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- PDB-2vpt: Clostridium thermocellum family 3 carbohydrate esterase -

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Basic information

Entry
Database: PDB / ID: 2vpt
TitleClostridium thermocellum family 3 carbohydrate esterase
ComponentsLIPOLYTIC ENZYME
KeywordsHYDROLASE / ESTERASE
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / Clostridium cellulosome enzymes repeated domain signature. / SGNH hydrolase superfamily / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily ...SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / Clostridium cellulosome enzymes repeated domain signature. / SGNH hydrolase superfamily / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipolytic protein G-D-S-L family
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsCorreia, M.A.S. / Prates, J.A.M. / Bras, J. / Fontes, C.M.G.A. / Newman, J.A. / Lewis, R.J. / Gilbert, H.J. / Flint, J.E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of a Cellulosomal Family 3 Carbohydrate Esterase from Clostridium Thermocellum Provides Insights Into the Mechanism of Substrate Recognition
Authors: Correia, M.A.S. / Prates, J.A.M. / Bras, J. / Fontes, C.M.G.A. / Newman, J.A. / Lewis, R.J. / Gilbert, H.J. / Flint, J.E.
History
DepositionMar 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPOLYTIC ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2722
Polymers24,2321
Non-polymers401
Water4,450247
1
A: LIPOLYTIC ENZYME
hetero molecules

A: LIPOLYTIC ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5444
Polymers48,4632
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1910 Å2
ΔGint-8.8 kcal/mol
Surface area18680 Å2
MethodPQS
Unit cell
Length a, b, c (Å)77.977, 77.977, 66.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein LIPOLYTIC ENZYME / FAMILY 3 CARBOHYDRATE ESTERASE


Mass: 24231.719 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A3DDK4, acetylxylan esterase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.44 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 7.5
Details: 2% PEG 400, 0.1 M HEPES-NAOH, PH 7.5, AND 2.0 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 16, 2005 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→47.5 Å / Num. obs: 46638 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.4
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.4→30.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.546 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17579 2352 5 %RANDOM
Rwork0.15353 ---
obs0.15468 44228 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.995 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 1 247 1824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221668
X-RAY DIFFRACTIONr_bond_other_d0.0010.021119
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9462278
X-RAY DIFFRACTIONr_angle_other_deg0.9532742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.3595214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81624.53375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69915281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.697158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021878
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02336
X-RAY DIFFRACTIONr_nbd_refined0.2280.2335
X-RAY DIFFRACTIONr_nbd_other0.1790.21200
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2835
X-RAY DIFFRACTIONr_nbtor_other0.0850.2807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.241.51062
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64621655
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5373727
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2284.5618
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.199 182
Rwork0.161 3260

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