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- PDB-2jep: Native family 5 xyloglucanase from Paenibacillus pabuli -

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Basic information

Entry
Database: PDB / ID: 2jep
TitleNative family 5 xyloglucanase from Paenibacillus pabuli
ComponentsXYLOGLUCANASE
KeywordsHYDROLASE / FAMILY 5 / XYLOGLUCANASE / PLANT CELL WALL
Function / homology
Function and homology information


xyloglucan-specific endo-beta-1,4-glucanase / cellulase activity / cellulose catabolic process
Similarity search - Function
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / 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 speciesPAENIBACILLUS PABULI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K. ...Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K. / Borchert, T.V. / Wilson, K.S. / Brumer, H. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Characterization and Three-Dimensional Structures of Two Distinct Bacterial Xyloglucanases from Families Gh5 and Gh12.
Authors: Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K. / Borchert, T.V. / Wilson, K.S. ...Authors: Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K. / Borchert, T.V. / Wilson, K.S. / Brumer, H. / Davies, G.J.
History
DepositionJan 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
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.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.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.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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XYLOGLUCANASE
B: XYLOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2067
Polymers87,9402
Non-polymers2665
Water23,0231278
1
A: XYLOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1344
Polymers43,9701
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: XYLOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0723
Polymers43,9701
Non-polymers1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.416, 89.574, 90.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9999, -0.01231, 0.009834), (0.01236, 0.9999, -0.004817), (-0.009774, 0.004938, 0.9999)
Vector: -41.97, -3.843, 0.8027)

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Components

#1: Protein XYLOGLUCANASE


Mass: 43969.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PAENIBACILLUS PABULI (bacteria) / Strain: DSM13330 / Production host: BACILLUS SUBTILIS (bacteria)
References: UniProt: H9KVH3*PLUS, xyloglucan-specific endo-beta-1,4-glucanase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1278 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 32 RESIDUES CANNOT BE OBSERVED, AND ARE LIKELY TO CORRESPOND TO A SIGNAL PEPTIDE CLEAVED ...THE FIRST 32 RESIDUES CANNOT BE OBSERVED, AND ARE LIKELY TO CORRESPOND TO A SIGNAL PEPTIDE CLEAVED DURING EXPRESSION OF THE PROTEIN.

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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: 41.7 %
Crystal growpH: 8.5 / Details: 20-25% PEG 8000, 0.2 M CACL2, 0.1 M TRIS, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 134851 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 42.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 9.1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.3.0011refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ECG

1ecg


Resolution: 1.4→63.25 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.272 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 34-37 IN THE B CHAIN DO NOT FIT THE DENSITY WELL, BUT HAVE BEEN MODELLED AS IN THE A CHAIN STRUCTURE WHICH IS MORE ORDERED. THERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 34-37 IN THE B CHAIN DO NOT FIT THE DENSITY WELL, BUT HAVE BEEN MODELLED AS IN THE A CHAIN STRUCTURE WHICH IS MORE ORDERED. THERE IS ALSO DENSITY IN THE ACTIVE SITE (NEAR TO RESIDUES 182 & 323) WHICH CANNOT BE MODELLED AS ANY SMALL MOLECULE KNOWN TO BE PRESENT AND HAS INSTEAD CONTAINS WATER MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.144 6771 5 %RANDOM
Rwork0.115 ---
obs0.116 128009 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.4→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5729 0 14 1278 7021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226235
X-RAY DIFFRACTIONr_bond_other_d0.0010.024067
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9118559
X-RAY DIFFRACTIONr_angle_other_deg0.96339991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34625.671328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.485151003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.081519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021277
X-RAY DIFFRACTIONr_nbd_refined0.2230.21338
X-RAY DIFFRACTIONr_nbd_other0.1930.24598
X-RAY DIFFRACTIONr_nbtor_refined0.190.23180
X-RAY DIFFRACTIONr_nbtor_other0.0870.22928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.2109
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2481.53873
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74826124
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.50832808
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2764.52388
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.203 463
Rwork0.151 9206

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