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- PDB-1qfe: THE STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE FROM SALMONE... -

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Basic information

Entry
Database: PDB / ID: 1qfe
TitleTHE STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE FROM SALMONELLA TYPHI
ComponentsPROTEIN (3-DEHYDROQUINATE DEHYDRATASE)
KeywordsLYASE / DEHYDRATASE / CONVERSION OF 3-DEHYDROQUINATE TO DEHYDROSHIKIMATE / 3RD ENZYME IN THE SHIKIMATE PATHWAY / TIM BARREL
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 / MIR / Resolution: 2.1 Å
AuthorsShrive, A.K. / Polikarpov, I. / Sawyer, L. / Coggins, J.R. / Hawkins, A.R.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction.
Authors: Gourley, D.G. / Shrive, A.K. / Polikarpov, I. / Krell, T. / Coggins, J.R. / Hawkins, A.R. / Isaacs, N.W. / Sawyer, L.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallisation of the Type I 3-Dehydroquinase from Salmonella Typhi
Authors: Boys, C.W.G. / Bury, S.M. / Sawyer, L. / Moore, J.D. / Charles, I.G. / Hawkins, A.R. / Deka, R. / Kleanthous, C. / Coggins, J.R.
History
DepositionApr 5, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: PROTEIN (3-DEHYDROQUINATE DEHYDRATASE)
B: PROTEIN (3-DEHYDROQUINATE DEHYDRATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6544
Polymers55,3102
Non-polymers3442
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-15 kcal/mol
Surface area18980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.490, 45.390, 85.470
Angle α, β, γ (deg.)90.00, 95.48, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.16579, -0.98198, 0.09069), (-0.98345, 0.15782, -0.08894), (0.07302, -0.10394, -0.9919)
Vector: 35.57699, 35.23283, 61.5108)

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Components

#1: Protein PROTEIN (3-DEHYDROQUINATE DEHYDRATASE) / EC 4.2.1.10 / 3-DEHYDROQUINASE


Mass: 27654.912 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C7H10NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHETEROGEN DHS: THE PRODUCT IS COVALENTLY LINKED TO LYS170 THROUGH FORMATION OF A SCHIFF BASE (IMINE) ...HETEROGEN DHS: 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.

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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: 2.17 Å3/Da / Density % sol: 42 %
Crystal growpH: 6
Details: 30% PEG 4000, PH BETWEEN 5 AND 6.5, 100MM CITRATE-PHOSPHATE BUFFER, pH 6.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Boys, C.W.G., (1992) J.Mol.Biol., 227, 352.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMphosphate1drop
20.5 mMdithiothreitol1drop
314 mg/mlprotein1drop
5100 mMcitrate phosphate1reservoir
433 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→17 Å / Num. obs: 23517 / % possible obs: 86.1 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.104
Reflection shellHighest resolution: 2.1 Å / % possible all: 74.7
Reflection
*PLUS
Num. measured all: 66770

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Processing

Software
NameVersionClassification
VECREFmodel building
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
VECREFphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→12 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -5 %RANDOM
Rwork0.199 ---
obs-23517 86.1 %-
Displacement parametersBiso mean: 22.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 22 137 4027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 12 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.6

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