[English] 日本語
Yorodumi
- PDB-1pii: THREE-DIMENSIONAL STRUCTURE OF THE BIFUNCTIONAL ENZYME PHOSPHORIB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pii
TitleTHREE-DIMENSIONAL STRUCTURE OF THE BIFUNCTIONAL ENZYME PHOSPHORIBOSYLANTHRANILATE ISOMERASE: INDOLEGLYCEROLPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI REFINED AT 2.0 ANGSTROMS RESOLUTION
ComponentsN-(5'PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE
KeywordsBIFUNCTIONAL(ISOMERASE AND SYNTHASE)
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function
N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain / N-(5'phosphoribosyl)anthranilate (PRA) isomerase / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel ...N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain / N-(5'phosphoribosyl)anthranilate (PRA) isomerase / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tryptophan biosynthesis protein TrpCF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWilmanns, M. / Priestle, J.P. / Jansonius, J.N.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 A resolution.
Authors: Wilmanns, M. / Priestle, J.P. / Niermann, T. / Jansonius, J.N.
#1: Journal: Biochemistry / Year: 1991
Title: Structural Conservation in Parallel Beta(Slash)Alpha-Barrel Enzymes that Catalyze Three Sequential Reactions in the Pathway of Tryptophan Biosynthesis
Authors: Wilmanns, M. / Hyde, C.C. / Davies, D.R. / Kirschner, K. / Jansonius, J.N.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Three-Dimensional Structure of the Bifunctional Enzyme N-(5'-Phosphoribosyl)Anthranilate Isomerase-Indole-3-Glycerol-Phosphate Synthase from Escherichia Coli
Authors: Priestle, J.P. / Gruetter, M.G. / White, J.L. / Vincent, M.G. / Kania, M. / Wilson, E. / Jardetzky, T.S. / Kirschner, K. / Jansonius, J.N.
#3: Journal: FEBS Lett. / Year: 1982
Title: Crystallization and Preliminary X-Ray Crystallographic Data of the Bifunctional Enzyme Phosphoribosyl-Anthranilate Isomerase-Indole-3-Glycerol-Phosphate Synthase from Escherichia Coli
Authors: White, J.L. / Gruetter, M.G. / Wilson, E. / Thaller, C. / Ford, G.C. / Smit, J.D.G. / Jansonius, J.N. / Kirschner, K.
History
DepositionJun 21, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_residues ...pdbx_database_status / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET PRAI:IGPS CONSISTS OF TWO BETA/ALPHA-BARRELS, WHICH CAN BE SUPERIMPOSED ON EACH OTHER. IGPS ...SHEET PRAI:IGPS CONSISTS OF TWO BETA/ALPHA-BARRELS, WHICH CAN BE SUPERIMPOSED ON EACH OTHER. IGPS HAS AN N-TERMINAL EXTENSION OUTSIDE OF THE BETA/ALPHA-BARREL, COMPRISING RESIDUES 1-48. THE SHEET PRESENTED AS *I* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS *P* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-(5'PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6033
Polymers49,4131
Non-polymers1902
Water11,313628
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.700, 104.700, 68.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note1: RESIDUES 380 - 388 HAVE VERY HIGH TEMPERATURE FACTORS.

-
Components

#1: Protein N-(5'PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE


Mass: 49412.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P00909, indole-3-glycerol-phosphate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECONDARY STRUCTURAL ELEMENTS (ALPHA-HELICES, BETA-STRANDS, TURNS) WERE DETERMINED WITH THE ...THE SECONDARY STRUCTURAL ELEMENTS (ALPHA-HELICES, BETA-STRANDS, TURNS) WERE DETERMINED WITH THE PROGRAM DSSP (KABSCH AND SANDER, 1983).
Sequence detailsRESIDUE 329 IS IDENTIFIED AS VAL IN PIR ENTRY GWEC. RECENT RESEQUENCING CONFIRMED THAT RESIDUE 329 ...RESIDUE 329 IS IDENTIFIED AS VAL IN PIR ENTRY GWEC. RECENT RESEQUENCING CONFIRMED THAT RESIDUE 329 IS ALA. IT IS PRESENTED AS ALA IN THIS ENTRY. SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME:TRPC_ECOLI SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ARG 94 GLN 94 SER 319 VAL 319 VAL 329 ALA 329 THR 398 SER 398

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.38 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Details: taken from White, J.L. et al (1982). FEBS Lett., 148, 87-90.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlenzyme1drop
20.8 Mammonium sulfate1drop
350 mMpotassium phosphate1drop
45 mMEDTA1drop
51-2 mMDTE1drop
61.6 Mammonium sulfate1reservoir
750 mMpotassium phosphate1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 45216 / % possible obs: 92.3 % / Observed criterion σ(I): 3 / Num. measured all: 130573 / Rmerge(I) obs: 0.133

-
Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→15 Å
Details: THE REFINED CRYSTAL STRUCTURE OF PRAI:IGPS INCLUDES TWO PHOSPHATE IONS, ONE BOUND TO EACH ACTIVE SITE OF THIS BIFUNCTIONAL ENZYME.
RfactorNum. reflection
obs0.173 44611
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 10 628 4162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg3.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / Num. reflection obs: 44611 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.017

+
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