[English] 日本語
Yorodumi
- PDB-1vmj: CRYSTAL STRUCTURE OF A PUTATIVE THIAMIN PHOSPHATE SYNTHASE (TM072... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vmj
TitleCRYSTAL STRUCTURE OF A PUTATIVE THIAMIN PHOSPHATE SYNTHASE (TM0723) FROM THERMOTOGA MARITIMA MSB8 AT 1.52 A RESOLUTION
Componentshypothetical protein TM0723
KeywordsTRANSFERASE / PUTATIVE THIAMIN PHOSPHATE SYNTHASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homologyYjbQ-like / Uncharacterised protein family UPF0047, YjbQ / YjbQ-like superfamily / UPF0047 protein YjbQ-like / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (TM0723) from Thermotoga maritima at 1.52 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_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_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein TM0723
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1295
Polymers17,8171
Non-polymers3114
Water3,837213
1
A: hypothetical protein TM0723
hetero molecules

A: hypothetical protein TM0723
hetero molecules

A: hypothetical protein TM0723
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,38615
Polymers53,4523
Non-polymers93412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8770 Å2
ΔGint-179 kcal/mol
Surface area15720 Å2
MethodPISA, PQS
2
A: hypothetical protein TM0723
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)108,77230
Polymers106,9056
Non-polymers1,86724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_666-y+5/4,-x+5/4,-z+5/41
crystal symmetry operation19_666-x+5/4,-z+5/4,-y+5/41
crystal symmetry operation24_666-z+5/4,-y+5/4,-x+5/41
Buried area18420 Å2
ΔGint-395 kcal/mol
Surface area30550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.194, 110.194, 110.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-143-

SO4

21A-150-

HOH

31A-207-

HOH

41A-233-

HOH

51A-300-

HOH

-
Components

#1: Protein hypothetical protein TM0723


Mass: 17817.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0723 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZI2
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.85 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6
Details: 3.2M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.024627
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2001 / Details: flat mirror
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.024627 Å / Relative weight: 1
ReflectionResolution: 1.52→27.55 Å / Num. obs: 35764 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 24.03 Å2 / Rsym value: 0.115 / Net I/σ(I): 19.2
Reflection shellResolution: 1.52→1.6 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 5117 / Rsym value: 0.01166 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata scaling
SCALA5.0)data scaling
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VMF

1vmf


Resolution: 1.52→27.55 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.965 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE DENSITY FOR SO4 4 IS LOCATED ON CRYSTALLOGRAPHIC 2-FOLD AXIS. THERE ARE SOME EXTRA DIFFERENCE DENSITY AFTER THE MODELLING OF 1/2 OCCUPIED SULFATE.
RfactorNum. reflection% reflectionSelection details
Rfree0.16302 1790 5 %RANDOM
Rwork0.144 ---
obs0.14495 33973 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.684 Å2
Refinement stepCycle: LAST / Resolution: 1.52→27.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 16 213 1367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221209
X-RAY DIFFRACTIONr_bond_other_d0.0020.021104
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9631630
X-RAY DIFFRACTIONr_angle_other_deg0.79532566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85823.22662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83615228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9071511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021302
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
X-RAY DIFFRACTIONr_nbd_refined0.240.2226
X-RAY DIFFRACTIONr_nbd_other0.1960.21121
X-RAY DIFFRACTIONr_nbtor_other0.0840.2729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.223
X-RAY DIFFRACTIONr_mcbond_it1.4023696
X-RAY DIFFRACTIONr_mcbond_other0.4113283
X-RAY DIFFRACTIONr_mcangle_it2.27751134
X-RAY DIFFRACTIONr_scbond_it3.6748531
X-RAY DIFFRACTIONr_scangle_it5.3511496
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2575
X-RAY DIFFRACTIONr_metal_ion_refined0.2660.25
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 136 5.24 %
Rwork0.284 2460 -
obs--99.77 %
Refinement TLS params.Method: refined / Origin x: 48.981 Å / Origin y: 64.142 Å / Origin z: 50.498 Å
111213212223313233
T-0.0032 Å20.0021 Å2-0.018 Å2--0.0335 Å2-0.0058 Å2---0.0182 Å2
L0.5901 °20.1699 °20.2322 °2-0.3079 °20.1462 °2--0.5262 °2
S-0.0439 Å °-0.0317 Å °0.0728 Å °-0.0709 Å °0.0071 Å °0.0529 Å °-0.0954 Å °-0.0463 Å °0.0368 Å °
Refinement TLS groupSelection: ALL

+
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