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- PDB-5g56: THE TETRA-MODULAR CELLULOSOMAL ARABINOXYLANASE CtXyl5A STRUCTURE ... -

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Basic information

Entry
Database: PDB / ID: 5g56
TitleTHE TETRA-MODULAR CELLULOSOMAL ARABINOXYLANASE CtXyl5A STRUCTURE AS REVEALED BY X-RAY CRYSTALLOGRAPHY
ComponentsCARBOHYDRATE BINDING FAMILY 6
KeywordsCARBOHYDRATE BINDING PROTEIN / ARABINOXYLANASE / CTXYL5A / GH5 / CBM6 / CBM13 / FN3 / CLOSTRIDIUM THERMOCELLUM / CELLULOSOME
Function / homology
Function and homology information


cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / metal ion binding
Similarity search - Function
Ricin-type beta-trefoil lectin domain-like / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. ...Ricin-type beta-trefoil lectin domain-like / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Ricin B, lectin domain / Ricin B-like lectins / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Carbohydrate binding family 6
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsBras, J.L.A. / Gilbert, H.J. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S.
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: The Mechanism by which Arabinoxylanases Can Recognise Highly Decorated Xylans.
Authors: Labourel, A. / Crouch, L.I. / Bras, J.L. / Jackson, A. / Rogowski, A. / Gray, J. / Yadav, M.P. / Henrissat, B. / Fontes, C.M. / Gilbert, H.J. / Najmudin, S. / Basle, A. / Cuskin, F.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Purification, Crystallization and Preliminary X-Ray Characterization of the Pentamodular Arabinoxylanase Ctxyl5A from Clostridium Thermocellum.
Authors: Bras, J.L.A. / Correia, M.A.S. / Romao, M.J. / Prates, J.A.M. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionMay 21, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionJun 29, 2016ID: 5AK1
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Other
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Nov 9, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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: CARBOHYDRATE BINDING FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3066
Polymers93,9501
Non-polymers3575
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.410, 191.730, 50.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CARBOHYDRATE BINDING FAMILY 6 / ARABINOXYLANASE


Mass: 93949.648 Da / Num. of mol.: 1 / Fragment: RESIDUES 36-889
Source method: isolated from a genetically manipulated source
Details: SEMET DERIVATIVE / Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A3DHG6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEMET DERIVATIVE

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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: 3.66 Å3/Da / Density % sol: 68 % / Description: CBM13 MODEL WAS BUILT IN MANUALLY USING COOT.
Crystal growpH: 7 / Details: 40% (V/V) 2-METHYL-2-4PENTANEDIOL (MPD), pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.64→50.7 Å / Num. obs: 42246 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8
Reflection shellResolution: 2.64→2.78 Å / Redundancy: 5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2Y8K, 3MPC, 2Y8M, 2Y9I AND 2Y9S

2y8k

3mpc

2y8m
PDB Unreleased entry

2y9i
PDB Unreleased entry

2y9s
PDB Unreleased entry


Resolution: 2.64→50.7 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.85 / SU B: 22.967 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED FOR GH5, CBM6,CBM13 AND FN3 MODULES. CBM62 WAS NOT FITTED IN THE SOLVENT CHANNEL. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2125 5 %RANDOM
Rwork0.23726 ---
obs0.23928 40074 97.7 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.64→50.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5446 0 19 227 5692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.025626
X-RAY DIFFRACTIONr_bond_other_d0.0020.025065
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9267683
X-RAY DIFFRACTIONr_angle_other_deg0.886311610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39123.9259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72615780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9711530
X-RAY DIFFRACTIONr_chiral_restr0.0710.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021390
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_it0.7652.4642826
X-RAY DIFFRACTIONr_mcbond_other0.7652.4632825
X-RAY DIFFRACTIONr_mcangle_it1.4113.6943530
X-RAY DIFFRACTIONr_mcangle_other1.4113.6953531
X-RAY DIFFRACTIONr_scbond_it0.6462.5432800
X-RAY DIFFRACTIONr_scbond_other0.6462.5452801
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.123.7954154
X-RAY DIFFRACTIONr_long_range_B_refined3.75529.1026450
X-RAY DIFFRACTIONr_long_range_B_other3.57528.8796400
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.642→2.711 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 153 -
Rwork0.32 2626 -
obs--89.18 %
Refinement TLS params.Method: refined / Origin x: 80.9645 Å / Origin y: 24.6616 Å / Origin z: 7.6844 Å
111213212223313233
T0.2184 Å2-0.0123 Å2-0.0088 Å2-0.0422 Å20.0232 Å2--0.0242 Å2
L0.6237 °2-0.0127 °2-0.186 °2-0.7674 °2-0.2373 °2--0.5875 °2
S-0.029 Å °-0.1441 Å °-0.0454 Å °0.0205 Å °-0.0544 Å °-0.1107 Å °-0.2581 Å °0.1034 Å °0.0833 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 373
2X-RAY DIFFRACTION1A374 - 516
3X-RAY DIFFRACTION1A517 - 652
4X-RAY DIFFRACTION1A653 - 742

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