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- PDB-6kjd: lovastatin esterase PcEST inactive mutant S57A in complex with lo... -

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Basic information

Entry
Database: PDB / ID: 6kjd
Titlelovastatin esterase PcEST inactive mutant S57A in complex with lovastatin
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 / Chem-LVA / Lovastatin esterase
Similarity search - Component
Biological speciesPenicillium rubens Wisconsin 54-1255 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 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)88,3689
Polymers86,9122
Non-polymers1,4567
Water10,521584
1
B: Pc15g00720 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1234
Polymers43,4561
Non-polymers6673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint7 kcal/mol
Surface area15540 Å2
MethodPISA
2
A: Pc15g00720 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2455
Polymers43,4561
Non-polymers7894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint7 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.909, 91.016, 139.849
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 0:42 or resseq 44:100 or resseq...
21(chain B and (resseq 0:42 or resseq 44:100 or resseq...

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
11HISHISGLYGLY(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB0 - 421 - 43
12LYSLYSASPASP(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB44 - 10045 - 101
13GLUGLUGLUGLU(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB102 - 145103 - 146
14GLUGLUGLUGLU(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB147148
15PROPROALAALA(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB149 - 230150 - 231
16LEULEULEULEU(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB231232
17HISHISGLNGLN(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB0 - 3991 - 400
18HISHISGLNGLN(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB0 - 3991 - 400
19HISHISGLNGLN(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB0 - 3991 - 400
110HISHISGLNGLN(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB0 - 3991 - 400
111HISHISGLNGLN(chain A and (resseq 0:42 or resseq 44:100 or resseq...AB0 - 3991 - 400
21HISHISGLYGLY(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA0 - 421 - 43
22LYSLYSASPASP(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA44 - 10045 - 101
23GLUGLUGLUGLU(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA102 - 145103 - 146
24GLUGLUGLUGLU(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA147148
25PROPROALAALA(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA149 - 230150 - 231
26LEULEULEULEU(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA231232
27HISHISGLNGLN(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA0 - 3991 - 400
28HISHISGLNGLN(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA0 - 3991 - 400
29HISHISGLNGLN(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA0 - 3991 - 400
210HISHISGLNGLN(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA0 - 3991 - 400
211HISHISGLNGLN(chain B and (resseq 0:42 or resseq 44:100 or resseq...BA0 - 3991 - 400

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Components

#1: Protein Pc15g00720 protein / PcEST


Mass: 43456.137 Da / Num. of mol.: 2 / Mutation: S57A
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-LVA / (3R,5R)-7-((1R,2R,6S,8R,8AS)-2,6-DIMETHYL-8-{[(2R)-2-METHYLBUTANOYL]OXY}-1,2,6,7,8,8A-HEXAHYDRONAPHTHALEN-1-YL)-3,5-DIHYDROXYHEPTANOIC ACID


Mass: 422.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H38O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200 mM calcium acetate, 100 mM Tris-HCl (pH 7.0) and 20% (w/v) PEG3000

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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: 2.299→30 Å / Num. obs: 50590 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.44 Å2 / Rmerge(I) obs: 0.117 / Χ2: 0.552 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.3-2.345.30.50724700.678199.7
2.34-2.385.80.4725020.663199.9
2.38-2.4360.47224760.617199.9
2.43-2.486.30.42824930.574199.8
2.48-2.536.60.39625150.5811100
2.53-2.596.70.34324930.5471100
2.59-2.656.90.30224920.5221100
2.65-2.736.90.2825010.5141100
2.73-2.816.90.24325080.5081100
2.81-2.970.20725190.5061100
2.9-370.18325040.5111100
3-3.127.10.15125120.5221100
3.12-3.267.20.1225430.5051100
3.26-3.437.20.09525150.533199.9
3.43-3.657.20.07525310.5351100
3.65-3.937.30.06425470.5761100
3.93-4.337.20.05425600.5381100
4.33-4.957.20.05125620.5581100
4.95-6.237.10.06226050.5461100
6.23-306.80.03827420.5771100

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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: 2.299→29.649 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.69
RfactorNum. reflection% reflection
Rfree0.2105 1994 3.95 %
Rwork0.168 --
obs0.1697 50526 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.95 Å2 / Biso mean: 26.6937 Å2 / Biso min: 6.9 Å2
Refinement stepCycle: final / Resolution: 2.299→29.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6118 0 100 584 6802
Biso mean--36.18 29.22 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086359
X-RAY DIFFRACTIONf_angle_d1.058639
X-RAY DIFFRACTIONf_chiral_restr0.056957
X-RAY DIFFRACTIONf_plane_restr0.0071120
X-RAY DIFFRACTIONf_dihedral_angle_d11.9143737
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3617X-RAY DIFFRACTION4.817TORSIONAL
12B3617X-RAY DIFFRACTION4.817TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.299-2.35630.27281390.2279334198
2.3563-2.420.28171450.21023419100
2.42-2.49120.25311360.19533434100
2.4912-2.57160.24171400.18663409100
2.5716-2.66340.25811460.18433443100
2.6634-2.770.22171380.18113443100
2.77-2.8960.23591440.17963444100
2.896-3.04850.24121380.19123453100
3.0485-3.23930.21691480.1893465100
3.2393-3.4890.23581430.16923464100
3.489-3.83950.1691430.14933488100
3.8395-4.39350.14811450.12973507100
4.3935-5.52950.18271440.1353529100
5.5295-29.6490.19421450.16353693100

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