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- PDB-5dpn: Engineered CBM X-2 L110F in complex with branched carbohydrate XXXG. -

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Basic information

Entry
Database: PDB / ID: 5dpn
TitleEngineered CBM X-2 L110F in complex with branched carbohydrate XXXG.
ComponentsXylanase
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding module hydrogen bond H/D exchanged
Function / homology
Function and homology information


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 / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / 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 / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / 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
DEUTERATED WATER / Xylanase
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOhlin, M.
CitationJournal: Biochemistry / Year: 2015
Title: Neutron Crystallographic Studies Reveal Hydrogen Bond and Water-Mediated Interactions between a Carbohydrate-Binding Module and Its Bound Carbohydrate Ligand.
Authors: Fisher, S.Z. / von Schantz, L. / Hakansson, M. / Logan, D.T. / Ohlin, M.
History
DepositionSep 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 28, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)19,0433
Polymers17,9401
Non-polymers1,1032
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint28 kcal/mol
Surface area7520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.977, 49.856, 45.091
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 Xylanase


Mass: 17939.734 Da / Num. of mol.: 1 / Fragment: UNP residues 212-376 / Mutation: L110F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WTN6
#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1062.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-1-2-2-2/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Large crystals were grown in 9-well glass plates using Hampton sandwich box set-up.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
22931
11001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
NUCLEAR REACTORFRM II BIODIFF22.66
SYNCHROTRONMAX II I911-211.04
Detector
TypeIDDetectorDate
FUJI2IMAGE PLATENov 25, 2014
MAR CCD 165 mm1CCDOct 28, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2SINGLE WAVELENGTHMneutron2
1SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
12.661
21.041
Reflection

Entry-ID: 5DPN

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.6-452053091.130.04126.6
1.6-29.32161097.75.50.093128.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.6-1.75.50.2317.83389197.2
1.6-1.652.50.4491.81485297.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
Cootmodel building
Refinement

SU ML: 0.19 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 4bj0

4bj0

/ Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDPhase errorStereochemistry target valuesStereochEM target val spec case
1.6-45X-RAY DIFFRACTION0.250.22250.22391027205125.0191.09124.18ML
1.606-29.445NEUTRON DIFFRACTION0.2040.16280.1648108121609597.692ML
Refinement step
CycleResolution (Å)Cycle-IDRefine-ID#notag 0
LAST1.6-45LASTX-RAY DIFFRACTION
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 73 60 1393
LAST1.596-45.091LASTNEUTRON DIFFRACTION
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 73 60 1393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013158
X-RAY DIFFRACTIONf_angle_d1.2685564
X-RAY DIFFRACTIONf_dihedral_angle_d22.277856
X-RAY DIFFRACTIONf_chiral_restr0.08251
X-RAY DIFFRACTIONf_plane_restr0.006617
NEUTRON DIFFRACTIONf_bond_d0.013158
NEUTRON DIFFRACTIONf_angle_d1.2685564
NEUTRON DIFFRACTIONf_dihedral_angle_d22.277856
NEUTRON DIFFRACTIONf_chiral_restr0.08251
NEUTRON DIFFRACTIONf_plane_restr0.006617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5965-1.68070.32021270.2742420NEUTRON DIFFRACTION80
1.6807-1.7860.27821310.24822470NEUTRON DIFFRACTION83
1.786-1.92390.26571390.23712643NEUTRON DIFFRACTION88
1.9239-2.11750.22531450.21252761NEUTRON DIFFRACTION91
2.1175-2.42380.23541540.20172929NEUTRON DIFFRACTION96
2.4238-3.05370.24411630.2223083NEUTRON DIFFRACTION100
3.0537-45.1090.24181680.21253179NEUTRON DIFFRACTION99
1.6056-1.67870.2311320.18382497X-RAY DIFFRACTION97
1.6787-1.76720.22711320.17232516X-RAY DIFFRACTION98
1.7672-1.87790.22131330.16542544X-RAY DIFFRACTION98
1.8779-2.02280.1771350.16092546X-RAY DIFFRACTION98
2.0228-2.22630.21661350.15732565X-RAY DIFFRACTION99
2.2263-2.54830.20541360.16432598X-RAY DIFFRACTION99
2.5483-3.210.23031380.17962625X-RAY DIFFRACTION98
3.21-29.44990.18021400.14872637X-RAY DIFFRACTION95

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