[English] 日本語
Yorodumi
- PDB-2c4v: H. pylori type II DHQase in complex with citrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c4v
TitleH. pylori type II DHQase in complex with citrate
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / 3-DEHYDROQUINASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS
Function / homology
Function and homology information


quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsRobinson, D.A. / Lapthorn, A.J.
Citation
Journal: J.Med.Chem. / Year: 2006
Title: Crystal Structures of Helicobacter Pylori Type II Dehydroquinase Inhibitor Complexes: New Directions for Inhibitor Design.
Authors: Robinson, D.A. / Stewart, K.A. / Price, N.C. / Chalk, P.A. / Coggins, J.R. / Lapthorn, A.J.
#1: Journal: Proteins: Struct.,Funct., Genet. / Year: 2003
Title: Crystal Structure of the Type II 3-Dehydroquinase from Helicobacter Pylori
Authors: Lee, B.I. / Kwak, J.E. / Suh, S.W.
History
DepositionOct 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 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: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6912
Polymers18,4991
Non-polymers1921
Water72140
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3834
Polymers36,9982
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_757-x+2,y,-z+21
MethodPQS
Unit cell
Length a, b, c (Å)98.910, 98.910, 98.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

21A-2010-

HOH

31A-2017-

HOH

-
Components

#1: Protein 3-DEHYDROQUINATE DEHYDRATASE / 3-DEHYDROQUINASE / DHQASE / TYPE II DEHYDROQUINASE


Mass: 18499.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q48255, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES A TRANS-DEHYDRATION VIA AN ENOLATE INTERMEDIATE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.1 %
Description: DATA USED WAS THAT OF ENTRY 1J2Y NO SIGMA CUTOFF WAS USED AND ALL DATA TO 2.5A RESOLUTION WAS USED
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 4000, SODIUM CHOLRIDE, SODIUM CITRATE, EDTA, 2-MERCAPTOETHANOL, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→44 Å / Num. obs: 6146 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 38 % / Biso Wilson estimate: 53.5 Å2 / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.48 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 15.034 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY IS A REINTERPRETATION OF ENTRY 1J2Y USING DEPOSITED STRUCTURE FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 311 5.2 %RANDOM
Rwork0.17 ---
obs0.172 5726 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.82 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 13 40 1274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221259
X-RAY DIFFRACTIONr_bond_other_d0.0020.021150
X-RAY DIFFRACTIONr_angle_refined_deg2.241.9561696
X-RAY DIFFRACTIONr_angle_other_deg1.93332686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0495157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.94225.93259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.17615228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.708154
X-RAY DIFFRACTIONr_chiral_restr0.1290.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
X-RAY DIFFRACTIONr_nbd_refined0.2280.2299
X-RAY DIFFRACTIONr_nbd_other0.2080.21158
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2614
X-RAY DIFFRACTIONr_nbtor_other0.1030.2742
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4851.5987
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81721252
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6053535
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8054.5444
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 22
Rwork0.223 378
Refinement TLS params.Method: refined / Origin x: 90.1067 Å / Origin y: -31.3267 Å / Origin z: 91.8471 Å
111213212223313233
T0.1848 Å2-0.0929 Å2-0.0507 Å2--0.0895 Å2-0.066 Å2--0.2208 Å2
L1.9165 °2-0.4771 °20.1179 °2-1.514 °2-0.6252 °2--2.8505 °2
S0.0369 Å °0.1113 Å °-0.6059 Å °-0.2133 Å °0.0556 Å °0.1233 Å °0.6452 Å °-0.1632 Å °-0.0925 Å °

+
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