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- PDB-1gwk: Carbohydrate binding module family29 -

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Basic information

Entry
Database: PDB / ID: 1gwk
TitleCarbohydrate binding module family29
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 / MAD / Resolution: 2.34 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 / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag
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
B: NON-CATALYTIC PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)34,8072
Polymers34,8072
Non-polymers00
Water1,65792
1
A: NON-CATALYTIC PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)17,4041
Polymers17,4041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NON-CATALYTIC PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)17,4041
Polymers17,4041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.270, 93.270, 83.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein NON-CATALYTIC PROTEIN 1 / NCP1


Mass: 17403.738 Da / Num. of mol.: 2 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUE 335-478
Source method: isolated from a genetically manipulated source
Details: SELENO-METHIONINE LABELLED CBM29 / Source: (gene. exp.) PIROMYCES EQUI (fungus) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9C171
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 58.8 %
Crystal growpH: 7.5
Details: 100MM NA HEPES, 150MM KSCN 20% ETHYLENE GLYCOL, 20% PEG3350, pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMsodium HEPES1reservoirpH7.5
3150 mM1reservoirKSCN
420 %(v/v)ethylene glycol1reservoir
516-21 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.34→20 Å / Num. obs: 29468 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.45
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 6.75 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.11refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.34→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.193 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.243 798 5 %RANDOM
Rwork0.193 ---
obs0.196 15158 100 %-
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: 28.78 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å20 Å20 Å2
2---2.49 Å20 Å2
3---4.98 Å2
Refinement stepCycle: LAST / Resolution: 2.34→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 0 92 2352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212330
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9383154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5785285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52424.878123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09815376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3971512
X-RAY DIFFRACTIONr_chiral_restr0.120.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021830
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2840
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7561.51413
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41722274
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8353917
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2054.5880
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: 2.34→2.4 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 66
Rwork0.214 1084
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7781-0.21190.05921.7441-0.17072.57810.02270.2240.1562-0.2998-0.0420.2402-0.281-0.21510.01930.0940.0283-0.0510.01470.00030.06768.455223.773627.2155
22.8243-0.7802-0.69344.57490.99062.90390.01550.31340.1103-0.2840.0188-0.06830.0155-0.1034-0.03430.0229-0.0313-0.00980.0766-0.00440.015146.224319.983137.1533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 144
2X-RAY DIFFRACTION2B3 - 148
Refinement
*PLUS
Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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