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- PDB-1wcu: CBM29_1, A Family 29 Carbohydrate Binding Module from Piromyces equi -

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Basic information

Entry
Database: PDB / ID: 1wcu
TitleCBM29_1, A Family 29 Carbohydrate Binding Module from Piromyces equi
ComponentsNON-CATALYTIC PROTEIN 1
KeywordsCARBOHYDRATE BINDING / CBM29 / CBM29_1 / CARBOHYDRATE BINDING MODULE
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: 1.5 Å
AuthorsFlint, J. / Bolam, D.N. / Nurizzo, D. / Taylor, E.J. / Williamson, M.P. / Walters, C. / Davis, G.J. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Probing the Mechanism of Ligand Recognition in Family 29 Carbohydrate-Binding Modules
Authors: Flint, J. / Bolam, D.N. / Nurizzo, D. / Taylor, E.J. / Williamson, M.P. / Walters, C. / Davies, G.J. / Gilbert, H.J.
History
DepositionNov 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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)17,5592
Polymers17,4671
Non-polymers921
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.054, 57.512, 76.130
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 NON-CATALYTIC PROTEIN 1 / CBM29_1


Mass: 17467.186 Da / Num. of mol.: 1 / Fragment: RESIDUES 174-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PIROMYCES EQUI (fungus) / Strain: NCP1 / Plasmid: PET 22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMIB PLYSS / References: UniProt: Q9C171
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 1.9 Å3/Da / Density % sol: 33.7 %
Crystal growDetails: 0.6M LITHIUM ACETATE, 20% PEG 3350. WITH PROTEIN AT A FINAL CONCENTRATION OF 10 MG / ML FINAL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.025
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2002
Details: A ZEISS MIRROR WITH DIMENSIONS OF 800X95X78 MM3. MADE OF MONOCRYSTALLINE SILICON AND COATED WITH 20-50 NM RH. SPECIFICATIONS SAGITTAL RADIUS 77.15, BENDING RADIUS 9KM
RadiationMonochromator: KHOZU MONOCHROMATOR WITH A MCKHOZU MONOCHROMATOR WITH A MCLENNON CONTROLLER CONTAINING A LN2 COOLED SI111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.025 Å / Relative weight: 1
ReflectionResolution: 1.5→46.12 Å / Num. obs: 21737 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 40
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 13 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GWK

1gwk


Resolution: 1.5→46.13 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.945 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.164 1114 5.1 %RANDOM
Rwork0.14 ---
obs0.141 20621 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.64 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 6 250 1449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221226
X-RAY DIFFRACTIONr_bond_other_d0.0020.021014
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9331655
X-RAY DIFFRACTIONr_angle_other_deg2.68832378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2955146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16525.29468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5815199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.77154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
X-RAY DIFFRACTIONr_nbd_refined0.2370.2199
X-RAY DIFFRACTIONr_nbd_other0.1780.2984
X-RAY DIFFRACTIONr_nbtor_refined0.220.2592
X-RAY DIFFRACTIONr_nbtor_other0.0820.2682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0511.5939
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26621176
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3513604
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2264.5479
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.168 69
Rwork0.151 1484

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