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- PDB-4ckx: Structure of the Mycobacterium tuberculosis Type II Dehydroquinas... -

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Basic information

Entry
Database: PDB / ID: 4ckx
TitleStructure of the Mycobacterium tuberculosis Type II Dehydroquinase N12S mutant (Crystal Form 2)
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / BACTERIAL PROTEINS / BINDING SITES / TYPE 2 DEHYDROQUINASE / INHIBITOR / PROTEIN BINDING / SHIKIMIS ACID PATHWAY / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


quinate catabolic process / Chorismate via Shikimate Pathway / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol
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 / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOtero, J.M. / Llamas-Saiz, A.L. / Maneiro, M. / Peon, A. / Sedes, A. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J.
CitationJournal: To be Published
Title: Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase
Authors: Maneiro, M. / Otero, J.M. / Peon, A. / Sedes, A. / Llamas-Saiz, A.L. / Lamb, H. / Hawkins, A.R. / van Raaij, M.J. / Gonzalez-Bello, C.
History
DepositionJan 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7722
Polymers15,6501
Non-polymers1221
Water61334
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)189,26224
Polymers187,79712
Non-polymers1,46612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation48_555-y+1/2,-z+1/2,x1
crystal symmetry operation32_555-z+1/2,x,-y+1/21
crystal symmetry operation38_555-x+1/2,-y+1/2,z1
crystal symmetry operation43_555-z+1/2,-x+1/2,y1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation23_555y,-z+1/2,-x+1/21
crystal symmetry operation27_555-x+1/2,y,-z+1/21
crystal symmetry operation34_555-y+1/2,z,-x+1/21
crystal symmetry operation9_555y,z,x1
crystal symmetry operation18_555z,-x+1/2,-y+1/21
crystal symmetry operation16_555x,-y+1/2,-z+1/21
Buried area29370 Å2
ΔGint-57.4 kcal/mol
Surface area68890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)125.610, 125.610, 125.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-201-

TRS

21A-201-

TRS

31A-2025-

HOH

41A-2031-

HOH

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Components

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


Mass: 15649.712 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SK3430
References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.9 Å3/Da / Density % sol: 57.1 % / Description: NONE
Crystal growpH: 8.5
Details: 26% PEG 8000, 0.2 M NA-K PHOSPHATE, 0.1 M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97922
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2013 / Details: PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR)
RadiationMonochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.6→72.52 Å / Num. obs: 5170 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y71

2y71


Resolution: 2.6→22.21 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.251 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.495 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GAP BY DISORDERED REGION BETWEEN ARG-18 AND GLY-25
RfactorNum. reflection% reflectionSelection details
Rfree0.19809 238 4.6 %RANDOM
Rwork0.14256 ---
obs0.14506 4914 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.462 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→22.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 8 34 1060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191054
X-RAY DIFFRACTIONr_bond_other_d0.0010.021049
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9661432
X-RAY DIFFRACTIONr_angle_other_deg0.77132391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65122.97947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49415171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6361510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
X-RAY DIFFRACTIONr_nbd_refined0.2390.2250
X-RAY DIFFRACTIONr_nbd_other0.1770.2996
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2510
X-RAY DIFFRACTIONr_nbtor_other0.0840.2679
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6723.4571054
X-RAY DIFFRACTIONr_mcbond_other0.6153.4671048
X-RAY DIFFRACTIONr_mcangle_it4.2285.1181432
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.14434.3591935
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.195.1932391
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: 2.602→2.742 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.206 37 -
Rwork0.179 712 -
obs--100 %

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