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- PDB-2e4t: Crystal structure of Cel44A, GH family 44 endoglucanase from Clos... -

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Basic information

Entry
Database: PDB / ID: 2e4t
TitleCrystal structure of Cel44A, GH family 44 endoglucanase from Clostridium thermocellum
ComponentsEndoglucanase
KeywordsHYDROLASE / TIM barrel / TIM-like barrel / Composite domain of glycosyl hydrolase families 5 / 30 / 39 and 51
Function / homology
Function and homology information


cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
: / Carbohydrate binding domain 30 / Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / PKD domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Polycystic kidney disease (PKD) domain profile. ...: / Carbohydrate binding domain 30 / Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / PKD domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.96 Å
AuthorsKitago, Y. / Karita, S. / Watanabe, N. / Sakka, K. / Tanaka, I.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellum.
Authors: Kitago, Y. / Karita, S. / Watanabe, N. / Kamiya, M. / Aizawa, T. / Sakka, K. / Tanaka, I.
History
DepositionDec 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1988
Polymers57,6891
Non-polymers5097
Water10,341574
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.077, 59.155, 170.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endoglucanase / xyloglucanase


Mass: 57688.516 Da / Num. of mol.: 1 / Fragment: Cel44A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: F1 / Gene: celJ / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P71140, cellulase, xyloglucan-specific endo-beta-1,4-glucanase

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Non-polymers , 5 types, 581 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 14% PEG 3350, 0.1M MES-NaOH pH 5.8, 6mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.0000, 1.2824, 0.9800
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2005 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.28241
30.981
ReflectionResolution: 0.96→50 Å / Num. all: 295816 / Num. obs: 292562 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 6.373 Å2 / Rsym value: 0.127 / Net I/σ(I): 22.1
Reflection shellResolution: 0.96→0.99 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.32 / Num. unique all: 26836 / Rsym value: 0.375 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PFnativedata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 0.96→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.408 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The position of the CB atom of Thr426 must be correct in the electron density map. And The author beleives that the 2fo-fc electron density ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The position of the CB atom of Thr426 must be correct in the electron density map. And The author beleives that the 2fo-fc electron density map and the model fit well with each other and reliable because of the resolution 0.96A and the free R value.
RfactorNum. reflection% reflectionSelection details
Rfree0.14606 14789 5.1 %RANDOM
Rwork0.13264 ---
obs0.13332 277615 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.397 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.1999 Å0.1969 Å
Luzzati d res low-5 Å
Luzzati sigma a0.0567 Å0.0388 Å
Refinement stepCycle: LAST / Resolution: 0.96→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 27 574 4613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224243
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.9535779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12124.856208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87815731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.821517
X-RAY DIFFRACTIONr_chiral_restr0.2250.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023279
X-RAY DIFFRACTIONr_nbd_refined0.2120.22024
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22961
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2472
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0320.21
X-RAY DIFFRACTIONr_mcbond_it1.4521.52564
X-RAY DIFFRACTIONr_mcangle_it2.03224115
X-RAY DIFFRACTIONr_scbond_it2.90731928
X-RAY DIFFRACTIONr_scangle_it3.8594.51644
X-RAY DIFFRACTIONr_rigid_bond_restr1.51434492
X-RAY DIFFRACTIONr_sphericity_free9.9993577
X-RAY DIFFRACTIONr_sphericity_bonded3.84334121
LS refinement shellResolution: 0.96→0.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 1027 -
Rwork0.272 18219 -
obs--100 %

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