[English] 日本語
Yorodumi
- PDB-1vpb: CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF DNA GYRASE (BT3649) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vpb
TitleCRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF DNA GYRASE (BT3649) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 A RESOLUTION
Componentsputative modulator of DNA gyrase
KeywordsHYDROLASE / PUTATIVE MODULATOR OF DNA GYRASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


metallopeptidase activity / cytosol
Similarity search - Function
PmbA/TldD fold / PmbA/TldD superfamily / PmbA/TldA metallopeptidase C-terminal domain / Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily / PmbA/TldA metallopeptidase domain 1 / PmbA/TldA metallopeptidase central domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative modulator of DNA gyrase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Putative modulator of DNA gyrase (bt3649) from Bacteroides thetaiotaomicron vpi-5482 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: putative modulator of DNA gyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9693
Polymers49,8451
Non-polymers1242
Water6,810378
1
A: putative modulator of DNA gyrase
hetero molecules

A: putative modulator of DNA gyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9386
Polymers99,6902
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)73.541, 154.968, 106.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein putative modulator of DNA gyrase


Mass: 49845.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: bt3649 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A1L2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.855.65DATA FROM A CRYSTAL OF SE-MET SUBSTITUTED PROTEIN WAS USED FOR THE MAD PHASING EXPERIMENTS AND DATA FROM A CRYSTAL OF NATIVE PROTEIN WAS USED FOR THE FINAL REFINEMENT.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop7.30.2M KFormate, 20.0% PEG-3350, No Buffer pH 7.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop720.0% PEG-6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL11-110.979224
SYNCHROTRONALS 8.3.121.020035,0.979718,0.979811
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJul 6, 2004flat mirror
ADSC2CCDSep 18, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(311) bent monochromatorSINGLE WAVELENGTHMx-ray1
2Double Crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792241
21.0200351
30.9797181
40.9798111
ReflectionResolution: 1.74→99 Å / Num. obs: 61062 / % possible obs: 98.69 % / Redundancy: 4.73 % / Biso Wilson estimate: 32.84 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 30.27
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.61 / Num. unique all: 2652 / % possible all: 86.87

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 1.75→43.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.635 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ELECTRON DENSITY FOR RESIDUES ALA42 AND LYS43 ARE POOR, SO THESE TWO RESIDUES ARE NOT INCLUDED IN THE FINAL MODEL. THE DATA USED IN THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ELECTRON DENSITY FOR RESIDUES ALA42 AND LYS43 ARE POOR, SO THESE TWO RESIDUES ARE NOT INCLUDED IN THE FINAL MODEL. THE DATA USED IN THE FINAL REFINEMENT WAS FROM A NATIVE CRYSTAL. THE REFINEMENT OF THE COORDINATES WAS RESTRAINED WITH THE EXPERIMENTAL PHASES FROM A SELENOMETHIONINE MAD EXPERIMENT FROM A SECOND CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.20393 3091 5.1 %RANDOM
Rwork0.17822 ---
obs0.17951 57756 99.22 %-
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: 34.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.8 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 8 378 3715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223555
X-RAY DIFFRACTIONr_bond_other_d0.0010.023199
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9594820
X-RAY DIFFRACTIONr_angle_other_deg0.83237468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.565471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04424.768151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44215630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0421520
X-RAY DIFFRACTIONr_chiral_restr0.1020.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02713
X-RAY DIFFRACTIONr_nbd_refined0.2060.2684
X-RAY DIFFRACTIONr_nbd_other0.1780.23303
X-RAY DIFFRACTIONr_nbtor_other0.0880.22226
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.224
X-RAY DIFFRACTIONr_mcbond_it2.32432336
X-RAY DIFFRACTIONr_mcbond_other0.5933942
X-RAY DIFFRACTIONr_mcangle_it3.2253636
X-RAY DIFFRACTIONr_scbond_it5.42781420
X-RAY DIFFRACTIONr_scangle_it7.32111184
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21791
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 252 5.71 %
Rwork0.218 4159 -
obs--98.59 %
Refinement TLS params.Method: refined / Origin x: 12.6584 Å / Origin y: 20.6205 Å / Origin z: 35.9151 Å
111213212223313233
T-0.1574 Å20.0004 Å2-0.0079 Å2--0.1988 Å2-0.0163 Å2---0.2017 Å2
L0.3612 °2-0.1214 °2-0.0927 °2-0.6376 °2-0.2372 °2--0.7103 °2
S0.0339 Å °0.0806 Å °-0.104 Å °-0.1519 Å °-0.0737 Å °0.0142 Å °0.2131 Å °0.0184 Å °0.0398 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://pdbjlvh1.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