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- PDB-4zc1: Crystal Structure of type II Dehydroquinate dehydratase from Acin... -

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Basic information

Entry
Database: PDB / ID: 4zc1
TitleCrystal Structure of type II Dehydroquinate dehydratase from Acinetobacter baumannii with a different crystal form at 2.52 A Resolution
Components3-dehydroquinate dehydratase
KeywordsLYASE / 3-DEHYDROQUINASE / TYPE II DHQASE
Function / homology
Function and homology information


quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid 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: 2.52 Å
AuthorsIqbal, N. / Kumar, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal Structure of type II Dehydroquinate dehydratase from Acinetobacter baumannii with different crystal form at 2.52 A Resolution
Authors: Iqbal, N. / Kumar, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

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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


Theoretical massNumber of molelcules
Total (without water)192,08712
Polymers192,08712
Non-polymers00
Water7,080393
1
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

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)384,17524
Polymers384,17524
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area57400 Å2
ΔGint-290 kcal/mol
Surface area128260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.914, 136.008, 142.878
Angle α, β, γ (deg.)90.00, 97.59, 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: 16007.288 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 17978 / NCDC KC 755) (bacteria)
Strain: ATCC 17978 / NCDC KC 755 / Gene: aroQ, A1S_2009 / Plasmid: Pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: A3M692, 3-dehydroquinate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.95 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% PEG3350, MgSO4, Tris buffer / PH range: 8

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Data collection

DiffractionMean temperature: 77 K / Ambient temp details: CCD
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 14, 2014
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. all: 248902 / Num. obs: 62069 / % possible obs: 100 % / Redundancy: 4 % / Rsym value: 0.1 / Net I/σ(I): 13.3
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 4 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RC9

4rc9


Resolution: 2.52→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.859 / SU B: 13.157 / SU ML: 0.286 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.15 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27325 3142 5.1 %RANDOM
Rwork0.21451 ---
obs0.21751 58927 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.165 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å2-0 Å2-0.36 Å2
2---0.14 Å20 Å2
3---1.73 Å2
Refinement stepCycle: 1 / Resolution: 2.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13536 0 0 393 13929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01913788
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213560
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.94518732
X-RAY DIFFRACTIONr_angle_other_deg0.763331008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88551740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14824.314612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.468152316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2781572
X-RAY DIFFRACTIONr_chiral_restr0.0660.22220
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023204
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_it1.9973.8426996
X-RAY DIFFRACTIONr_mcbond_other1.9973.8416995
X-RAY DIFFRACTIONr_mcangle_it3.4345.7488724
X-RAY DIFFRACTIONr_mcangle_other3.4335.7488725
X-RAY DIFFRACTIONr_scbond_it1.74.0726792
X-RAY DIFFRACTIONr_scbond_other1.74.0736793
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9546.01810009
X-RAY DIFFRACTIONr_long_range_B_refined5.79630.74616001
X-RAY DIFFRACTIONr_long_range_B_other5.75330.74315908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.525→2.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 227 -
Rwork0.288 4203 -
obs--96.68 %

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