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- PDB-3s4k: Structure of a putative esterase Rv1847/MT1895 from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 3s4k
TitleStructure of a putative esterase Rv1847/MT1895 from Mycobacterium tuberculosis
ComponentsPutative esterase Rv1847/MT1895
KeywordsHYDROLASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


acyl-CoA hydrolase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / hydrolase activity / cytosol
Similarity search - Function
Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Putative esterase MT1895 / Putative esterase Rv1847
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structure of a putative esterase Rv1847/MT1895 from Mycobacterium tuberculosis
Authors: Clifton, M.C. / Edwards, T.E. / Sankaran, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative esterase Rv1847/MT1895
B: Putative esterase Rv1847/MT1895
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,40312
Polymers30,8212
Non-polymers58210
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-50 kcal/mol
Surface area12620 Å2
MethodPISA
2
A: Putative esterase Rv1847/MT1895
B: Putative esterase Rv1847/MT1895
hetero molecules

A: Putative esterase Rv1847/MT1895
B: Putative esterase Rv1847/MT1895
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,80624
Polymers61,6414
Non-polymers1,16420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9170 Å2
ΔGint-124 kcal/mol
Surface area22060 Å2
MethodPISA
3
A: Putative esterase Rv1847/MT1895
hetero molecules

A: Putative esterase Rv1847/MT1895
hetero molecules

B: Putative esterase Rv1847/MT1895
hetero molecules

B: Putative esterase Rv1847/MT1895
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,80624
Polymers61,6414
Non-polymers1,16420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_666-x+1,y+1,-z+11
Buried area6840 Å2
ΔGint-91 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.722, 50.642, 60.506
Angle α, β, γ (deg.)90.000, 92.760, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-143-

CL

21B-143-

CL

31A-165-

HOH

41B-173-

HOH

51B-186-

HOH

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Components

#1: Protein Putative esterase Rv1847/MT1895


Mass: 15410.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1847, MT1895, MTCY359.26c / Production host: Escherichia coli (E. coli)
References: UniProt: P95162, UniProt: P9WIM3*PLUS, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M LiCl, 0.1M MES pH 6.0, 20% PEG6000. Cryo protection in 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 14, 2011
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionRedundancy: 4.3 % / Av σ(I) over netI: 16.24 / Number: 117551 / Rmerge(I) obs: 0.083 / Χ2: 0.99 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 27452 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.615099.510.0520.9734.3
3.664.6199.610.0550.9574.1
3.23.6699.810.070.9564.2
2.913.210010.0770.9954.3
2.72.9199.910.08314.4
2.542.710010.0870.994.4
2.412.5410010.0890.984.4
2.312.4199.910.0940.9814.4
2.222.3110010.0970.9754.4
2.142.2299.910.1010.9484.4
2.072.1410010.1160.9794.4
2.022.0799.710.1221.0284.4
1.962.0299.610.1330.9924.4
1.911.9699.310.1441.0134.4
1.871.9199.310.1571.0464.4
1.831.8799.310.1710.9244.4
1.791.8398.910.1920.9824.4
1.761.7998.910.2051.0754.2
1.731.7697.110.2290.9893.7
1.71.7386.710.2350.9383.4
ReflectionResolution: 1.7→50 Å / Num. obs: 27452 / % possible obs: 98.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.083 / Χ2: 0.987 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.733.40.23511970.938186.7
1.73-1.763.70.22913210.989197.1
1.76-1.794.20.20513671.075198.9
1.79-1.834.40.19213710.982198.9
1.83-1.874.40.17113760.924199.3
1.87-1.914.40.15713611.046199.3
1.91-1.964.40.14413601.013199.3
1.96-2.024.40.13313830.992199.6
2.02-2.074.40.12213761.028199.7
2.07-2.144.40.11613810.9791100
2.14-2.224.40.10113770.948199.9
2.22-2.314.40.09713980.9751100
2.31-2.414.40.09413690.981199.9
2.41-2.544.40.08913950.981100
2.54-2.74.40.08713760.991100
2.7-2.914.40.08313931199.9
2.91-3.24.30.07713960.9951100
3.2-3.664.20.0714050.956199.8
3.66-4.614.10.05514150.957199.6
4.61-504.30.05214350.973199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.43 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.82 Å
Translation2.5 Å38.82 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q4T

1q4t


Resolution: 1.7→38.82 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2044 / WRfactor Rwork: 0.1788 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8952 / SU B: 3.461 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0225 / SU Rfree: 0.0211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1376 5 %RANDOM
Rwork0.1714 ---
obs0.1727 27400 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 42.12 Å2 / Biso mean: 12.5794 Å2 / Biso min: 2.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å2-0.11 Å2
2---3.57 Å20 Å2
3---2.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 30 221 2125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212002
X-RAY DIFFRACTIONr_bond_other_d0.0020.021361
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9612725
X-RAY DIFFRACTIONr_angle_other_deg0.86233299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93622.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46915325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.881522
X-RAY DIFFRACTIONr_chiral_restr0.0850.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
X-RAY DIFFRACTIONr_mcbond_it0.7071.51264
X-RAY DIFFRACTIONr_mcbond_other0.21.5524
X-RAY DIFFRACTIONr_mcangle_it1.31222036
X-RAY DIFFRACTIONr_scbond_it2.2263738
X-RAY DIFFRACTIONr_scangle_it3.4944.5679
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 90 -
Rwork0.218 1641 -
all-1731 -
obs--83.38 %
Refinement TLS params.

T11: 0.0014 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.33650.10630.08360.28240.14480.1213-0.01410.02420.0266-0.01380.00360.004-0.0008-0.01180.0105-0.0010.00130.02020.00340.0110.558210.513417.7473
20.32170.1438-0.06820.2659-0.10420.1106-0.01610.0194-0.0165-0.00320.0058-0.01610.00230.01040.01030.00250.00250.0185-0.00140.008628.28981.929517.6787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 140
2X-RAY DIFFRACTION2B15 - 140

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