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- PDB-6kjf: lovastatin esterase PcEST in complex with simvastatin -

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Basic information

Entry
Database: PDB / ID: 6kjf
Titlelovastatin esterase PcEST in complex with simvastatin
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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Simvastatin acid / Lovastatin esterase
Similarity search - Component
Biological speciesPenicillium rubens Wisconsin 54-1255 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
B: Pc15g00720 protein
A: Pc15g00720 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4289
Polymers86,9442
Non-polymers1,4847
Water8,125451
1
B: Pc15g00720 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2755
Polymers43,4721
Non-polymers8034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-4 kcal/mol
Surface area15720 Å2
MethodPISA
2
A: Pc15g00720 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1534
Polymers43,4721
Non-polymers6813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-4 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.725, 91.957, 142.474
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))
21(chain B and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))

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
11HISHISALAALA(chain A and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))AB0 - 1351 - 136
12TRPTRPASNASN(chain A and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))AB137 - 146138 - 147
13PROPROLEULEU(chain A and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))AB149 - 216150 - 217
14ALAALAGLYGLY(chain A and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))AB218 - 397219 - 398
15GLNGLNGLNGLN(chain A and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))AB399400
21HISHISALAALA(chain B and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))BA0 - 1351 - 136
22TRPTRPASNASN(chain B and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))BA137 - 146138 - 147
23PROPROLEULEU(chain B and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))BA149 - 216150 - 217
24ALAALAGLYGLY(chain B and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))BA218 - 397219 - 398
25GLNGLNGLNGLN(chain B and (resseq 0:135 or resseq 137:146 or resseq 149:216 or resseq 218:397 or resseq 399))BA399400

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Components

#1: Protein Pc15g00720 protein / PcEST


Mass: 43472.137 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-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12NO3
#3: Chemical ChemComp-SIM / Simvastatin acid / DIMETHYL-COMPACTIN / Simvastatin


Mass: 436.582 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200 mM calcium acetate, 100 mM sodium cacodylate trihydrate pH 6.5, and 18% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 45464 / % possible obs: 98.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.27 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.036 / Net I/σ(I): 9.2 / Num. measured all: 292393
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.4-2.445.60.31421630.646196.2
2.44-2.495.90.27122250.652196.8
2.49-2.535.90.24421920.678196.3
2.53-2.5960.2222390.692197.4
2.59-2.6460.21122180.749198.1
2.64-2.76.10.20222371.119196.7
2.7-2.776.20.17222370.764197.8
2.77-2.856.20.14822570.752198.3
2.85-2.936.20.1322450.776198.5
2.93-3.026.40.11522400.82198
3.02-3.136.40.122610.86198.3
3.13-3.266.50.08422770.903198.5
3.26-3.416.60.08522951.205198.3
3.41-3.586.60.08622631.762199
3.58-3.816.40.07323011.77199.3
3.81-4.16.80.06523041.585199
4.1-4.527.20.04723161.181199.3
4.52-5.177.30.04623611.099199.5
5.17-6.517.20.04923671.017199.2
6.51-506.80.03824661.261197.8

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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: 6KJC

6kjc


Resolution: 2.4→31.153 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 22.05
RfactorNum. reflection% reflection
Rfree0.2208 2000 4.41 %
Rwork0.178 --
obs0.1799 45362 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.39 Å2 / Biso mean: 32.1876 Å2 / Biso min: 13.1 Å2
Refinement stepCycle: final / Resolution: 2.4→31.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 102 451 6673
Biso mean--42.61 32.38 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016363
X-RAY DIFFRACTIONf_angle_d1.1458647
X-RAY DIFFRACTIONf_chiral_restr0.058957
X-RAY DIFFRACTIONf_plane_restr0.0071120
X-RAY DIFFRACTIONf_dihedral_angle_d12.8473739
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3652X-RAY DIFFRACTION6.517TORSIONAL
12B3652X-RAY DIFFRACTION6.517TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4002-2.46020.29361380.2091298896
2.4602-2.52670.28831500.2048298697
2.5267-2.6010.25961300.2014303597
2.601-2.68490.25991420.1967303598
2.6849-2.78080.28091390.2046307898
2.7808-2.8920.23071430.2021305598
2.892-3.02360.27261350.2051308098
3.0236-3.18280.25241410.2131309098
3.1828-3.3820.26211460.2041308799
3.382-3.64280.22721470.1901311698
3.6428-4.00870.24441400.1736314599
4.0087-4.58720.17031520.1372313299
4.5872-5.77330.15651420.1395320599
5.7733-31.1530.14851550.1474333099

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