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- PDB-2xfg: Reassembly and co-crystallization of a family 9 processive endogl... -

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Basic information

Entry
Database: PDB / ID: 2xfg
TitleReassembly and co-crystallization of a family 9 processive endoglucanase from separately expressed GH9 and CBM3c modules
Components(ENDOGLUCANASE 1) x 2
KeywordsHYDROLASE/SUGAR BINDING PROTEIN / HYDROLASE-SUGAR BINDING PROTEIN COMPLEX / FAMILY-9 GLYCOSIDE HYDROLASE / HYDROLASE / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / identical protein binding
Similarity search - Function
Glycosyl hydrolases family 9 (GH9) active site signature 1. / Endoglucanase-like / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily ...Glycosyl hydrolases family 9 (GH9) active site signature 1. / Endoglucanase-like / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.679 Å
AuthorsPetkun, S. / Lamed, R. / Jindou, S. / Burstein, T. / Yaniv, O. / Shoham, Y. / Shimon, J.W.L. / Bayer, E.A. / Frolow, F.
CitationJournal: Peerj / Year: 2015
Title: Reassembly and Co-Crystallization of a Family 9 Processive Endoglucanase from its Component Parts: Structural and Functional Significance of Intermodular Linker
Authors: Petkun, S. / Grinberg, I.R. / Lamed, R. / Jindou, S. / Burstein, T. / Yaniv, O. / Shoham, Y. / Shimon, J.W.L. / Bayer, E.A. / Frolow, F.
History
DepositionMay 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references / Version format compliance
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Jan 13, 2016Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE 1
B: ENDOGLUCANASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5867
Polymers72,4002
Non-polymers1875
Water17,691982
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-67.1 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.399, 88.541, 106.486
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 ENDOGLUCANASE 1 / ENDOGLUCANASE I / EGI / ENDO-1 / 4-BETA-GLUCANASE / CELLULASE I


Mass: 52818.062 Da / Num. of mol.: 1 / Fragment: GH9 CATALYTIC DOMAIN, RESIDUES 54-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q02934, cellulase
#2: Protein ENDOGLUCANASE 1 / ENDOGLUCANASE I / EGI / ENDO-1 / 4-BETA-GLUCANASE / CELLULASE I


Mass: 19581.607 Da / Num. of mol.: 1 / Fragment: CBM3C CELLULOSE BINDING MODULE, RESIDUES 517-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q02934
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 982 / 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: 2.37 Å3/Da / Density % sol: 48.17 % / Description: NONE
Crystal growpH: 8
Details: 24% PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.1 M HEPES, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.68→43.81 Å / Num. obs: 76727 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 16.06 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 34.72
Reflection shellResolution: 1.68→1.71 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.08 / % possible all: 74.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G87

1g87


Resolution: 1.679→20.868 Å / SU ML: 0.16 / σ(F): 0.02 / Phase error: 16.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1759 3580 5 %
Rwork0.1414 --
obs0.1432 71559 93.52 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.314 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 21.12 Å2
Baniso -1Baniso -2Baniso -3
1--3.9913 Å20 Å20 Å2
2--2.3609 Å20 Å2
3---1.6304 Å2
Refinement stepCycle: LAST / Resolution: 1.679→20.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4925 0 5 982 5912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145286
X-RAY DIFFRACTIONf_angle_d1.3717211
X-RAY DIFFRACTIONf_dihedral_angle_d13.321897
X-RAY DIFFRACTIONf_chiral_restr0.101715
X-RAY DIFFRACTIONf_plane_restr0.007955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6793-1.73930.27572660.22564926X-RAY DIFFRACTION69
1.7393-1.80890.24113240.17346274X-RAY DIFFRACTION87
1.8089-1.89110.18713450.1536668X-RAY DIFFRACTION93
1.8911-1.99080.18194170.14816800X-RAY DIFFRACTION95
1.9908-2.11540.20993590.14716993X-RAY DIFFRACTION97
2.1154-2.27850.17033480.12147113X-RAY DIFFRACTION98
2.2785-2.50750.15813760.11617114X-RAY DIFFRACTION98
2.5075-2.86950.16693420.12977234X-RAY DIFFRACTION99
2.8695-3.61220.18083870.13997297X-RAY DIFFRACTION99
3.6122-20.86990.1554160.14597560X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.1181 Å / Origin y: -31.0663 Å / Origin z: 24.4566 Å
111213212223313233
T0.0785 Å20.015 Å2-0.0138 Å2-0.0623 Å20.0008 Å2--0.0521 Å2
L0.637 °2-0.066 °2-0.3269 °2-0.2291 °20.0709 °2--0.2724 °2
S0.0209 Å °-0.0198 Å °0.0064 Å °0.0083 Å °-0.0282 Å °0.0581 Å °-0.0297 Å °-0.0086 Å °0.0037 Å °
Refinement TLS groupSelection details: ALL

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