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- PDB-3qh4: Crystal structure of esterase LipW from Mycobacterium marinum -

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Basic information

Entry
Database: PDB / ID: 3qh4
TitleCrystal structure of esterase LipW from Mycobacterium marinum
ComponentsEsterase LipW
KeywordsHYDROLASE / Structural Genomics / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Mycobacterium / tuberculosis / marinum / ortholog / LipW / esterase / heroin esterase / multidrug resistance / TB
Function / homology
Function and homology information


: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Biochemistry / Year: 2016
Title: Structural Basis for the Strict Substrate Selectivity of the Mycobacterial Hydrolase LipW.
Authors: McKary, M.G. / Abendroth, J. / Edwards, T.E. / Johnson, R.J.
#1: Journal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJan 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Dec 21, 2016Group: Database references
Revision 1.5Sep 13, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase LipW


Theoretical massNumber of molelcules
Total (without water)33,8371
Polymers33,8371
Non-polymers00
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.270, 86.990, 46.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Esterase LipW


Mass: 33837.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: lipW, MMAR_0404 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HLX2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: protein at 55.6 mg/mL, 0.2 M MgCl2, 0.1 M Tris, 20 % PEG 6000, cryo-protected with 25 % ethylene glycol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 30513 / Num. obs: 30172 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 17.905 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 21.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.75-1.81.90.0739.1339132212210195
1.8-1.840.06310.264230213997.9
1.84-1.90.05611.624216206899.3
1.9-1.960.05312.694306201698.4
1.96-2.020.05114.14392198098.9
2.02-2.090.0515.634461191699.5
2.09-2.170.04718.464799181398.5
2.17-2.260.04521.575309176798.8
2.26-2.360.04422.765555173399.1
2.36-2.470.04224.075478163399.6
2.47-2.610.04225.525620156899.7
2.61-2.770.04127.255818148399.7
2.77-2.960.0431.036522140699.9
2.96-3.20.03933.046341132999.9
3.2-3.50.03735.035736121199.7
3.5-3.910.03437.285177111099.8
3.91-4.520.03337.43453698599.7
4.52-5.530.03236.97390684099.6
5.53-7.830.0335.23129682100
7.830.02935.69160739297.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.52 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å46.19 Å
Translation3 Å46.19 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1lzk

1lzk


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.1537 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9169 / SU B: 3.834 / SU ML: 0.057 / SU R Cruickshank DPI: 0.1031 / SU Rfree: 0.1047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 1515 5 %RANDOM
Rwork0.1445 ---
obs0.1466 30076 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 40.88 Å2 / Biso mean: 11.4448 Å2 / Biso min: 2.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 0 419 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212417
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9613317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5775323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43222.212104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07615336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7181525
X-RAY DIFFRACTIONr_chiral_restr0.0960.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211908
X-RAY DIFFRACTIONr_mcbond_it0.7331.51585
X-RAY DIFFRACTIONr_mcangle_it1.28722534
X-RAY DIFFRACTIONr_scbond_it2.1013832
X-RAY DIFFRACTIONr_scangle_it3.3084.5778
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 122 -
Rwork0.165 1967 -
all-2089 -
obs--94.4 %
Refinement TLS params.Method: refined / Origin x: 61.8631 Å / Origin y: 13.3035 Å / Origin z: 36.1235 Å
111213212223313233
T0.0143 Å20.0059 Å20.0018 Å2-0.0077 Å2-0.0027 Å2--0.0074 Å2
L0.3364 °2-0.1242 °2-0.0166 °2-0.192 °20.0868 °2--0.2835 °2
S0.0048 Å °0.0211 Å °-0.0036 Å °-0.0027 Å °-0.0213 Å °-0.0021 Å °-0.0426 Å °-0.0292 Å °0.0165 Å °

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