[English] 日本語
Yorodumi
- PDB-2y88: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL IS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y88
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL ISOMERASE (VARIANT D11N) WITH BOUND PRFAR
ComponentsPHOSPHORIBOSYL ISOMERASE A
KeywordsISOMERASE / AROMATIC AMINO ACID BIOSYNTHESIS / TIM-BARREL / HISTIDINE BIOSYNTHESIS / TRYPTOPHAN BIOSYNTHESIS
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / phosphoribosylanthranilate isomerase activity / histidine biosynthetic process / tryptophan biosynthetic process / cytoplasm
Similarity search - Function
HisA/PriA, Actinobacteria / Histidine biosynthesis, HisA-like / HisA/PriA, bacterial-type / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-2ER / Phosphoribosyl isomerase A / Phosphoribosyl isomerase A
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsKuper, J. / Due, A.V. / Geerlof, A. / Wilmanns, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Bisubstrate Specificity in Histidine/Tryptophan Biosynthesis Isomerase from Mycobacterium Tuberculosis by Active Site Metamorphosis.
Authors: Due, A.V. / Kuper, J. / Geerlof, A. / Kries, J.P. / Wilmanns, M.
History
DepositionFeb 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_sheet / struct_site
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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHORIBOSYL ISOMERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2352
Polymers25,6581
Non-polymers5771
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.270, 63.270, 131.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein PHOSPHORIBOSYL ISOMERASE A / N-(5'-PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE / 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) ...N-(5'-PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE / 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE / PHOSPHORIBOSYLFORMIMINO-5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMERASE / PRAI


Mass: 25657.781 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P60578, UniProt: P9WMM5*PLUS, phosphoribosylanthranilate isomerase, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical ChemComp-2ER / [(2R,3S,4R,5R)-5-[4-AMINOCARBONYL-5-[[(Z)-[(3R,4R)-3,4-DIHYDROXY-2-OXO-5-PHOSPHONOOXY-PENTYL]IMINOMETHYL]AMINO]IMIDAZOL-1-YL]-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE


Mass: 577.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N5O15P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 10 TO ASN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.01 % / Description: NONE
Crystal growDetails: 0.1M HEPES PH7.5, 1.4M TRI-SODIUM CITRATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 1.33→20 Å / Num. obs: 61458 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 0.58
Reflection shellResolution: 1.33→1.4 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.4 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y85

2y85


Resolution: 1.33→56.98 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.056 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1836 3082 5 %RANDOM
Rwork0.1379 ---
obs0.14 58387 99.709 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 14.109 Å2
Baniso -1Baniso -2Baniso -3
1-0.109 Å20 Å20 Å2
2--0.109 Å20 Å2
3----0.218 Å2
Refinement stepCycle: LAST / Resolution: 1.33→56.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 37 394 2235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211968
X-RAY DIFFRACTIONr_bond_other_d0.0030.021278
X-RAY DIFFRACTIONr_angle_refined_deg2.2061.9832700
X-RAY DIFFRACTIONr_angle_other_deg1.1833.0043087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.42223.90887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9515305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8981519
X-RAY DIFFRACTIONr_chiral_restr0.1610.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022309
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02395
X-RAY DIFFRACTIONr_nbd_refined0.2420.2424
X-RAY DIFFRACTIONr_nbd_other0.2360.21604
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21036
X-RAY DIFFRACTIONr_nbtor_other0.1160.21189
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2325
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3440.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7551546
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.12962023
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.0546766
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.2617.5675
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: 1.331→1.366 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 215 -
Rwork0.246 4096 -
obs--95.8 %

+
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