[English] 日本語
Yorodumi
- PDB-2ntk: Crystal structure of PurO/IMP from Methanothermobacter thermoauto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ntk
TitleCrystal structure of PurO/IMP from Methanothermobacter thermoautotrophicus
ComponentsIMP cyclohydrolase
KeywordsHYDROLASE / alpha-beta-beta-alpha NTN hydrolase fold
Function / homology
Function and homology information


IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
IMP cyclohydrolase / Inosine monophosphate cyclohydrolase-like / Inosine monophosphate cyclohydrolase-like / Inosine monophosphate cyclohydrolase-like superfamily / IMP cyclohydrolase-like protein / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / IMP cyclohydrolase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsKang, Y.N. / Tran, A. / White, R.H. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2007
Title: A novel function for the N-terminal nucleophile hydrolase fold demonstrated by the structure of an archaeal inosine monophosphate cyclohydrolase.
Authors: Kang, Y.N. / Tran, A. / White, R.H. / Ealick, S.E.
History
DepositionNov 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IMP cyclohydrolase
B: IMP cyclohydrolase
C: IMP cyclohydrolase
D: IMP cyclohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5168
Polymers96,1234
Non-polymers1,3934
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-12 kcal/mol
Surface area29440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.975, 85.975, 124.442
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
IMP cyclohydrolase / / Inosinicase / IMP synthetase


Mass: 24030.787 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (unknown)
Gene: PurO / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (unknown) / Strain (production host): BL21 / References: UniProt: O27099, IMP cyclohydrolase
#2: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25-30% MPD, 0.2M ammonium acetate, 0.1M sodium citrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97949
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 66529 / Num. obs: 65280 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.043 / Net I/σ(I): 26.99
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 6.27 / Num. unique all: 6678 / Rsym value: 0.215 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KUU
Resolution: 2.03→27.45 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 862209.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 6017 10.1 %RANDOM
Rwork0.218 ---
obs0.218 59591 89.6 %-
all-66507 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.7496 Å2 / ksol: 0.412293 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.32 Å26.91 Å20 Å2
2--8.32 Å20 Å2
3----16.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.03→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6179 0 92 200 6471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it3.121.5
X-RAY DIFFRACTIONc_mcangle_it3.872
X-RAY DIFFRACTIONc_scbond_it4.832
X-RAY DIFFRACTIONc_scangle_it6.032.5
LS refinement shellResolution: 2.03→2.16 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 958 10.5 %
Rwork0.281 8195 -
obs-8195 82.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4imp_pimp_p

+
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