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- PDB-5ydb: Crystal structure of the complex of type II dehydroquinate dehydr... -

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Basic information

Entry
Database: PDB / ID: 5ydb
TitleCrystal structure of the complex of type II dehydroquinate dehydratase from Acinetobacter baumannii with dehydroquinic acid at 1.76 Angstrom 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
1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsIqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the complex of type II dehydroquinate dehydratase from Acinetobacter baumannii with dehydroquinic acid at 1.76 Angstrom resolution
Authors: Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionSep 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Jul 11, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Nov 22, 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,59012
Polymers64,7384
Non-polymers8538
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-72 kcal/mol
Surface area25130 Å2
Unit cell
Length a, b, c (Å)139.117, 139.117, 79.587
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 16184.426 Da / Num. of mol.: 4 / Fragment: UNP residues 3-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Gene: aroQ, A1S_2009 / Production host: Escherichia coli (E. coli) / References: UniProt: A3M692, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-DQA / 1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID / 3-DEHYDROQUINIC ACID


Mass: 190.151 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C7H10O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M Cadmium sulfate hydrate, 0.1M HEPES, PH 7.5, IM Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 5, 2017 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.76→69.56 Å / Num. obs: 56929 / % possible obs: 98.3 % / Redundancy: 2.8 % / Net I/σ(I): 8.2
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.7 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6P

5b6p


Resolution: 1.76→69.56 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.02 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24766 2666 4.8 %RANDOM
Rwork0.19723 ---
obs0.19926 53283 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.76→69.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 56 202 4742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0194626
X-RAY DIFFRACTIONr_bond_other_d0.0030.024520
X-RAY DIFFRACTIONr_angle_refined_deg2.1531.966303
X-RAY DIFFRACTIONr_angle_other_deg1.222310345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12724.244205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4515755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5061525
X-RAY DIFFRACTIONr_chiral_restr0.1540.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025241
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021064
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_it3.1283.6492316
X-RAY DIFFRACTIONr_mcbond_other3.1223.6472315
X-RAY DIFFRACTIONr_mcangle_it4.8325.4472888
X-RAY DIFFRACTIONr_mcangle_other4.8315.452889
X-RAY DIFFRACTIONr_scbond_it3.7184.2082310
X-RAY DIFFRACTIONr_scbond_other3.7144.2052306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5016.1683412
X-RAY DIFFRACTIONr_long_range_B_refined9.90934.70119332
X-RAY DIFFRACTIONr_long_range_B_other9.90934.69919331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 227 -
Rwork0.369 3758 -
obs--94.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84890.28110.18570.17870.13030.32220.0865-0.07660.01950.0281-0.04720.00370.0335-0.0599-0.03940.0572-0.02220.02470.09220.0320.1032-17.0506-5.1799-26.8503
20.1964-0.07280.02090.3426-0.16161.1050.0377-0.0062-0.07560.00230.03660.0481-0.004-0.1661-0.07430.0088-0.0027-0.0230.12610.0550.1331-31.2141-7.1055-47.0185
30.733-0.04250.02510.72470.06990.32230.02090.1330.0057-0.0335-0.02980.0073-0.0269-0.07040.00890.05060.0371-0.0390.13470.03220.0706-25.82548.9275-72.6231
41.37870.3135-0.07640.25980.22210.3089-0.02520.22940.31140.03330.0430.07780.0444-0.0172-0.01780.0420.00010.00330.07770.11830.1827-8.92526.7006-71.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 147
2X-RAY DIFFRACTION2B3 - 147
3X-RAY DIFFRACTION3C3 - 147
4X-RAY DIFFRACTION4D3 - 147

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