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- PDB-3aja: Crystal Structure of MSMEG_6394 -

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Basic information

Entry
Database: PDB / ID: 3aja
TitleCrystal Structure of MSMEG_6394
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / alpha-beta hydrolase / serine esterase / cutinase / lipase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxylesterase Culp6 homolog
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsVivian, J.P. / Scoble, J. / Beddoe, T. / Rossjohn, J.
CitationJournal: To be Published
Title: Functional characterisation of a lipase essential for mycobacterial viability
Authors: Crellin, P.K. / Vivian, J.P. / Scoble, J. / Chow, F.M. / West, N.P. / Brammananth, R. / Proellocks, N.I. / Shahine, A. / Le Nours, J. / Wilce, M.C.J. / Britton, W.J. / Coppel, R.L. / Rossjohn, J. / Beddoe, T.
History
DepositionMay 27, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)64,3002
Polymers64,3002
Non-polymers00
Water57632
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,1501
Polymers32,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,1501
Polymers32,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.434, 130.434, 209.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
/ NCS ensembles :
ID
1
2

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Components

#1: Protein Putative uncharacterized protein / MSMEG_6394 protein


Mass: 32149.891 Da / Num. of mol.: 2 / Fragment: residues 36-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: strain ATCC 700084 / mc(2)155 / Gene: MSMEG_6394 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: A0R619
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 2.1M sodium formate, 0.1M BisTris-propane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.97941, 0.97930, 0.96411
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979411
20.97931
30.964111
ReflectionResolution: 2.9→50 Å / Num. all: 20363 / Num. obs: 20363 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 114 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2909 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→29.17 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 37.613 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24973 932 5.2 %RANDOM
Rwork0.21302 ---
obs0.21488 17098 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 0 32 3956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224025
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9575503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60525.169178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.03515589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8521520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223160
X-RAY DIFFRACTIONr_mcbond_it0.4621.52612
X-RAY DIFFRACTIONr_mcangle_it0.84924213
X-RAY DIFFRACTIONr_scbond_it1.54731413
X-RAY DIFFRACTIONr_scangle_it2.4014.51290
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
111645tight positional0.10.05
22250medium positional0.150.5
111645tight thermal0.160.5
22250medium thermal0.962
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 34 -
Rwork0.367 560 -
obs--100 %
Refinement TLS params.

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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.62631.41580.53664.33751.38393.84620.35370.409-0.18020.0312-0.0145-0.12410.39750.119-0.33920.78130.24940.0260.1106-0.00060.279771.1631.3829.465
23.5250.3102-0.67134.259-0.14664.45640.0480.243-0.00980.1795-0.00930.4574-0.3667-0.6912-0.03870.5756-0.07010.11150.20420.01640.24440.83913.50333.592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A71 - 334
2X-RAY DIFFRACTION2B71 - 334

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