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

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Basic information

Entry
Database: PDB / ID: 1nve
TitleCrystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+ and NAD
Components3-DEHYDROQUINATE SYNTHASE
KeywordsLYASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / DHQS / OPEN FORM / FORM E / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pentafunctional AROM polypeptide
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.58 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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
C: 3-DEHYDROQUINATE SYNTHASE
D: 3-DEHYDROQUINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,85214
Polymers171,8664
Non-polymers2,98610
Water12,430690
1
A: 3-DEHYDROQUINATE SYNTHASE
B: 3-DEHYDROQUINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4267
Polymers85,9332
Non-polymers1,4935
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-105 kcal/mol
Surface area30870 Å2
MethodPISA
2
C: 3-DEHYDROQUINATE SYNTHASE
D: 3-DEHYDROQUINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4267
Polymers85,9332
Non-polymers1,4935
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-104 kcal/mol
Surface area30770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.640, 70.350, 144.320
Angle α, β, γ (deg.)90.00, 90.78, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two crystallographic dimers chains A+B and C+D respectively, each equivalent to the biological dimer.

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Components

#1: Protein
3-DEHYDROQUINATE SYNTHASE / DHQS


Mass: 42966.535 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.43 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG3350, HEPES, DMSO, NA/K-TARTRATE, pH 8.0, 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
218 %PEG33501reservoir
430 %DMSO1reservoir
50.2 Msodium potassium tartrate1reservoir
3HEPES1reservoirpH8.0

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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 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: 2.58→30 Å / Num. all: 53149 / Num. obs: 52135 / % possible obs: 98.1 % / Observed criterion σ(I): -1.5 / Redundancy: 3.66 % / Biso Wilson estimate: 67.3 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.25
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 2.64 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.17 / Num. unique all: 5327 / % possible all: 78.8
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 97.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Lowest resolution: 2.63 Å / % possible obs: 68.6 % / Redundancy: 1.89 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.09

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NRX

1nrx


Resolution: 2.58→25.57 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1396837.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 5121 9.8 %RANDOM
Rwork0.208 ---
obs0.208 52135 98.4 %-
all-53149 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9276 Å2 / ksol: 0.289413 e/Å3
Displacement parametersBiso mean: 55.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.98 Å20 Å2-0.32 Å2
2--10.23 Å20 Å2
3----14.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.58→25.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11621 0 182 690 12493
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.58→2.67 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.39 319 7.1 %
Rwork0.316 4197 -
obs--85.4 %
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
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0061
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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