[English] 日本語
Yorodumi
- PDB-2gt2: Structure of the E. coli GDP-mannose mannosyl hydrolase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gt2
TitleStructure of the E. coli GDP-mannose mannosyl hydrolase
ComponentsGDP-mannose mannosyl hydrolase
KeywordsHYDROLASE / GDP-mannose hydrolase GDP-glucose hydrolase NUDIX
Function / homology
Function and homology information


GDP-glucosidase activity / GDP-mannose mannosyl hydrolase activity / lipopolysaccharide biosynthetic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / manganese ion binding / magnesium ion binding / protein homodimerization activity / identical protein binding
Similarity search - Function
GDP-mannose mannosyl hydrolase, Enterobacteria / GDP-mannose mannosyl hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...GDP-mannose mannosyl hydrolase, Enterobacteria / GDP-mannose mannosyl hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GDP-mannose mannosyl hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGabelli, S.B. / Bianchet, M.A. / Azurmendi, H.F. / MIldvan, A.S. / Amzel, L.M.
Citation
Journal: Biochemistry / Year: 2006
Title: X-ray, NMR, and mutational studies of the catalytic cycle of the GDP-mannose mannosyl hydrolase reaction.
Authors: Gabelli, S.B. / Azurmendi, H.F. / Bianchet, M.A. / Amzel, L.M. / Mildvan, A.S.
#1: Journal: Structure / Year: 2004
Title: Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus.
History
DepositionApr 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GDP-mannose mannosyl hydrolase
B: GDP-mannose mannosyl hydrolase
C: GDP-mannose mannosyl hydrolase
D: GDP-mannose mannosyl hydrolase


Theoretical massNumber of molelcules
Total (without water)73,6994
Polymers73,6994
Non-polymers00
Water6,323351
1
A: GDP-mannose mannosyl hydrolase
B: GDP-mannose mannosyl hydrolase


Theoretical massNumber of molelcules
Total (without water)36,8492
Polymers36,8492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-15 kcal/mol
Surface area14580 Å2
MethodPISA
2
C: GDP-mannose mannosyl hydrolase
D: GDP-mannose mannosyl hydrolase


Theoretical massNumber of molelcules
Total (without water)36,8492
Polymers36,8492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-17 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.767, 48.767, 210.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Detailsthe biological assembly is a dimer (A,B) or (C,D)

-
Components

#1: Protein
GDP-mannose mannosyl hydrolase / GDPMH / Colanic acid biosynthesis protein wcaH


Mass: 18424.627 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nudD, gmm, wcaH / Plasmid: pet11b / Production host: Escherichia coli (E. coli)
References: UniProt: P32056, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 0
Details: 0.4M Potassium Sodium Tartrate tetra-hydrate, pH 0.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→223.61 Å / Num. obs: 34871 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Χ2: 3.275 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.03 / Num. unique all: 2405 / Rsym value: 0.206 / Χ2: 1.199 / % possible all: 63.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MADNESSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RYA

1rya


Resolution: 2→223.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.166 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1747 5 %RANDOM
Rwork0.201 ---
all0.204 34871 --
obs0.204 34871 92.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.477 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å20 Å2
2---0.35 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2→223.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4937 0 0 351 5288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225060
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9416858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28722.574272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6315791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6641552
X-RAY DIFFRACTIONr_chiral_restr0.0660.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023966
X-RAY DIFFRACTIONr_nbd_refined0.1810.22148
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23374
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2380
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.230
X-RAY DIFFRACTIONr_mcbond_it0.5981.53070
X-RAY DIFFRACTIONr_mcangle_it1.0624815
X-RAY DIFFRACTIONr_scbond_it1.16932268
X-RAY DIFFRACTIONr_scangle_it1.7794.52043
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 87 -
Rwork0.231 1592 -
obs-1679 59.86 %

+
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