[English] 日本語
Yorodumi
- PDB-1kuu: CRYSTAL STRUCTURE OF METHANOBACTERIUM THERMOAUTOTROPHICUM CONSERV... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kuu
TitleCRYSTAL STRUCTURE OF METHANOBACTERIUM THERMOAUTOTROPHICUM CONSERVED PROTEIN MTH1020 REVEALS AN NTN-HYDROLASE FOLD
Componentsconserved proteinConservation
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved protein / NTN-hydrolase fold
Function / homology
Function and homology information


IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
Inosine monophosphate cyclohydrolase-like / IMP cyclohydrolase / 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
Biological speciesMethanothermobacter (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsSaridakis, V. / Christendat, D. / Thygesen, A. / Arrowsmith, C.H. / Edwards, A.M. / Pai, E.F.
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2002
Title: CRYSTAL STRUCTURE OF METHANOBACTERIUM THERMOAUTOTROPHICUM CONSERVED PROTEIN MTH1020 REVEALS AN NTN-HYDROLASE FOLD
Authors: Saridakis, V. / Christendat, D. / Thygesen, A. / Arrowsmith, C.H. / Edwards, A.M. / Pai, E.F.
History
DepositionJan 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: conserved protein


Theoretical massNumber of molelcules
Total (without water)21,8591
Polymers21,8591
Non-polymers00
Water57632
1
A: conserved protein

A: conserved protein

A: conserved protein

A: conserved protein


Theoretical massNumber of molelcules
Total (without water)87,4384
Polymers87,4384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Unit cell
Length a, b, c (Å)107.033, 107.033, 87.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein conserved protein / Conservation


Mass: 21859.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter (archaea) / Genus: Methanothermobacter / Gene: MTH1020 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O27099
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14 % MPD, 0.2 M Mg Acetate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: Christendat, D., (2000) J.Biol.Chem., 275, 24608.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 %MPD1reservoir
20.2 Mmagnesium acetate1reservoir
3100 mMHEPES1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 13025 / Num. obs: 13025 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 9 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 35.6
Reflection shellResolution: 2.2→2.34 Å / Rsym value: 0.374 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 113676
Reflection shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.33 Å / % possible obs: 96.5 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.3

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SDMSdata reduction
SOLVEphasing
CNS1refinement
SDMSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→14.5 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 245271.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 656 5.1 %RANDOM
Rwork0.229 ---
obs0.229 12746 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1196 Å2 / ksol: 0.349789 e/Å3
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20 Å2
2---2.57 Å20 Å2
3---5.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 0 32 1568
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.342.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 91 4.7 %
Rwork0.27 1865 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor obs: 0.27

+
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