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- PDB-4hty: Crystal Structure of a metagenome-derived cellulase Cel5A -

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Basic information

Entry
Database: PDB / ID: 4hty
TitleCrystal Structure of a metagenome-derived cellulase Cel5A
ComponentsCellulase
KeywordsHYDROLASE / (alpha/beta)8 barrel / family 5 endoglucanase
Function / homology
Function and homology information


: / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhuang, N. / Lee, K.H.
CitationJournal: To be Published
Title: Crystal structure and substrate-binding mode of cellulase Cel5A from a metagenome library
Authors: Zhuang, N. / Lee, K.H.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1386
Polymers41,6781
Non-polymers4605
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.771, 137.771, 137.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-807-

HOH

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Components

#1: Protein Cellulase


Mass: 41677.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6PLH5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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

Crystal growTemperature: 291 K / pH: 6.5
Details: PEG4000, MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97916, 0.97933, 0.96394
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979161
20.979331
30.963941
ReflectionResolution: 2→30 Å / Num. obs: 59067 / % possible obs: 99.9 %
Reflection shellResolution: 2→2.07 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→28.12 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.779 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 2974 5.1 %RANDOM
Rwork0.154 ---
obs0.155 55884 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.59 Å2
Refinement stepCycle: LAST / Resolution: 2→28.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 30 150 2887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.0222818
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7981.9173825
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7685329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52823.836146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45915441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4311517
X-RAY DIFFRACTIONr_chiral_restr0.2950.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0212206
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9781.51645
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.43422661
X-RAY DIFFRACTIONr_scbond_it4.9731173
X-RAY DIFFRACTIONr_scangle_it7.944.51164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 198 -
Rwork0.181 4094 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: 83.5485 Å / Origin y: 60.5772 Å / Origin z: 94.315 Å
111213212223313233
T0.0414 Å2-0.0002 Å2-0.0063 Å2-0.0353 Å20.0368 Å2--0.0483 Å2
L0.252 °2-0.0938 °20.0986 °2-0.3347 °2-0.2084 °2--0.5428 °2
S0.0143 Å °-0.0093 Å °-0.0038 Å °-0.0198 Å °-0.0374 Å °-0.025 Å °0.0137 Å °-0.0195 Å °0.0231 Å °

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