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- PDB-4cnp: Structure of the Salmonella typhi type I dehydroquinase inhibited... -

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Basic information

Entry
Database: PDB / ID: 4cnp
TitleStructure of the Salmonella typhi type I dehydroquinase inhibited by a 3-epiquinic acid derivative
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / SHIKIMIS ACID PATHWAY
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
(2S)-2-HYDROXY-3-EPIQUINIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsOtero, J.M. / Llamas-Saiz, A.L. / Maneiro, M. / Peon, A. / Lence, E. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J.
CitationJournal: To be Published
Title: Mechanistic Insight Into the Reaction Catalyzed by Type I Dehydroquinase
Authors: Maneiro, M. / Peon, A. / Lence, E. / Otero, J.M. / Llamas-Saiz, A.L. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C.
History
DepositionJan 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)55,97512
Polymers55,3622
Non-polymers61310
Water12,034668
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-62.4 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.216, 44.473, 84.702
Angle α, β, γ (deg.)90.00, 95.20, 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-9C4 / (2S)-2-HYDROXY-3-EPIQUINIC ACID


Mass: 208.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12O7
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O

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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: 39.9 % / Description: NONE
Crystal growpH: 6.4 / Details: 30% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.09723
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 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: 1.09723 Å / Relative weight: 1
ReflectionResolution: 1.15→84.35 Å / Num. obs: 156242 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.9
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.2 / % possible all: 95.9

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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: 1.15→51.17 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.944 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INHIBITOR INCLUDED IN ENZYME ACTIVE SITE BY SOAKING OF APO- CRYSTALS IN INHIBITOR SOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.16031 3124 2 %RANDOM
Rwork0.13344 ---
obs0.13396 153096 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.232 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.25 Å2
2---0.03 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.15→51.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 36 668 4564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194310
X-RAY DIFFRACTIONr_bond_other_d0.0010.024356
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9685882
X-RAY DIFFRACTIONr_angle_other_deg0.7843.00210054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6955545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23724.011182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90515838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7151530
X-RAY DIFFRACTIONr_chiral_restr0.0760.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02929
X-RAY DIFFRACTIONr_nbd_refined0.2440.21734
X-RAY DIFFRACTIONr_nbd_other0.1710.24121
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22053
X-RAY DIFFRACTIONr_nbtor_other0.0850.22465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0010.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.2172
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7241.0214310
X-RAY DIFFRACTIONr_mcbond_other1.4941.0574356
X-RAY DIFFRACTIONr_mcangle_it5.0961.515866
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.02110.1677544
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7971.56110054
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.35838666
X-RAY DIFFRACTIONr_sphericity_free22.142597
X-RAY DIFFRACTIONr_sphericity_bonded5.69759160
LS refinement shellResolution: 1.15→1.212 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.222 437 -
Rwork0.185 21634 -
obs--95.78 %

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