[English] 日本語
Yorodumi
- PDB-1b6r: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1b6r
TitleN5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI
ComponentsPROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
KeywordsLYASE / ATP-GRASP / CARBOXYPHOSPHATE / PURINE BIOSYNTHESIS
Function / homologyRudiment single hybrid motif / ATP-grasp fold / ATP-grasp fold profile. / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp domain / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / Phosphoribosylaminoimidazole carboxylase, ATPase subunit / ATP-grasp fold, subdomain 1 ...Rudiment single hybrid motif / ATP-grasp fold / ATP-grasp fold profile. / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp domain / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / Phosphoribosylaminoimidazole carboxylase, ATPase subunit / ATP-grasp fold, subdomain 1 / 5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytosol / N5-carboxyaminoimidazole ribonucleotide synthase
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / 2.1 Å resolution
AuthorsThoden, J.B. / Kappock, T.J. / Stubbe, J. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1999
Title: Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily.
Authors: Thoden, J.B. / Kappock, T.J. / Stubbe, J. / Holden, H.M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 17, 1999 / Release: Nov 30, 1999
RevisionDateData content typeGroupProviderType
1.0Nov 30, 1999Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6242
Polyers39,5281
Non-polymers961
Water1,65792
1
A: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
hetero molecules

A: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2484
Polyers79,0562
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
Unit cell
γ
α
β
Length a, b, c (Å)93.400, 95.200, 120.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC 2 2 21

-
Components

#1: Protein/peptide PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE) / AIRC / PURK


Mass: 39528.000 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia
References: UniProt: P09029, phosphoribosylaminoimidazole carboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4 / Sulfate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.4 / Density percent sol: 64 %
Crystal growpH: 7.8 / Details: 100MM HEPPS, PH 7.8 0.575 M AMMONIUM SULFATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: macroseeding
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
110 mg/mlprotein1drop
20.525 Mammonium sulfate1reservoir
3100 mMHEPPS1reservoir

-
Data collection

DiffractionMean temperature: 280 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: BRUKER / Details: GOBEL MIRRORS / Detector: AREA DETECTOR / Collection date: Feb 15, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2.1 Å / D resolution low: 3 Å / Number obs: 30332 / Observed criterion sigma I: 0 / Rmerge I obs: 0.047 / Rsym value: 0.047 / NetI over sigmaI: 24.3 / Redundancy: 3.9 % / Percent possible obs: 95.6
Reflection shellRmerge I obs: 0.292 / Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / MeanI over sigI obs: 2.4 / Rsym value: 0.292 / Redundancy: 2 % / Percent possible all: 78.9
Reflection shell
*PLUS
Percent possible obs: 78.9

-
Processing

Software
NameVersionClassification
TNT5Drefinement
SAINTdata reduction
XCALIBREdata scaling
RefineMethod to determine structure: MIR / Sigma F: 0 / Stereochemistry target values: TNT PROTGEO
Solvent computationSolvent model details: TNT / Solvent model param bsol: 696.7 / Solvent model param ksol: 1.032
Least-squares processR factor R work: 0.197 / R factor all: 0.197 / Highest resolution: 2.1 Å / Lowest resolution: 3 Å / Number reflection obs: 30332 / Percent reflection obs: 95.6
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 2737 / Nucleic acid: 0 / Ligand: 5 / Solvent: 92 / Total: 2834
Refine LS restraints
Refine IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01341940.600
X-RAY DIFFRACTIONt_angle_deg2.32055381.000
X-RAY DIFFRACTIONt_dihedral_angle_d17.64426840.000
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.007752.500
X-RAY DIFFRACTIONt_gen_planes0.0117502.750
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.064535.000
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Least-squares process
*PLUS
R factor all: 0.196
Refine LS restraints
*PLUS
Refine IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.33
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.60.000
X-RAY DIFFRACTIONt_plane_restr0.0112.75

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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