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- PDB-5ch9: Gkap mutant B12 -

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Basic information

Entry
Database: PDB / ID: 5ch9
TitleGkap mutant B12
ComponentsPhosphotriesterase
KeywordsHYDROLASE / insert mutation
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / catabolic process / hydrolase activity / zinc ion binding
Similarity search - Function
Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Phosphotriesterase
Similarity search - Component
Biological speciesGeobacillus kaustophilus HTA426 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsChen, L.-Q.
CitationJournal: To Be Published
Title: Active site loop architecture enhance the promiscuous PTE activity in lactonase from Geobacillus kaustophilus HTA426
Authors: Chen, L.-Q.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_struct_oper_list ...pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn
Item: _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: Phosphotriesterase
B: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0546
Polymers80,8182
Non-polymers2364
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-67 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.822, 79.643, 90.066
Angle α, β, γ (deg.)90.00, 99.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphotriesterase / phospho-triesterase-like lactonase


Mass: 40408.980 Da / Num. of mol.: 2 / Mutation: insert mutation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus HTA426 (bacteria)
Strain: HTA426 / Gene: GK1506 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5KZU5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.44 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 3350 Tacsimate sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 55188 / % possible obs: 98.8 % / Redundancy: 3.8 % / Net I/σ(I): 4.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.538 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21268 2797 5.1 %RANDOM
Rwork0.18349 ---
obs0.18504 52371 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.481 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å2-0 Å2-0.46 Å2
2---0.37 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 4 176 5348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195309
X-RAY DIFFRACTIONr_bond_other_d0.0020.025003
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9627162
X-RAY DIFFRACTIONr_angle_other_deg0.804311509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3085656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55323.647255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11215881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.861540
X-RAY DIFFRACTIONr_chiral_restr0.0780.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021229
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_it2.0243.5372624
X-RAY DIFFRACTIONr_mcbond_other2.0233.5352623
X-RAY DIFFRACTIONr_mcangle_it3.1515.2933277
X-RAY DIFFRACTIONr_mcangle_other3.1515.2943278
X-RAY DIFFRACTIONr_scbond_it2.6993.9062685
X-RAY DIFFRACTIONr_scbond_other2.643.9052683
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0885.723884
X-RAY DIFFRACTIONr_long_range_B_refined5.81728.3936013
X-RAY DIFFRACTIONr_long_range_B_other5.81328.3785998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 185 -
Rwork0.261 3645 -
obs--93.07 %

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