[English] 日本語
Yorodumi
- PDB-4clm: Structure of Salmonella typhi type I dehydroquinase irreversibly ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4clm
TitleStructure of Salmonella typhi type I dehydroquinase irreversibly inhibited with a 1,3,4-trihydroxyciclohexane-1-carboxylic acid derivative
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / TYPE I DEHYDROQUINASE / INHIBITOR / SHIKIMIS ACID PATHWAY / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
: / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Chem-WPL / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOtero, J.M. / Llamas-Saiz, A.L. / Tizon, L. / Maneiro, M. / Lence, E. / Poza, S. / Lamb, H. / Hawkins, A.R. / Blanco, B. / Sedes, A. ...Otero, J.M. / Llamas-Saiz, A.L. / Tizon, L. / Maneiro, M. / Lence, E. / Poza, S. / Lamb, H. / Hawkins, A.R. / Blanco, B. / Sedes, A. / Peon, A. / Gonzalez-Bello, C. / van Raaij, M.J.
CitationJournal: Org. Biomol. Chem. / Year: 2015
Title: Irreversible covalent modification of type I dehydroquinase with a stable Schiff base.
Authors: Tizon, L. / Maneiro, M. / Peon, A. / Otero, J.M. / Lence, E. / Poza, S. / van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C.
History
DepositionJan 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Aug 1, 2018Group: Data collection / Database references / Structure summary
Category: citation_author / struct / Item: _citation_author.identifier_ORCID / _struct.title
Revision 2.0Aug 29, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Aug 28, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Dec 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_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-DEHYDROQUINATE DEHYDRATASE
B: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6657
Polymers55,3622
Non-polymers3035
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-50.6 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.590, 44.470, 84.980
Angle α, β, γ (deg.)90.00, 95.17, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 27680.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24670, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Chemical ChemComp-WPL / (1~{S},3~{S},4~{R},5~{R})-3-methyl-1,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid


Mass: 190.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsWPL: THE PROTEIN IS MODIFIED USING AN IRREVERSIBLE INHIBITOR. A THE INHIBITION TAKE PLACE VIA A ...WPL: THE PROTEIN IS MODIFIED USING AN IRREVERSIBLE INHIBITOR. A THE INHIBITION TAKE PLACE VIA A NUCLEOPHILIC RING OPENING OF THE EPOXIDE GROUP OF THE INHIBITOR BY THE NZ-ATOM OF LYS-170 WHICH IS FOLLOWED BY ELIMINATION OF A WATER MOLECULE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.6 % / Description: NONE
Crystal growpH: 5.6 / Details: 34% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.8729
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2013 / Details: PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR)
RadiationMonochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.4→47.17 Å / Num. obs: 85495 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.1 / % possible all: 76.1

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QFE

1qfe


Resolution: 1.4→47.21 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.702 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. GAP BY DISORDERED REGION BETWEEN VAL-228 AND ILE-237 IN CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.15498 4293 5 %RANDOM
Rwork0.1199 ---
obs0.12168 81186 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.231 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.47 Å2
2--0.69 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 17 665 4472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194090
X-RAY DIFFRACTIONr_bond_other_d0.0020.024097
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9645555
X-RAY DIFFRACTIONr_angle_other_deg0.9473.0029430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36924.382178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35315774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1351527
X-RAY DIFFRACTIONr_chiral_restr0.0910.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024490
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02879
X-RAY DIFFRACTIONr_nbd_refined0.2840.21646
X-RAY DIFFRACTIONr_nbd_other0.1710.23819
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21930
X-RAY DIFFRACTIONr_nbtor_other0.0830.22350
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1190.25
X-RAY DIFFRACTIONr_metal_ion_refined0.1510.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.21575
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.26450.213
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0710.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.77671.1014090
X-RAY DIFFRACTIONr_mcbond_other2.28971.1514097
X-RAY DIFFRACTIONr_mcangle_it7.5511.6235551
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.56811.137053
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2471.6919430
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.84738187
X-RAY DIFFRACTIONr_sphericity_free28.7175120
X-RAY DIFFRACTIONr_sphericity_bonded7.92158673
LS refinement shellResolution: 1.4→1.476 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.214 478 -
Rwork0.152 9343 -
obs--75.96 %

+
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