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- PDB-6kjc: lovastatin esterase PcEST, wild type -

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Basic information

Entry
Database: PDB / ID: 6kjc
Titlelovastatin esterase PcEST, wild type
ComponentsPc15g00720 protein
KeywordsHYDROLASE / family VIII esterase / lovastatin hydrolysis / monacolin J / simvastatin
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity
Similarity search - Function
Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Lovastatin esterase
Similarity search - Component
Biological speciesPenicillium rubens Wisconsin 54-1255 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å
AuthorsLiang, Y.J. / Lu, X.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31700051 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural insights into the catalytic mechanism of lovastatin hydrolase
Authors: Liang, Y.J. / Lu, X.F.
History
DepositionJul 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pc15g00720 protein
B: Pc15g00720 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9216
Polymers90,7372
Non-polymers1844
Water4,035224
1
A: Pc15g00720 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4603
Polymers45,3681
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-1 kcal/mol
Surface area16290 Å2
MethodPISA
2
B: Pc15g00720 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4603
Polymers45,3681
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-2 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.576, 129.576, 272.664
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-616-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq -13:140 or resseq 142:144 or resseq 146:396))
21(chain B and (resseq -13:140 or resseq 142:144 or resseq 146:396))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLNGLN(chain A and (resseq -13:140 or resseq 142:144 or resseq 146:396))AA-13 - 1405 - 158
12ALAALAPROPRO(chain A and (resseq -13:140 or resseq 142:144 or resseq 146:396))AA142 - 144160 - 162
13ASNASNLYSLYS(chain A and (resseq -13:140 or resseq 142:144 or resseq 146:396))AA146 - 396164 - 414
21HISHISGLNGLN(chain B and (resseq -13:140 or resseq 142:144 or resseq 146:396))BB-13 - 1405 - 158
22ALAALAPROPRO(chain B and (resseq -13:140 or resseq 142:144 or resseq 146:396))BB142 - 144160 - 162
23ASNASNLYSLYS(chain B and (resseq -13:140 or resseq 142:144 or resseq 146:396))BB146 - 396164 - 414

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Components

#1: Protein Pc15g00720 protein / PcEST


Mass: 45368.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium rubens Wisconsin 54-1255 (fungus)
Strain: Wisconsin 54-1255 / Gene: Pc15g00720, PCH_Pc15g00720 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B6H6L7
#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 4M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.297→30 Å / Num. obs: 60901 / % possible obs: 99.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 39.53 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.025 / Rrim(I) all: 0.093 / Χ2: 1.097 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.386.30.51159480.10.2130.5561.06199.7
2.38-2.487.10.49359740.2320.1930.5311.10199.6
2.48-2.597.80.46459770.5360.1710.4961.11799.8
2.59-2.739.20.4360030.7430.1450.4561.16399.9
2.73-2.910.20.37860280.8960.1210.3971.21299.9
2.9-3.1211.80.27260380.9740.0790.2841.23299.9
3.12-3.4313.10.16560850.9930.0450.1721.19899.9
3.43-3.9316.40.09961280.9980.0240.1021.09799.9
3.93-4.9516.30.06861870.9990.0170.071.0399.8
4.95-3017.30.048653310.0120.050.91399.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LCL

4lcl


Resolution: 2.297→29.258 Å / SU ML: 0.42 / Cross valid method: NONE / σ(F): 1.48 / Phase error: 30.12
RfactorNum. reflection% reflection
Rfree0.2624 2000 3.29 %
Rwork0.2207 --
obs0.2221 60851 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.38 Å2 / Biso mean: 52.0086 Å2 / Biso min: 22.03 Å2
Refinement stepCycle: final / Resolution: 2.297→29.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 12 224 6572
Biso mean--44.3 42.6 -
Num. residues----828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096498
X-RAY DIFFRACTIONf_angle_d1.1918819
X-RAY DIFFRACTIONf_chiral_restr0.061965
X-RAY DIFFRACTIONf_plane_restr0.0081154
X-RAY DIFFRACTIONf_dihedral_angle_d14.0053801
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3743X-RAY DIFFRACTION7.218TORSIONAL
12B3743X-RAY DIFFRACTION7.218TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2972-2.35460.39381390.3928408999
2.3546-2.41830.4221400.38694104100
2.4183-2.48940.39611400.37424150100
2.4894-2.56970.37171400.34744099100
2.5697-2.66150.38291410.32694147100
2.6615-2.7680.34491410.30964163100
2.768-2.89380.31761420.28644166100
2.8938-3.04630.33741410.25364161100
3.0463-3.23690.28161440.23884205100
3.2369-3.48640.28691420.22524188100
3.4864-3.83660.21941430.17944226100
3.8366-4.39020.21291450.15884260100
4.3902-5.52510.19891470.15454325100
5.5251-29.2580.19551550.16194568100

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