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- PDB-4rc9: Crystal Structure of the type II Dehydroquinate dehydratase from ... -

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Basic information

Entry
Database: PDB / ID: 4rc9
TitleCrystal Structure of the type II Dehydroquinate dehydratase from Acinetobacter baumannii at 2.03A Resolution
Components3-dehydroquinate dehydratase
KeywordsLYASE
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 speciesAcinetobacter baumannii ATCC 17978 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsIqbal, N. / Kumar, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of the type II Dehydroquinate dehydratase from Acinetobacter baumannii at 2.03 A Resolution
Authors: Iqbal, N. / Kumar, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionSep 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 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)199,35424
Polymers198,20212
Non-polymers1,15312
Water13,854769
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29740 Å2
ΔGint-337 kcal/mol
Surface area69800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.284, 95.279, 132.263
Angle α, β, γ (deg.)90.00, 95.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-dehydroquinate dehydratase / 3-dehydroquinase / Type II DHQase


Mass: 16516.803 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 17978 (bacteria)
Strain: ATCC 17978 / NCDC KC 755 / Gene: A1S_2009, aroQ, F911_01683, HMPREF0010_00310 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3M692, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG3350, MgSO4, Tris buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 8, 2014 / Details: mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 124546 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.09 / Net I/σ(I): 31
Reflection shellResolution: 2.03→2.07 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWZ

3lwz


Resolution: 2.05→47 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.53 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24488 6049 4.9 %RANDOM
Rwork0.1905 ---
obs0.19321 116575 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.311 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-0.08 Å2
2--0.07 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13968 0 60 769 14797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01914292
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213920
X-RAY DIFFRACTIONr_angle_refined_deg1.871.95119452
X-RAY DIFFRACTIONr_angle_other_deg0.948331872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98451800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64724.528636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.885152352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2361572
X-RAY DIFFRACTIONr_chiral_restr0.1280.22292
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02116272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023288
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4953.0517236
X-RAY DIFFRACTIONr_mcbond_other3.4873.057235
X-RAY DIFFRACTIONr_mcangle_it5.6634.5369024
X-RAY DIFFRACTIONr_mcangle_other5.6654.5389025
X-RAY DIFFRACTIONr_scbond_it3.6673.4487056
X-RAY DIFFRACTIONr_scbond_other3.6173.457009
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7325.0510357
X-RAY DIFFRACTIONr_long_range_B_refined8.91324.60716613
X-RAY DIFFRACTIONr_long_range_B_other8.87924.47816355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 435 -
Rwork0.187 8963 -
obs--100 %

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