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

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Basic information

Entry
Database: PDB / ID: 1nvd
TitleCrystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+ and carbaphosphonate
Components3-DEHYDROQUINATE SYNTHASE
KeywordsLYASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / DHQS / open form / form B / 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
Chem-CRB / Pentafunctional AROM polypeptide
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 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 / 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_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_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.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_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.value / _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)86,6407
Polymers85,9332
Non-polymers7075
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-93 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.030, 70.030, 197.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE CRYSTALLOGRAPHIC DIMER IS EQUIVALENMT 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-CRB / [1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID / CARBAPHOSPHONATE


Mass: 270.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.4 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG3350, HEPES, ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
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
27 %PEG60001reservoir
420 %ethylene glycol1reservoir
3HEPES1reservoirpH7.0

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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: Mar 20, 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: 2.51→30 Å / Num. all: 31211 / Num. obs: 29338 / % possible obs: 94 % / Observed criterion σ(I): -1.5 / Redundancy: 2.98 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 29.79
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 2.79 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 13.3 / Num. unique all: 3064 / % possible all: 88.3
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 97.8 % / Redundancy: 2.93 % / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 99.5 % / Redundancy: 2.99 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 15.41

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NR5

1nr5


Resolution: 2.51→30 Å / Data cutoff high absF: 1893027.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2929 -random
Rwork0.196 ---
obs0.196 29338 94.4 %-
all-31211 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.8433 Å2 / ksol: 0.331757 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---3.39 Å20 Å2
3---3.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.51→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5871 0 37 694 6602
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it3.853
X-RAY DIFFRACTIONc_mcangle_it5.746
X-RAY DIFFRACTIONc_scbond_it8.656
X-RAY DIFFRACTIONc_scangle_it10.7712
LS refinement shellResolution: 2.51→2.6 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.407 260 9.6 %
Rwork0.305 2736 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2lig.paramlig.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater_rep.top
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.19
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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