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- PDB-3fw6: Crystal structure of CelM2, a bifunctional glucanase-xylanase pro... -

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Basic information

Entry
Database: PDB / ID: 3fw6
TitleCrystal structure of CelM2, a bifunctional glucanase-xylanase protein from a metagenome library
ComponentsCellulase
KeywordsHYDROLASE / CelM2 / glucanase-xyanase / glucanase / xylanase / bifunctional enzyme
Function / homology
Function and homology information


Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHwang, K.Y. / Nam, K.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structure of CelM2, a bifunctional glucanase-xylanase protein from a metagenome library
Authors: Nam, K.H. / Kim, S.-J. / Hwang, K.Y.
History
DepositionJan 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3674
Polymers58,1711
Non-polymers1963
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.663, 86.952, 111.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cellulase /


Mass: 58170.977 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 31-549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Description: this protein was purified from Metagenome Library
Gene: celM2 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1E9A6, cellulase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.1M MES pH 5.9, 10% (v/v) PEG 3350, 2% ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2008
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 37615 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.137 / Χ2: 1.135 / Net I/av σ(I): 11.019 / Net I/σ(I): 5.8 / Num. measured all: 219990
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.332 / Num. unique all: 3686 / Χ2: 0.646 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EQD

2eqd


Resolution: 2.3→34.26 Å / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2418 3762 random
Rwork0.2073 --
obs0.2073 33817 -
all-38052 -
Displacement parametersBiso max: 90.14 Å2 / Biso min: 1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4004 0 3 252 4259
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2

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