[English] 日本語
Yorodumi
- PDB-3t31: Crystal structure of sulfide:quinone oxidoreductase from Acidithi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t31
TitleCrystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans in complex with decylubiquinone
ComponentsSulfide-quinone reductaseSulfide:quinone reductase
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / integral monotopic membrane protein / acidithiobacillus ferrooxidans / complex with decylubiquinone
Function / homology
Function and homology information


bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / quinone binding / nucleotide binding / membrane
Similarity search - Function
FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Chem-DCQ / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCherney, M.M. / Zhang, Y. / Solomonson, M. / Weiner, J.H. / James, M.N.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification.
Authors: Cherney, M.M. / Zhang, Y. / Solomonson, M. / Weiner, J.H. / James, M.N.
History
DepositionJul 24, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionAug 17, 2011ID: 3KPG
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 2.0Apr 3, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / refine / refine_hist / reflns / reflns_shell / software / struct_asym / struct_conn / struct_ref / struct_ref_seq_dif / 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.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_all / _refine.ls_percent_reflns_obs / _refine.solvent_model_param_bsol / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.number_all / _reflns.observed_criterion_sigma_F / _reflns.observed_criterion_sigma_I / _reflns_shell.d_res_high / _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all / _software.classification / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_ref.db_code / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5155
Polymers47,8621
Non-polymers1,6534
Water5,639313
1
A: Sulfide-quinone reductase
hetero molecules

A: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,03010
Polymers95,7242
Non-polymers3,3058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1710 Å2
ΔGint-11 kcal/mol
Surface area35060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.770, 150.770, 82.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

21A-734-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sulfide-quinone reductase / Sulfide:quinone reductase


Mass: 47862.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus ferrooxidans (bacteria)
Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_1792 / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: B7JBP8, bacterial sulfide:quinone reductase
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 4 types, 316 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-DCQ / 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / decylubiquinone


Mass: 322.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O4
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 600, 0.1 M bis-tris buffer, 0.1M MgSO4, 0.4mM DDM, 2 mM decylubiquinone, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2009
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 24845 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 21.4 % / Biso Wilson estimate: 38.36 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 23.67
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 21.5 % / Rmerge(I) obs: 0.987 / Mean I/σ(I) obs: 4.08 / Rsym value: 0.987 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.91 Å / SU ML: 0.63 / σ(F): 1.99 / Phase error: 20.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1242 5 %random
Rwork0.159 ---
obs0.161 24844 100 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.4 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0104 Å20 Å20 Å2
2---3.0104 Å2-0 Å2
3---6.0208 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 112 313 3650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083429
X-RAY DIFFRACTIONf_angle_d1.1434643
X-RAY DIFFRACTIONf_dihedral_angle_d17.0631287
X-RAY DIFFRACTIONf_chiral_restr0.073493
X-RAY DIFFRACTIONf_plane_restr0.008585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2999-2.39190.26511350.20882566X-RAY DIFFRACTION100
2.3919-2.50050.3031350.21292561X-RAY DIFFRACTION100
2.5005-2.63210.25771360.1912585X-RAY DIFFRACTION100
2.6321-2.79660.2881360.1852587X-RAY DIFFRACTION100
2.7966-3.01180.20861370.17042602X-RAY DIFFRACTION100
3.0118-3.31370.22791370.16462594X-RAY DIFFRACTION100
3.3137-3.79030.20521380.15722623X-RAY DIFFRACTION100
3.7903-4.76460.17321410.13032677X-RAY DIFFRACTION100
4.7646-19.91260.17551470.14522807X-RAY DIFFRACTION100
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)
11.96290.7869-0.29142.5309-0.55540.80420.0774-0.2212-0.00430.6016-0.04440.12340.0697-0.20640.00860.2103-0.09910.04080.26820.05930.174740.9026-26.907812.3328
21.3985-0.1233-0.20611.9895-0.23580.45590.2243-0.1387-0.0530.2651-0.3452-1.2116-0.07940.4420.04890.1779-0.1042-0.12910.22860.1220.611864.7343-17.12626.2272
32.54540.56150.06672.5362-0.52890.98650.02450.16570.07-0.21710.0429-0.1390.2241-0.176-0.05770.1825-0.04590.0280.25080.03770.162945.9912-25.9416-2.519
42.02450.943-0.55183.471-0.62521.43790.0592-0.03610.2241-0.23360.14590.33050.1696-0.4663-0.03460.1368-0.02390.03050.18640.03980.203343.7633-10.3989-1.9078
51.81191.5263-2.19973.173-2.35393.5380.00210.20080.68460.59390.18150.5914-0.0193-0.5696-0.13630.3020.01740.10320.3233-0.01770.371842.353-7.311511.7376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:161)
2X-RAY DIFFRACTION2chain 'A' and (resseq 162:232)
3X-RAY DIFFRACTION3chain 'A' and (resseq 233:341)
4X-RAY DIFFRACTION4chain 'A' and (resseq 342:377)
5X-RAY DIFFRACTION5chain 'A' and (resseq 378:410)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more