[English] 日本語
Yorodumi
- PDB-4cl0: Structure of the Mycobacterium tuberculosis Type II Dehydroquinas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cl0
TitleStructure of the Mycobacterium tuberculosis Type II Dehydroquinase inhibited by a 3-dehydroquinic acid derivative
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / BACTERIAL PROTEINS / TYPE 2 DEHYDROQUINASE / INHIBITOR / PROTEIN BINDING / SHIKIMIS ACID PATHWAY / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


quinate catabolic process / Chorismate via Shikimate Pathway / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol
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
(2R)-2-METHYL-3-DEHYDROQUINIC ACID / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsOtero, J.M. / Llamas-Saiz, A.L. / Maneiro, M. / Peon, A. / Sedes, A. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J.
CitationJournal: To be Published
Title: Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase
Authors: Maneiro, M. / Otero, J.M. / Peon, A. / Sedes, A. / Llamas-Saiz, A.L. / Lamb, H. / Hawkins, A.R. / van Raaij, M.J. / Gonzalez-Bello, C.
History
DepositionJan 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8812
Polymers15,6771
Non-polymers2041
Water23413
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)190,57124
Polymers188,12112
Non-polymers2,45012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation8_555-z,x,-y1
Buried area25690 Å2
ΔGint-37.7 kcal/mol
Surface area53970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.003, 126.003, 126.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-2006-

HOH

-
Components

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


Mass: 15676.737 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): SK3430
References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-9PY / (2R)-2-METHYL-3-DEHYDROQUINIC ACID


Mass: 204.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.8 Å3/Da / Density % sol: 55.7 % / Description: NONE
Crystal growpH: 7.5
Details: 32% (V/V) 2-METHYL-2,4-PENTANEDIOL, 0.3 M AMMONIUM SULFATE, 0.1 M 4-(2-HYDROXYETHYL)-PIPERAZINE- 1-ETHANESULFONIC ACID SODIUM SALT (HEPES) PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2013 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR
RadiationMonochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 3.1→44.55 Å / Num. obs: 3177 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.9
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 7.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y71

2y71


Resolution: 3.1→44.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.862 / SU B: 15.61 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. ARG-18 AND GLU-42 SIDE CHAINS ARE MISSING BY DISORDER IN THE STRUCTURE. INHIBITOR INCLUDED IN ENZYME ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. ARG-18 AND GLU-42 SIDE CHAINS ARE MISSING BY DISORDER IN THE STRUCTURE. INHIBITOR INCLUDED IN ENZYME ACTIVE SITE BY SOAKING OF APO-CRYSTALS IN INHIBITOR SOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.22814 137 4.4 %RANDOM
Rwork0.13199 ---
obs0.13607 2970 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.75 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.1→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 14 13 1078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191089
X-RAY DIFFRACTIONr_bond_other_d0.0010.021064
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9781489
X-RAY DIFFRACTIONr_angle_other_deg0.7853.0032430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.565141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29523.61747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86515170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.305159
X-RAY DIFFRACTIONr_chiral_restr0.0670.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
X-RAY DIFFRACTIONr_nbd_refined0.2140.2259
X-RAY DIFFRACTIONr_nbd_other0.1750.21060
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2542
X-RAY DIFFRACTIONr_nbtor_other0.0850.2680
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.211
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0350.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9384.8231089
X-RAY DIFFRACTIONr_mcbond_other0.5534.8791064
X-RAY DIFFRACTIONr_mcangle_it4.8587.1751488
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.42547.9881970
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.447.2982430
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: 3.1→3.465 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.289 42 -
Rwork0.173 823 -
obs--100 %

+
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