[English] 日本語
Yorodumi
- PDB-1w30: PyrR of Mycobacterium Tuberculosis as a potential drug target -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w30
TitlePyrR of Mycobacterium Tuberculosis as a potential drug target
ComponentsPYRR BIFUNCTIONAL PROTEIN
KeywordsTRANSFERASE / PYRR / GLYCOSYLTRANSFERASE / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TB / TBSGC
Function / homology
Function and homology information


uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / nucleoside metabolic process / peptidoglycan-based cell wall / regulation of DNA-templated transcription
Similarity search - Function
Bifunctional protein PyrR / : / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional protein PyrR / Bifunctional protein PyrR
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKantardjieff, K.A. / Vasquez, C. / Castro, P. / Warfel, N.N. / Rho, B.-S. / Lekin, T. / Kim, C.-Y. / Segelke, B.W. / Terwilliger, T. / Rupp, B. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Pyrr (Rv1379) from Mycobacterium Tuberculosis: A Persistence Gene and Protein Drug Target
Authors: Kantardjieff, K.A. / Vasquez, C. / Castro, P. / Warfel, N.N. / Rho, B.-S. / Lekin, T. / Kim, C.-Y. / Segelke, B.W. / Terwilliger, T. / Rupp, B.
History
DepositionJul 11, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2004Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PYRR BIFUNCTIONAL PROTEIN
B: PYRR BIFUNCTIONAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)43,2592
Polymers43,2592
Non-polymers00
Water5,927329
1
A: PYRR BIFUNCTIONAL PROTEIN
B: PYRR BIFUNCTIONAL PROTEIN

A: PYRR BIFUNCTIONAL PROTEIN
B: PYRR BIFUNCTIONAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)86,5184
Polymers86,5184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)66.638, 66.638, 154.716
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2161-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHRAA25 - 3725 - 37
21THRTHRTHRTHRBB25 - 3725 - 37
12VALVALASNASNAA51 - 6951 - 69
22VALVALASNASNBB51 - 6951 - 69
13VALVALLEULEUAA78 - 8378 - 83
23VALVALLEULEUBB78 - 8378 - 83
14ILEILELEULEUAA116 - 135116 - 135
24ILEILELEULEUBB116 - 135116 - 135
15GLNGLNVALVALAA145 - 176145 - 176
25GLNGLNVALVALBB145 - 176145 - 176

NCS oper: (Code: given
Matrix: (-0.3662, -0.3354, 0.868), (-0.3717, -0.8024, -0.4669), (0.8531, -0.4936, 0.1691)
Vector: -48, 70.31, 64.12)

-
Components

#1: Protein PYRR BIFUNCTIONAL PROTEIN / URACIL PHOSPHORIBOSYLTRANSFERASE / UPRTASE


Mass: 21629.594 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: GSHHHHHH C-TERMINAL TAG / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: HRV37 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P71807, UniProt: P9WHK3*PLUS, uracil phosphoribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE FOR CHAINS A, B: ASP (21) ASN
Sequence detailsD21N MUTATION, C-TERMINAL GSHHHHHH TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.5 %
Description: 3D-PSSM HOMOLOGY MODEL FROM 1A3C REFINED WITH SCWRL 3.0
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: SITTING DROPS 0.5UL + 0.5UL IN INTELLIPLATE, 0.1M IMIDAZOLE-MALEATE PH 7.5, 26% PEG-MME 2K, 2.8% EDTA. CRYSTAL APPROXIMATELY 50 MICRON RHOMBOID.

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2003 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→38.8 Å / Num. obs: 34571 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRV. 2.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3C

1a3c


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.611 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL REGION 1-11 ABSENT IN DENSITY. LOOPS 90-100 HIGHLY FLEXIBLE AND ABSENT FROM MODEL, ALTHOUGH INTERMITTENT DENSITY FRAGMENTS CAN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL REGION 1-11 ABSENT IN DENSITY. LOOPS 90-100 HIGHLY FLEXIBLE AND ABSENT FROM MODEL, ALTHOUGH INTERMITTENT DENSITY FRAGMENTS CAN BE TRACED. RESIDUE ATOMS. C -TERMINAL LINKER AND HIS TAG GSHHHHHH ABSENT FROM DENSITY, FRAGMENTS OF ISOLATED OR FRAGMENTED DENSITY ARE VISIBLE AND MAY BE REPRESENTED BY SOLVENT ATOMS. ALL REGIONS EXCLUDED FROM NCS SHOW HIGH MOBILITY AND VARIATION BETWEEN MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1589 5 %RANDOM
Rwork0.205 ---
obs0.206 30276 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 0 329 2985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212692
X-RAY DIFFRACTIONr_bond_other_d0.0020.022623
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.7981.9743655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.96736018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr6.655347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023012
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02549
X-RAY DIFFRACTIONr_nbd_refined0.2060.2561
X-RAY DIFFRACTIONr_nbd_other0.2660.23221
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.21870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2192
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3190.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2221.51738
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16722805
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9983954
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1674.5850
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 116
Rwork0.278 2213

+
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