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- PDB-4clm: Structure of Salmonella typhi type I dehydroquinase irreversibly ... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
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.

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Experimental details

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Experiment

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

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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

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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

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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 %

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