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- PDB-1gwl: Carbohydrate binding module family29 complexed with mannohexaose -

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Basic information

Entry
Database: PDB / ID: 1gwl
TitleCarbohydrate binding module family29 complexed with mannohexaose
ComponentsNON-CATALYTIC PROTEIN 1
KeywordsCARBOHYDRATE BINDING DOMAIN / GLUCOMANNAN / CELLOHEXAOSE / MANNOHEXAOSE / CELLULOSOME
Function / homology
Function and homology information


Fungal dockerin domain superfamily / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Galactose-binding lectin / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Non-catalytic protein 1
Similarity search - Component
Biological speciesPIROMYCES EQUI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsCharnock, S.J. / Nurizzo, D. / Davies, G.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Promiscuity in Ligand-Binding: The Three-Dimensional Structure of a Piromyces Carbohydrate-Binding Module,Cbm29-2,in Complex with Cello- and Mannohexaose
Authors: Charnock, S.J. / Bolam, D. / Nurizzo, D. / Szabo, L. / Mckie, V. / Gilbert, H. / Davies, G.J.
History
DepositionMar 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Atomic model / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NON-CATALYTIC PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2542
Polymers17,2631
Non-polymers9911
Water3,603200
1
A: NON-CATALYTIC PROTEIN 1
hetero molecules

A: NON-CATALYTIC PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5084
Polymers34,5262
Non-polymers1,9822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)51.619, 43.176, 60.731
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NON-CATALYTIC PROTEIN 1 / NCP1


Mass: 17263.053 Da / Num. of mol.: 1
Fragment: CARBOHYDRATE BINDING MODULE FAMILY 29 RESIDUES 335-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PIROMYCES EQUI (fungus) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9C171
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a1122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.2 Å3/Da / Density % sol: 44.9 %
Crystal growpH: 7.5
Details: 3.0M AMMONIUM SULFATE, 10MM MANNOHEXAOSE, 25% GLYCEROL, pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.0 Mammonium sulfate1drop
210 mg/mlprotein1drop
310 mMmannohexaose1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.52→20 Å / Num. obs: 20412 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.8
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.86 / % possible all: 92.7
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99 %
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
REFMAC5.1.11refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE CBM29 SOLVED BY MAD

Resolution: 1.51→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.239 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.179 1062 5.2 %RANDOM
Rwork0.154 ---
obs0.156 19556 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0.47 Å2
2---0.28 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 0 67 200 1377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211231
X-RAY DIFFRACTIONr_bond_other_d0.0020.021022
X-RAY DIFFRACTIONr_angle_refined_deg1.7652.0031672
X-RAY DIFFRACTIONr_angle_other_deg3.12432397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3295140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021316
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02248
X-RAY DIFFRACTIONr_nbd_refined0.2030.2147
X-RAY DIFFRACTIONr_nbd_other0.2520.21033
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.2617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3780.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8591.5694
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51321124
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4173537
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6084.5548
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: 1.51→1.55 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.198 59
Rwork0.187 1188
Refinement TLS params.Method: refined / Origin x: 6.8668 Å / Origin y: -0.0081 Å / Origin z: 14.5049 Å
111213212223313233
T0.0062 Å20.0122 Å20.0016 Å2-0.0249 Å20.0091 Å2--0.0357 Å2
L1.0611 °2-0.1349 °2-0.0295 °2-0.941 °20.2577 °2--1.3709 °2
S-0.0165 Å °0.0319 Å °0.0382 Å °0.0074 Å °0.0145 Å °0.0221 Å °-0.065 Å °-0.0559 Å °0.002 Å °
Refinement
*PLUS
Highest resolution: 1.51 Å / Rfactor Rfree: 0.18 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9

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