J.A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.
Authors: Youngblut, M.D. / Tsai, C.L. / Clark, I.C. / Carlson, H.K. / Maglaqui, A.P. / Gau-Pan, P.S. / Redford, S.A. / Wong, A. / Tainer, J.A. / Coates, J.D.
History
DepositionFeb 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DMSO reductase family type II enzyme, molybdopterin subunit
B: DMSO reductase family type II enzyme, iron-sulfur subunit
C: DMSO reductase family type II enzyme, molybdopterin subunit
D: DMSO reductase family type II enzyme, iron-sulfur subunit
E: DMSO reductase family type II enzyme, molybdopterin subunit
F: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,59051
Polymers417,4136
Non-polymers11,17745
Water50,1182782
1
A: DMSO reductase family type II enzyme, molybdopterin subunit
B: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,93719
Polymers139,1382
Non-polymers3,79917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15450 Å2
ΔGint-147 kcal/mol
Surface area37670 Å2
MethodPISA
2
C: DMSO reductase family type II enzyme, molybdopterin subunit
D: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,80115
Polymers139,1382
Non-polymers3,66413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14280 Å2
ΔGint-164 kcal/mol
Surface area37250 Å2
MethodPISA
3
E: DMSO reductase family type II enzyme, molybdopterin subunit
F: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,85217
Polymers139,1382
Non-polymers3,71415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-150 kcal/mol
Surface area37570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.827, 175.501, 193.160
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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DMSO reductase family type II enzyme, ... , 2 types, 6 molecules ACEBDF

#1: Protein DMSO reductase family type II enzyme, molybdopterin subunit


Mass: 102069.859 Da / Num. of mol.: 3 / Fragment: residues 29-927 / Source method: isolated from a natural source / Source: (natural) Dechlorosoma suillum (bacteria) / Strain: ATCC BAA-33 / DSM 13638 / PS / References: UniProt: G8QM55
#2: Protein DMSO reductase family type II enzyme, iron-sulfur subunit


Mass: 37067.809 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Dechlorosoma suillum (bacteria) / Strain: ATCC BAA-33 / DSM 13638 / PS / References: UniProt: G8QM54

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Non-polymers , 10 types, 2827 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mo
#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.: 3 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / References: EC: 1.97.1.1
#6: Chemical ChemComp-MD1 / PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER


Mass: 740.557 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2 / References: EC: 1.97.1.1
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2782 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20%PEG6000 and 0.1M Tris, pH 8.25 / PH range: 8.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2014
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.86→48.35 Å / Num. obs: 372024 / % possible obs: 99.1 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 13.2
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.1623 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIXdev_2299refinement
Aimless2.21data scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IVF

2ivf


Resolution: 1.86→48.35 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 18588 5 %random selection
Rwork0.2008 ---
obs0.2026 371511 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29138 0 488 2782 32408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0130561
X-RAY DIFFRACTIONf_angle_d1.43641579
X-RAY DIFFRACTIONf_dihedral_angle_d12.43118008
X-RAY DIFFRACTIONf_chiral_restr0.0634277
X-RAY DIFFRACTIONf_plane_restr0.0085327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.88110.3555840.314511540X-RAY DIFFRACTION98
1.8811-1.90330.33196200.300111580X-RAY DIFFRACTION98
1.9033-1.92650.32836110.299911598X-RAY DIFFRACTION98
1.9265-1.95090.32896280.290511549X-RAY DIFFRACTION98
1.9509-1.97650.33136420.281211520X-RAY DIFFRACTION98
1.9765-2.00360.32716170.281111636X-RAY DIFFRACTION98
2.0036-2.03220.32885670.277311614X-RAY DIFFRACTION98
2.0322-2.06260.30586500.272411600X-RAY DIFFRACTION98
2.0626-2.09480.3066750.274911592X-RAY DIFFRACTION98
2.0948-2.12920.29516260.260611604X-RAY DIFFRACTION99
2.1292-2.16590.31725760.25811768X-RAY DIFFRACTION99
2.1659-2.20530.30986310.255411631X-RAY DIFFRACTION99
2.2053-2.24770.2846140.248111683X-RAY DIFFRACTION99
2.2477-2.29350.28616380.243411687X-RAY DIFFRACTION99
2.2935-2.34340.28965780.241611776X-RAY DIFFRACTION99
2.3434-2.39790.28495730.231811744X-RAY DIFFRACTION99
2.3979-2.45790.26155770.225711755X-RAY DIFFRACTION99
2.4579-2.52430.27085890.223811794X-RAY DIFFRACTION99
2.5243-2.59860.25686190.221511754X-RAY DIFFRACTION99
2.5986-2.68250.25886130.215111854X-RAY DIFFRACTION99
2.6825-2.77840.2466300.213111774X-RAY DIFFRACTION99
2.7784-2.88960.25116350.209511818X-RAY DIFFRACTION99
2.8896-3.02110.26356210.205711859X-RAY DIFFRACTION99
3.0211-3.18030.23885970.200911907X-RAY DIFFRACTION100
3.1803-3.37950.24016570.191711851X-RAY DIFFRACTION100
3.3795-3.64040.21586310.179411924X-RAY DIFFRACTION100
3.6404-4.00660.18166400.15911956X-RAY DIFFRACTION100
4.0066-4.5860.15646600.128611988X-RAY DIFFRACTION100
4.586-5.77630.15616380.125212087X-RAY DIFFRACTION100
5.7763-48.36650.16286510.14812480X-RAY DIFFRACTION100

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