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- PDB-1l9w: CRYSTAL STRUCTURE OF 3-DEHYDROQUINASE FROM SALMONELLA TYPHI COMPL... -

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Basic information

Entry
Database: PDB / ID: 1l9w
TitleCRYSTAL STRUCTURE OF 3-DEHYDROQUINASE FROM SALMONELLA TYPHI COMPLEXED WITH REACTION PRODUCT
Components3-dehydroquinate dehydratase aroD
KeywordsLYASE / TIM-Barrel / complex with product
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
3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLee, W.H. / Perles, L.A. / Nagem, R.A.P. / Shrive, A.K. / Hawkins, A. / Sawyer, L. / Polikarpov, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Comparison of different crystal forms of 3-dehydroquinase from Salmonella typhi and its implication for the enzyme activity.
Authors: Lee, W.H. / Perles, L.A. / Nagem, R.A. / Shrive, A.K. / Hawkins, A. / Sawyer, L. / Polikarpov, I.
History
DepositionMar 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 8, 2012Group: Derived calculations
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN DHS: 3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE GROUP. Formula:4(C7 H8 N1 O4). THE ...HETEROGEN DHS: 3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE GROUP. Formula:4(C7 H8 N1 O4). THE PRODUCT IS COVALENTLY LINKED TO LYS170 THROUGH FORMATION OF A SCHIFF BASE (IMINE) INTERMEDIATE THAT IS THEN REDUCED WITH BOROHYDRIDE. THE EMPIRICAL FORMULA GIVEN CONTAINS THE CARBOXYLATE PROTON BUT NOT THE 3-KETO OXYGEN (WHICH IS REPLACED BY THE NZ OF LYS170 IN FORMING THE SCHIFF BASE). LYS 170 FORMS THE IMINE INTERMEDIATE WITH THE AID OF HIS 143. ARG 213 INTERACTS WITH THE CARBOXYL GROUP OF THE 3-DEHYDROQUINATE SUBSTRATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase aroD
B: 3-dehydroquinate dehydratase aroD
C: 3-dehydroquinate dehydratase aroD
D: 3-dehydroquinate dehydratase aroD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3088
Polymers110,6204
Non-polymers6894
Water3,729207
1
A: 3-dehydroquinate dehydratase aroD
B: 3-dehydroquinate dehydratase aroD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6544
Polymers55,3102
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-16 kcal/mol
Surface area18900 Å2
MethodPISA, PQS
2
C: 3-dehydroquinate dehydratase aroD
D: 3-dehydroquinate dehydratase aroD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6544
Polymers55,3102
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-14 kcal/mol
Surface area18840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.610, 158.560, 85.890
Angle α, β, γ (deg.)90.00, 93.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-dehydroquinate dehydratase aroD / 3-dehydroquinase


Mass: 27654.912 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: THE PRODUCT 3-DEHYDROSHIKIMATE IS COVALENTLY ATTACHED TO THE ACTIVE SITE LYS 170 BY BOROHYDRIDE REDUCTION OF THE IMINE (SCHIFF BASE)
Source: (natural) Salmonella typhi (bacteria) / References: UniProt: P24670, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-DHS / 3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE


Mass: 172.159 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H10NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, citrate-phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Method: sparse matrix method / PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
2100 mMcitrate-phosphate11pH5.0-6.0
1PEG400011

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.928 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. all: 49700 / Num. obs: 49700 / % possible obs: 76.45 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.15 Å / % possible all: 70.12
Reflection
*PLUS
Highest resolution: 2.1 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QFE

1qfe


Resolution: 2.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2485 5 %Random
Rwork0.177 ---
all-49700 --
obs-49700 --
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7736 0 44 207 7987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d2.4
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4

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