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- PDB-1uqr: Type II 3-dehydroquinate dehydratase (DHQase) from Actinobacillus... -

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Basic information

Entry
Database: PDB / ID: 1uqr
TitleType II 3-dehydroquinate dehydratase (DHQase) from Actinobacillus pleuropneumoniae
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS
Function / homology
Function and homology information


quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesACTINOBACILLUS PLEUROPNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMaes, D. / Gonzalez-Ramirez, L.A. / Lopez-Jaramillo, J. / Yu, B. / De Bondt, H. / Zegers, I. / Afonina, E. / Garcia-Ruiz, J.M. / Gulnik, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structural Study of the Type II 3-Dehydroquinate Dehydratase from Actinobacillus Pleuropneumoniae
Authors: Maes, D. / Gonzalez-Ramirez, L.A. / Lopez-Jaramillo, J. / Yu, B. / De Bondt, H. / Zegers, I. / Afonina, E. / Garcia-Ruiz, J.M. / Gulnik, S.
History
DepositionOct 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-DEHYDROQUINATE DEHYDRATASE
B: 3-DEHYDROQUINATE DEHYDRATASE
C: 3-DEHYDROQUINATE DEHYDRATASE
D: 3-DEHYDROQUINATE DEHYDRATASE
E: 3-DEHYDROQUINATE DEHYDRATASE
F: 3-DEHYDROQUINATE DEHYDRATASE
G: 3-DEHYDROQUINATE DEHYDRATASE
H: 3-DEHYDROQUINATE DEHYDRATASE
I: 3-DEHYDROQUINATE DEHYDRATASE
J: 3-DEHYDROQUINATE DEHYDRATASE
K: 3-DEHYDROQUINATE DEHYDRATASE
L: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,83647
Polymers206,37012
Non-polymers3,46735
Water40,7502262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)129.095, 131.333, 161.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
3-DEHYDROQUINATE DEHYDRATASE / 3-DEHYDROQUINASE / TYPE II DHQASE


Mass: 17197.488 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACTINOBACILLUS PLEUROPNEUMONIAE (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P43877, 3-dehydroquinate dehydratase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2262 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES A TRANS-DEHYDRATION VIA AN ENOLATE INTERMEDIATE. BELONGS TO THE TYPE-II 3-DEHYDROQUINASE ...CATALYZES A TRANS-DEHYDRATION VIA AN ENOLATE INTERMEDIATE. BELONGS TO THE TYPE-II 3-DEHYDROQUINASE FAMILY. CLASS-II ENZYMES ARE HOMODODECAMERIC ENZYMES OF ABOUT 17 KDA

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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: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growpH: 7.4 / Details: pH 7.40
Crystal grow
*PLUS
pH: 7.4 / Method: gel-acupuncture method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein11
2100 mMTris-HCl11pH7.4
33.5 Mammonium sulfate12
4100 mMTris-HCl12pH7.4
50.03 %(w/v)sodium azide12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8463
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8463 Å / Relative weight: 1
ReflectionResolution: 1.71→20 Å / Num. obs: 288020 / % possible obs: 98.2 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 28
Reflection shellResolution: 1.71→1.8 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 7.3 / % possible all: 96
Reflection
*PLUS
Highest resolution: 1.71 Å / Lowest resolution: 20 Å / Num. obs: 210933 / % possible obs: 71.5 % / Redundancy: 1.64 % / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 66.2 % / Num. unique obs: 27619 / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE SIDE CHAIN OF CYS 125 HAS THREE ALTERNATE CONFORMATIONS IN EVERY CHAIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 -5 %RANDOM
Rwork0.178 ---
obs0.178 288020 98 %-
Displacement parametersBiso mean: 23.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13650 0 187 2262 16099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 1.71 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3

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