[English] 日本語
Yorodumi
- PDB-2btu: Crystal structure of Phosphoribosylformylglycinamidine cyclo-liga... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2btu
TitleCrystal structure of Phosphoribosylformylglycinamidine cyclo-ligase from Bacillus Anthracis at 2.3A resolution.
ComponentsPHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE
KeywordsSYNTHASE / PURM / DE NOVO PURINE BIOSYNTHESIS / AIR SYNTHASE FAMILY / SPINE / SYNTHETASE / FGAR AMIDOTRANSFERASE / NOVEL FOLD / STRUCTURAL PROTEOMICS IN EUROPE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / 'de novo' IMP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsMoroz, O.V. / Blagova, E.V. / Levdikov, V.M. / Fogg, M.J. / Lebedev, A.A. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
CitationJournal: To be Published
Title: Crystal Structure of Phosphoribosylformylglycinamidine Cyclo-Ligase from Bacillus Anthracis at 2.3A Resolution.
Authors: Moroz, O.V. / Blagova, E.V. / Levdikov, V.M. / Fogg, M.J. / Lebedev, A.A. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
History
DepositionJun 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / 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
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE
B: PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)74,5942
Polymers74,5942
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.490, 89.490, 88.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE / PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE AIRS / PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE / AIR SYNTHASE


Mass: 37297.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q81ZH0, phosphoribosylformylglycinamidine cyclo-ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ATP + 2-(FORMAMIDO)-N(1)-(5-PHOSPHO-D- RIBOSYL)ACETAMIDINE = ADP + PHOSPHATE + ...CATALYTIC ACTIVITY: ATP + 2-(FORMAMIDO)-N(1)-(5-PHOSPHO-D- RIBOSYL)ACETAMIDINE = ADP + PHOSPHATE + 5-AMINO-1-(5-PHOSPHO-D- RIBOSYL)IMIDAZOLE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP VAPOUR DIFFUSION, 17% PEG2K, 0.1M TRIS-HCL PH 8.0, 0.1M TMAO (TRIMETHYLAMINE-N-OXIDE)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.00806
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00806 Å / Relative weight: 1
ReflectionResolution: 2.31→25 Å / Num. obs: 28479 / % possible obs: 93.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.4
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.4 / % possible all: 47.9

-
Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CLI

1cli


Resolution: 2.31→25 Å / Num. parameters: 19680 / Num. restraintsaints: 19478 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: MEROHEDRAL TWIN, TWINNING FRACTION 0.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 1375 5 %RANDOM
all0.1825 27092 --
obs--93.3 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4578.91
Refinement stepCycle: LAST / Resolution: 2.31→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 0 166 4584
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0246
X-RAY DIFFRACTIONs_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.09
X-RAY DIFFRACTIONs_approx_iso_adps0

+
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