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- PDB-1j83: STRUCTURE OF FAM17 CARBOHYDRATE BINDING MODULE FROM CLOSTRIDIUM C... -

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Basic information

Entry
Database: PDB / ID: 1j83
TitleSTRUCTURE OF FAM17 CARBOHYDRATE BINDING MODULE FROM CLOSTRIDIUM CELLULOVORANS
ComponentsENDO-1,4-BETA GLUCANASE ENGF
KeywordsHYDROLASE / CARBOHYDRATE BINDING MODULE
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls ...Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium cellulovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsNotenboom, V. / Boraston, A.B. / Chiu, P. / Freelove, A.C.J. / Kilburn, D.G. / Rose, D.R.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Recognition of cello-oligosaccharides by a family 17 carbohydrate-binding module: an X-ray crystallographic, thermodynamic and mutagenic study.
Authors: Notenboom, V. / Boraston, A.B. / Chiu, P. / Freelove, A.C. / Kilburn, D.G. / Rose, D.R.
History
DepositionMay 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO-1,4-BETA GLUCANASE ENGF
B: ENDO-1,4-BETA GLUCANASE ENGF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9024
Polymers38,8222
Non-polymers802
Water4,810267
1
A: ENDO-1,4-BETA GLUCANASE ENGF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4512
Polymers19,4111
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDO-1,4-BETA GLUCANASE ENGF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4512
Polymers19,4111
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.264, 37.678, 71.234
Angle α, β, γ (deg.)90.00, 91.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ENDO-1,4-BETA GLUCANASE ENGF


Mass: 19410.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cellulovorans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P94622, cellulase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: AMMONIUM SULFATE, HEPES, PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.6 mMammonium sulfate1reservoir
2100 mMHEPES1reservoirpH7.0
32 %(w/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9798, 0.9796, 0.9593
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.97961
30.95931
ReflectionResolution: 1.7→50 Å / Num. all: 38876 / Num. obs: 37972 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.9 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.186 / % possible all: 91.9
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. measured all: 249009
Reflection shell
*PLUS
% possible obs: 91.9 % / Mean I/σ(I) obs: 9.7

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→24.54 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 407968.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3517 5 %RANDOM
Rwork0.198 ---
all-70877 --
obs-70877 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.65 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso mean: 10.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20.03 Å2
2---1.94 Å20 Å2
3---3.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 2 267 2995
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it0.161.5
X-RAY DIFFRACTIONc_mcangle_it0.292
X-RAY DIFFRACTIONc_scbond_it0.212
X-RAY DIFFRACTIONc_scangle_it0.322.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 482 4.7 %
Rwork0.243 9794 -
obs--82.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 10.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it0.161.5
X-RAY DIFFRACTIONc_scbond_it0.212
X-RAY DIFFRACTIONc_mcangle_it0.292
X-RAY DIFFRACTIONc_scangle_it0.322.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.267 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.243

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