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- PDB-3rq0: The crystal structure of a glycosyl hydrolases (GH) family protei... -

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Basic information

Entry
Database: PDB / ID: 3rq0
TitleThe crystal structure of a glycosyl hydrolases (GH) family protein 16 from Mycobacterium smegmatis str. MC2 155
ComponentsGlycosyl hydrolases family protein 16
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2,2',2''-NITRILOTRIETHANOL / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Glycosyl hydrolases family protein 16
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsTan, K. / Chhor, G. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a glycosyl hydrolases (GH) family protein 16 from Mycobacterium smegmatis str. MC2 155
Authors: Tan, K. / Chhor, G. / Bearden, J. / Joachimiak, A.
History
DepositionApr 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: 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: Glycosyl hydrolases family protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,55016
Polymers29,6221
Non-polymers1,92815
Water3,351186
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.420, 117.420, 54.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glycosyl hydrolases family protein 16


Mass: 29622.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_5345 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE) magic / References: UniProt: A0R351

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Non-polymers , 7 types, 201 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-211 / 2,2',2''-NITRILOTRIETHANOL


Mass: 149.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M Na2HPO4:Citric Acid, 40% (v/v) PEG300, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2011 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.02→46 Å / Num. all: 24834 / Num. obs: 24834 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 23.76 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 19.8
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1156 / % possible all: 90.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.02→41.514 Å / SU ML: 0.2 / σ(F): 0 / σ(I): 0 / Phase error: 18.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 1197 5.13 %Random
Rwork0.1603 ---
all0.162 23354 --
obs0.162 23354 90.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.353 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.3664 Å2-0 Å20 Å2
2---9.3664 Å2-0 Å2
3---18.7328 Å2
Refinement stepCycle: LAST / Resolution: 2.02→41.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 125 186 2125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071990
X-RAY DIFFRACTIONf_angle_d1.0812678
X-RAY DIFFRACTIONf_dihedral_angle_d13.896705
X-RAY DIFFRACTIONf_chiral_restr0.083249
X-RAY DIFFRACTIONf_plane_restr0.004339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0198-2.10060.26691270.20672092X-RAY DIFFRACTION79
2.1006-2.19620.22381160.18672247X-RAY DIFFRACTION84
2.1962-2.3120.22071240.18492362X-RAY DIFFRACTION88
2.312-2.45690.22551240.1742442X-RAY DIFFRACTION91
2.4569-2.64650.20531560.16262446X-RAY DIFFRACTION92
2.6465-2.91280.18971330.15682546X-RAY DIFFRACTION94
2.9128-3.33410.18771500.15612614X-RAY DIFFRACTION96
3.3341-4.20.18311340.14532644X-RAY DIFFRACTION96
4.2-41.5230.16211330.15322764X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 41.1964 Å / Origin y: 16.9586 Å / Origin z: 13.3747 Å
111213212223313233
T0.1651 Å20.0028 Å20.0013 Å2-0.1591 Å2-0.0031 Å2--0.1766 Å2
L0.4856 °2-0.3199 °20.2292 °2-0.4906 °2-0.3609 °2--0.6912 °2
S0.0101 Å °0.0011 Å °0.0557 Å °0.0502 Å °0.0058 Å °0.0007 Å °-0.0163 Å °-0.0037 Å °-0.0072 Å °
Refinement TLS groupSelection details: all

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