[English] 日本語
Yorodumi
- PDB-2vli: Structure of Deinococcus radiodurans tunicamycin resistance protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vli
TitleStructure of Deinococcus radiodurans tunicamycin resistance protein
ComponentsANTIBIOTIC RESISTANCE PROTEINAntimicrobial resistance
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE
Function / homologyP-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / Antibiotic resistance protein
Function and homology information
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsMacedo, S. / Kapp, U. / Leiros, I. / Hall, D.R. / Mitchell, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of Deinococcus Radiodurans Tunicamycin-Resistance Protein (Tmrd), a Phosphotransferase.
Authors: Kapp, U. / Macedo, S. / Hall, D.R. / Leiros, I. / Mcsweeney, S.M. / Mitchell, E.
History
DepositionJan 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANTIBIOTIC RESISTANCE PROTEIN
B: ANTIBIOTIC RESISTANCE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9894
Polymers40,8412
Non-polymers1482
Water4,071226
1
A: ANTIBIOTIC RESISTANCE PROTEIN
hetero molecules

A: ANTIBIOTIC RESISTANCE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1376
Polymers40,8412
Non-polymers2964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1200 Å2
ΔGint-2 kcal/mol
Surface area20430 Å2
MethodPQS
2
B: ANTIBIOTIC RESISTANCE PROTEIN

B: ANTIBIOTIC RESISTANCE PROTEIN


Theoretical massNumber of molelcules
Total (without water)40,8412
Polymers40,8412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area920 Å2
ΔGint0.6 kcal/mol
Surface area21150 Å2
MethodPQS
Unit cell
Length a, b, c (Å)81.360, 118.160, 81.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2052-

HOH

21B-2125-

HOH

-
Components

#1: Protein ANTIBIOTIC RESISTANCE PROTEIN / Antimicrobial resistance / TUNICAMYCIN RESISTANCE PROTEIN


Mass: 20420.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RUG7
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCADMIUM ION (CD): FROM CRYSTALLISATION CONDITIONS CHLORIDE ION (CL): FROM CRYSTALLISATION CONDITIONS
Sequence detailsPROTEIN WAS EXPRESSED USING A CONSTRUCT GIVING A PRODUCT WITH A C-TERMINAL TRUNCATION FROM RESIDUE ...PROTEIN WAS EXPRESSED USING A CONSTRUCT GIVING A PRODUCT WITH A C-TERMINAL TRUNCATION FROM RESIDUE 184 FORWARDS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 48.4 %
Description: PHASING DATA WERE COLLECTED FROM A SECOND CRYSTAL. THE INITIAL MODEL WAS THEN TRANSFERRED TO HIGHER RESOLUTION DATA SET FROM ANOTHER CRYSTAL FOR REFINEMENT.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20 DEGREESC AFTER 3-6 DAYS USING HANGING DROPS CONTAINING 2 MICROL OF THE PROTEIN, 0.4-0.8 MICROL 0.1 M CDCL2 AND 1.6-1.2 MICROL OF A RESERVOIR SOLUTION CONTAINING 11-13% PEG 4000, 0.8 M ...Details: 20 DEGREESC AFTER 3-6 DAYS USING HANGING DROPS CONTAINING 2 MICROL OF THE PROTEIN, 0.4-0.8 MICROL 0.1 M CDCL2 AND 1.6-1.2 MICROL OF A RESERVOIR SOLUTION CONTAINING 11-13% PEG 4000, 0.8 M SODIUM FORMATE AND 0.1 M SODIUM ACETATE PH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9144, 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2006 / Details: RH COATED TOROIDAL MIRROR
RadiationMonochromator: SI DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91441
20.97921
ReflectionResolution: 1.95→22.93 Å / Num. obs: 28689 / % possible obs: 99.5 % / Observed criterion σ(I): -3.7 / Redundancy: 4.94 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.54
Reflection shellResolution: 1.95→1.97 Å / Redundancy: 5.09 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.95→22.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.354 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE N-TERMINAL HIS-TAGS AND RESIDUES TO A4 AND B3 AND FROM A176 AND B176 WERE NOT VISIBLE IN THE DENSITY MAPS. RESIDUES A15-18 AND A126-129 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE N-TERMINAL HIS-TAGS AND RESIDUES TO A4 AND B3 AND FROM A176 AND B176 WERE NOT VISIBLE IN THE DENSITY MAPS. RESIDUES A15-18 AND A126-129 WERE ALSO NOT VISIBLE. ALL THESE RESIDUES WERE THEREFORE NOT INCLUDED IN THE STRUCTURE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1486 5.2 %RANDOM
Rwork0.174 ---
obs0.176 27186 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---2.53 Å20 Å2
3---2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 2 226 2848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212699
X-RAY DIFFRACTIONr_bond_other_d0.0060.021862
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9643672
X-RAY DIFFRACTIONr_angle_other_deg0.98434524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3195337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16222.96125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27915442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0811527
X-RAY DIFFRACTIONr_chiral_restr0.10.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02536
X-RAY DIFFRACTIONr_nbd_refined0.2160.2554
X-RAY DIFFRACTIONr_nbd_other0.2070.21930
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21299
X-RAY DIFFRACTIONr_nbtor_other0.0880.21353
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9591.52020
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93322727
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.20631088
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8214.5943
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.234 102
Rwork0.2 1987

+
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