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- PDB-1nva: Crystal structure of 3-dehydroquinate synthase (DHQS) in complex ... -

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Basic information

Entry
Database: PDB / ID: 1nva
TitleCrystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+ and ADP
Components3-DEHYDROQUINATE SYNTHASE
KeywordsLYASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / DHQS / OPEN FORM / FORM D / DOMAIN MOVEMENT / CYCLASE
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate kinase activity / shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity ...3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate kinase activity / shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / : / 3-dehydroquinate synthase C-terminal / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase N-terminal / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / Shikimate kinase, conserved site ...Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / : / 3-dehydroquinate synthase C-terminal / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase N-terminal / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / Shikimate kinase, conserved site / Shikimate kinase signature. / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Rossmann fold - #1970 / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Aminoacid dehydrogenase-like, N-terminal domain superfamily / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Pentafunctional AROM polypeptide
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsNichols, C.E. / Ren, J. / Lamb, H.K. / Hawkins, A.R. / Stammers, D.K.
Citation
Journal: J.MOL.BIOL. / Year: 2003
Title: Ligand-induced Conformational Changes and a Mechanism for Domain Closure in Aspergillus nidulans Dehydroquinate Synthase
Authors: Nichols, C.E. / Ren, J. / Lamb, H.K. / Hawkins, A.R. / Stammers, D.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Identification of many crystal forms of Aspergillus nidulans Dehydroquinate Synthase
Authors: Nichols, C.E. / Ren, J. / Lamb, H. / Haldane, F. / Hawkins, A.R. / Stammers, D.K.
History
DepositionFeb 3, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / 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 / _struct_conn.pdbx_dist_value / _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.ptnr2_label_seq_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 SYNTHASE
B: 3-DEHYDROQUINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9547
Polymers85,9332
Non-polymers1,0215
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-104 kcal/mol
Surface area30950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.010, 68.910, 137.710
Angle α, β, γ (deg.)90.00, 94.71, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE CRYSTALLOGRAPHIC DIMER IS EQUIVALENT TO THE BIOLOGICAL DIMER

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Components

#1: Protein 3-DEHYDROQUINATE SYNTHASE / DHQS


Mass: 42966.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: AROMA / Plasmid: PTR51 / Production host: Escherichia coli (E. coli) / Strain (production host): GLW38 (AROB-) / References: UniProt: P07547, 3-dehydroquinate synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.25 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG6000, MPD, ETHYLENE GLYCOL, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
pH: 6.8
Details: Nichols, C.E., (2001) Acta Crystallogr., Sect.D, 57, 306.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115-25 mg/mlprotein1drop
217 %PEG33501reservoir
40.2 Mammonium tartrate1reservoir
3HEPES1reservoirpH6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2000 / Details: OSMIC MULTILAYER
RadiationMonochromator: OSMIC MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.62→30 Å / Num. all: 23231 / Num. obs: 22806 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1.5 / Redundancy: 4.48 % / Biso Wilson estimate: 66.48 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.06
Reflection shellResolution: 2.62→2.71 Å / Redundancy: 1.14 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 1.05 / Num. unique all: 2312 / % possible all: 81.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 35 Å / % possible obs: 99.6 % / Redundancy: 4.81 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.85 Å / % possible obs: 95.9 % / Redundancy: 3.38 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.32

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NRX

1nrx


Resolution: 2.62→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2264 -RANDOM
Rwork0.198 ---
all-23231 --
obs-22806 98.2 %-
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.62→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5836 0 57 253 6146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.62→2.71 Å / Rfactor Rfree error: 0.028
RfactorNum. reflection% reflection
Rfree0.427 192 -
Rwork0.384 --
obs-1863 88.3 %
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 35 Å / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0068
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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