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- PDB-1oh3: E78R mutant of a carbohydrate binding module family 29 -

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Basic information

Entry
Database: PDB / ID: 1oh3
TitleE78R mutant of a carbohydrate binding module family 29
ComponentsNON-CATALYTIC PROTEIN 1
KeywordsCARBOHYDRATE BINDING DOMAIN / GLUCOMANNAN / CELLOHEXAOSE / MANNOHEXAOSE / CELLULOSOME / NCP1
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
AuthorsNurizzo, D. / Gilbert, H.J. / Davies, G.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Ligand-Mediated Dimerization of a Carbohydrate -Binding Module Reveals a Novel Mechanism for Protein-Carbohydrate Recognition
Authors: Flint, J. / Nurizzo, D. / Harding, S.E. / Longman, E. / Davies, G.J. / Gilbert, H.J. / Bolam, D.N.
History
DepositionMay 21, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / 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 / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: NON-CATALYTIC PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1143
Polymers32,1242
Non-polymers9911
Water5,044280
1
A: NON-CATALYTIC PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0532
Polymers16,0621
Non-polymers9911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NON-CATALYTIC PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)16,0621
Polymers16,0621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.671, 56.549, 129.770
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 / NCP1


Mass: 16061.758 Da / Num. of mol.: 2 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 334-477 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PIROMYCES EQUI (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9C171
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE GLU 411 ARG

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 6
Details: 25 % PEG 3350 15 % ETHYLENEGLYCOL, 0.1 M CALCIUM CHLORIDE 5 MM CELLOHEXAOASE, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→42.631 Å / Num. obs: 42994 / % possible obs: 92.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.8 / % possible all: 68.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GWM

1gwm


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.375 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2163 5 %RANDOM
Rwork0.17 ---
obs0.171 40754 92.3 %-
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: 12.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--0.99 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 67 280 2571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212375
X-RAY DIFFRACTIONr_bond_other_d0.0020.022033
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9793216
X-RAY DIFFRACTIONr_angle_other_deg0.93534721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4625280
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_restr0.1410.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022599
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02498
X-RAY DIFFRACTIONr_nbd_refined0.3190.2396
X-RAY DIFFRACTIONr_nbd_other0.2560.22397
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.21491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2183
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3910.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6951.51390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27122234
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0393985
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1114.5982
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
Rfree0.339 102
Rwork0.274 2025
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)
12.2534-0.3096-0.04261.21810.03091.44430.03760.118-0.0092-0.0961-0.02180.0119-0.01910.0304-0.01580.041-0.0080.00330.00740.01480.041513.723-0.29930.0477
21.7820.2647-0.88041.5987-1.13824.29450.0343-0.2638-0.04030.2579-0.0370.0053-0.13070.08890.00270.0914-0.01040.00030.09030.02090.076627.8371-2.657827.8814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 144
2X-RAY DIFFRACTION2B4 - 144

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