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- PDB-4rhc: Crystal structure of 3-Dehydroquinate dehydratase from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 4rhc
TitleCrystal structure of 3-Dehydroquinate dehydratase from Acinetobacter baumannii at 2.68 A resolution
Components3-dehydroquinate dehydratase
KeywordsLYASE
Function / homology
Function and homology information


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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsIqbal, N. / Singh, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of 3-Dehydroquinate dehydratase from Acinetobacter baumannii at 2.68 A resolution
Authors: Iqbal, N. / Singh, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)196,62712
Polymers196,62712
Non-polymers00
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26340 Å2
ΔGint-133 kcal/mol
Surface area65660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.827, 133.243, 136.851
Angle α, β, γ (deg.)90.00, 97.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 16385.605 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 17978 / NCDC KC 755 / Gene: A1S_2009, aroQ / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(De3) / References: UniProt: A3M692, 3-dehydroquinate dehydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCL, 1M Ammonium Sulfate, pH 8.5, 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 29, 2013 / 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: 2.68→38.5 Å / Num. obs: 50314 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.063 / Net I/σ(I): 8.2
Reflection shellResolution: 2.68→2.78 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.18 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
AMoREphasing
CNS0.9refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LWZ

3lwz


Resolution: 2.68→38.38 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.846 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28701 2560 5.1 %RANDOM
Rwork0.22709 ---
obs0.2301 47733 99.06 %-
all-50314 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.085 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0 Å20.08 Å2
2--0.78 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.68→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13508 0 0 464 13972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913774
X-RAY DIFFRACTIONr_bond_other_d00.0213508
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.94618736
X-RAY DIFFRACTIONr_angle_other_deg3.587330890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14851737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62924.351616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.193152285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.31572
X-RAY DIFFRACTIONr_chiral_restr0.1250.22217
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215739
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023205
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_it2.1134.0346984
X-RAY DIFFRACTIONr_mcbond_other2.1134.0346983
X-RAY DIFFRACTIONr_mcangle_it3.476.0358709
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9314.1436789
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 193 -
Rwork0.308 3512 -
obs--99.89 %

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