[English] 日本語
Yorodumi
- PDB-1xdq: Structural and Biochemical Identification of a Novel Bacterial Ox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xdq
TitleStructural and Biochemical Identification of a Novel Bacterial Oxidoreductase
ComponentsBacterial Sulfite Oxidase
KeywordsOXIDOREDUCTASE / Bioinformatics / sequence analysis / electron transfer / molybdoenzymes / molybdopterin
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on a heme group of donors / response to hypochlorite / oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / protein repair / molybdopterin cofactor binding / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Protein-methionine-sulfoxide reductase subunit MsrP / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MOLYBDENUM ATOM / Chem-MTE / OXYGEN ATOM / UREA / Protein-methionine-sulfoxide reductase catalytic subunit MsrP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsLoschi, L. / Brokx, S.J. / Hills, T.L. / Zhang, G. / Bertero, M.G. / Lovering, A.L. / Weiner, J.H. / Strynadka, N.C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural and biochemical identification of a novel bacterial oxidoreductase.
Authors: Loschi, L. / Brokx, S.J. / Hills, T.L. / Zhang, G. / Bertero, M.G. / Lovering, A.L. / Weiner, J.H. / Strynadka, N.C.
History
DepositionSep 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN Due to the presence of adjacent electron density from a bound molecule, we cannot ...HETEROGEN Due to the presence of adjacent electron density from a bound molecule, we cannot distinguish unambiguously the position of the second coordinating atom as it can be refined with similar parameters at the typical length for an oxo group (1.6-1.8 and a direct hydrogen bond to bound molecule) or for a water molecule (2.1-2.4 and a direct hydrogen bond to bound urea).
Remark 999SEQUENCE THE AUTHORS BELIEVE THAT THERE IS AN AN ERROR IN THE DATABASE SEQUENCE SINCE THE OTHER E. ...SEQUENCE THE AUTHORS BELIEVE THAT THERE IS AN AN ERROR IN THE DATABASE SEQUENCE SINCE THE OTHER E.COLI STRAINS WITH PUBLISHED SEQUENCES LIKE THE PATHOGENIC STRAINS O157:H7 EDL933, AND CFT073 ALSO HAVE AN ASP AT THAT POSITION.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacterial Sulfite Oxidase
B: Bacterial Sulfite Oxidase
C: Bacterial Sulfite Oxidase
D: Bacterial Sulfite Oxidase
E: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,16825
Polymers168,3315
Non-polymers2,83720
Water3,081171
1
A: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2345
Polymers33,6661
Non-polymers5674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2345
Polymers33,6661
Non-polymers5674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2345
Polymers33,6661
Non-polymers5674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2345
Polymers33,6661
Non-polymers5674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2345
Polymers33,6661
Non-polymers5674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.345, 165.064, 181.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Bacterial Sulfite Oxidase


Mass: 33666.258 Da / Num. of mol.: 5 / Fragment: residues 45-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Plasmid details: plasmid pMSYZ3 (construcy with YedYZ cloned) which is derived from plasmid pMS119
Plasmid: pMSYZ3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 and SBJ20 / References: UniProt: P76342

-
Non-polymers , 5 types, 191 molecules

#2: Chemical
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH4N2O
#3: Chemical
ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mo
#4: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: O
#5: Chemical
ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.5 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: Li2SO4, TEA, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97965 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 19, 2003
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 51827 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 50.1 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 82.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→39.75 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2827727.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3650 7.1 %RANDOM
Rwork0.23 ---
obs0.23 51741 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.5168 Å2 / ksol: 0.328455 e/Å3
Displacement parametersBiso mean: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1-14.33 Å20 Å20 Å2
2---21.34 Å20 Å2
3---7.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.55→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10450 0 150 171 10771
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.991.5
X-RAY DIFFRACTIONc_mcangle_it4.512
X-RAY DIFFRACTIONc_scbond_it4.682
X-RAY DIFFRACTIONc_scangle_it6.252.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.461 481 6.8 %
Rwork0.39 6572 -
obs--79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MTQ.PARURE.TOP
X-RAY DIFFRACTION4URE.PARMTQ.TOP

+
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://pdbjlc1.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