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- PDB-2y6j: X-2 engineered mutated CBM4-2 Carbohydrate Binding Module from a ... -

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Basic information

Entry
Database: PDB / ID: 2y6j
TitleX-2 engineered mutated CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase
ComponentsXYLANASE
KeywordsHYDROLASE
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / endo-1,4-beta-xylanase / xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Secretion system C-terminal sorting domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...Secretion system C-terminal sorting domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Xylanase / endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
Authorsvon Schantz, L. / Hakansson, M. / Logan, D.T. / Walse, B. / Osterlin, J. / Nordberg-Karlsson, E. / Ohlin, M.
CitationJournal: Glycobiology / Year: 2012
Title: Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules.
Authors: von Schantz, L. / Hakansson, M. / Logan, D.T. / Walse, B. / Osterlin, J. / Nordberg-Karlsson, E. / Ohlin, M.
History
DepositionJan 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / diffrn_source
Item: _audit_author.name / _citation.journal_id_ISSN ..._audit_author.name / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9462
Polymers17,9061
Non-polymers401
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.360, 49.680, 62.150
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 XYLANASE / CBM4-2


Mass: 17905.717 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): T7 EXPRESS
References: UniProt: Q6V8M0, UniProt: Q7WTN6*PLUS, endo-1,4-beta-xylanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TRP 68 TO PHE ENGINEERED RESIDUE IN CHAIN A, ASP 69 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, TRP 68 TO PHE ENGINEERED RESIDUE IN CHAIN A, ASP 69 TO ASN ENGINEERED RESIDUE IN CHAIN A, GLU 71 TO GLN ENGINEERED RESIDUE IN CHAIN A, PHE 75 TO LEU ENGINEERED RESIDUE IN CHAIN A, TRP 90 TO ARG ENGINEERED RESIDUE IN CHAIN A, PHE 109 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLN 110 TO ASP ENGINEERED RESIDUE IN CHAIN A, GLU 117 TO HIS
Sequence detailsTHIS CONSTRUCT STARTS WITH M (POSITION 1) AND ENDS WITH ONE L

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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: 41.2 % / Description: NONE
Crystal growpH: 6.5 / Details: 1.4 M SODIUM CITRATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Dec 13, 2007 / Details: MIRRORS
RadiationMonochromator: GERMANIUM CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.7→17 Å / Num. obs: 16932 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K42

1k42


Resolution: 1.7→17 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.04 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 853 5 %RANDOMN
Rwork0.153 ---
obs0.156 16078 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WTH MASK
Displacement parametersBiso mean: 14 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20 Å2
2---1.18 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 1 201 1461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221320
X-RAY DIFFRACTIONr_bond_other_d0.0010.02814
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9311821
X-RAY DIFFRACTIONr_angle_other_deg0.95732008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2425.48462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43915187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.545155
X-RAY DIFFRACTIONr_chiral_restr0.0990.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
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_it0.931.5845
X-RAY DIFFRACTIONr_mcbond_other0.2641.5346
X-RAY DIFFRACTIONr_mcangle_it1.65521382
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5543475
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1994.5433
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: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 64 -
Rwork0.259 1106 -
obs--96.5 %

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