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- PDB-4cno: Structure of the Salmonella typhi Type I dehydroquinase inhibited... -

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Basic information

Entry
Database: PDB / ID: 4cno
TitleStructure of the Salmonella typhi Type I dehydroquinase inhibited by a 3-dehydroquinic acid derivative
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / INHIBITOR / PROTEIN BINDING / 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
(2R)-2-METHYL-3-DEHYDROQUINIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Biochem. J. / Year: 2014
Title: Insights into substrate binding and catalysis in bacterial type I dehydroquinase.
Authors: Maneiro, M. / Peon, A. / Lence, E. / Otero, J.M. / Van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C.
History
DepositionJan 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,5418
Polymers110,7244
Non-polymers8174
Water5,350297
1
C: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

D: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7704
Polymers55,3622
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area2210 Å2
ΔGint-20.2 kcal/mol
Surface area19750 Å2
MethodPISA
2
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

B: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7704
Polymers55,3622
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area2250 Å2
ΔGint-19.2 kcal/mol
Surface area19620 Å2
MethodPISA
3
B: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7704
Polymers55,3622
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2250 Å2
ΔGint-19.2 kcal/mol
Surface area19720 Å2
MethodPISA
4
D: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

C: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7704
Polymers55,3622
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area2210 Å2
ΔGint-20.2 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.670, 39.406, 155.130
Angle α, β, γ (deg.)90.00, 104.68, 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.: 4
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-9PY / (2R)-2-METHYL-3-DEHYDROQUINIC ACID


Mass: 204.177 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H12O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 42.6 % / Description: NONE
Crystal growpH: 5.2 / Details: 32% PEG 4000, 0.1 M NA-CITRATE PH 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97922
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 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: 0.97922 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.522
11-H, -K, H+L20.478
ReflectionResolution: 1.5→150.07 Å / Num. obs: 131130 / % possible obs: 88.4 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 50.7

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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: 1.5→150.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.207 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. GAP BY DISORDERED REGION BETWEEN LYS-229 AND PRO-234 IN CHAINS A, B, C AND D.
RfactorNum. reflection% reflectionSelection details
Rfree0.21363 6690 5.1 %RANDOM
Rwork0.18005 ---
obs0.18177 124425 88.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.804 Å2
Baniso -1Baniso -2Baniso -3
1--12.53 Å2-0 Å20.42 Å2
2--16.29 Å20 Å2
3----3.76 Å2
Refinement stepCycle: LAST / Resolution: 1.5→150.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7617 0 56 297 7970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197971
X-RAY DIFFRACTIONr_bond_other_d0.0020.027881
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.96410835
X-RAY DIFFRACTIONr_angle_other_deg0.763.00218115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82751022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51324.102334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.953151434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2051551
X-RAY DIFFRACTIONr_chiral_restr0.0710.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021734
X-RAY DIFFRACTIONr_nbd_refined0.2160.21992
X-RAY DIFFRACTIONr_nbd_other0.1650.27711
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23872
X-RAY DIFFRACTIONr_nbtor_other0.0830.24946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2184
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1220.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.266
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1320.2171
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0992.0727971
X-RAY DIFFRACTIONr_mcbond_other0.2312.1057881
X-RAY DIFFRACTIONr_mcangle_it1.7213.08510815
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.48720.53714408
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8413.14518115
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: 1.5→1.581 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 486 -
Rwork0.302 10314 -
obs--50.16 %

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