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- PDB-2x34: Structure of a polyisoprenoid binding domain from Saccharophagus ... -

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Basic information

Entry
Database: PDB / ID: 2x34
TitleStructure of a polyisoprenoid binding domain from Saccharophagus degradans implicated in plant cell wall breakdown
ComponentsCELLULOSE-BINDING PROTEIN, X158
KeywordsCARBOHYDRATE-BINDING PROTEIN / OXIDOREDUCTION / MARINE BACTERIA / POLYISOPRENOID TRANSPORT
Function / homology
Function and homology information


polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / membrane
Similarity search - Function
: / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II ...: / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Ubiquinone-8 / Cellulose-binding protein
Similarity search - Component
Biological speciesSACCHAROPHAGUS DEGRADANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsVincent, F. / Dal Molin, D. / Weiner, R.M. / Bourne, Y. / Henrissat, B.
CitationJournal: FEBS Lett. / Year: 2010
Title: Structure of a Polyisoprenoid Binding Domain from Saccharophagus Degradans Implicated in Plant Cell Wall Breakdown
Authors: Vincent, F. / Dalmolin, D. / Weiner, R.M. / Bourne, Y. / Henrissat, B.
History
DepositionJan 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2018Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_sheet / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: CELLULOSE-BINDING PROTEIN, X158
B: CELLULOSE-BINDING PROTEIN, X158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0044
Polymers39,5502
Non-polymers1,4542
Water6,557364
1
A: CELLULOSE-BINDING PROTEIN, X158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5022
Polymers19,7751
Non-polymers7271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELLULOSE-BINDING PROTEIN, X158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5022
Polymers19,7751
Non-polymers7271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.979, 64.964, 84.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.961, 0.072, 0.268), (0.077, -0.997, -0.011), (0.266, 0.031, -0.963)
Vector: -5.37555, 33.34503, 31.8741)

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Components

#1: Protein CELLULOSE-BINDING PROTEIN, X158


Mass: 19774.775 Da / Num. of mol.: 2 / Fragment: YCEI-LIKE DOMAIN, RESIDUES 199-371
Source method: isolated from a genetically manipulated source
Details: UBIQUINONE-8 BOUND TO THE PROTEIN / Source: (gene. exp.) SACCHAROPHAGUS DEGRADANS (bacteria) / Strain: 2-40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS / References: UniProt: Q21LI5
#2: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H74O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS DOMAIN IS PART OF A MODULAR PROTEIN. MK AT THE BEGINNING AND 6XHIS AT THE END ARE FROM THE ...THIS DOMAIN IS PART OF A MODULAR PROTEIN. MK AT THE BEGINNING AND 6XHIS AT THE END ARE FROM THE CLONING PROCESS.

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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: 48.53 % / Description: NONE
Crystal growpH: 5.5 / Details: 42% PEG600, 0.2M IMIDAZOL-MALATE PH 5.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→51 Å / Num. obs: 27856 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→51.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.6 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1399 5 %RANDOM
Rwork0.175 ---
obs0.178 26470 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→51.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 106 364 3088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222802
X-RAY DIFFRACTIONr_bond_other_d0.0010.021685
X-RAY DIFFRACTIONr_angle_refined_deg1.4792.0083826
X-RAY DIFFRACTIONr_angle_other_deg1.00734168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12524.766107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08915442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.931514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02512
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6951.51753
X-RAY DIFFRACTIONr_mcbond_other0.1561.5714
X-RAY DIFFRACTIONr_mcangle_it1.26322849
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.09231049
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2044.5970
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 92 -
Rwork0.268 1901 -
obs--99.06 %
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)
13.0051-1.08760.27241.048-0.85270.86760.10580.1121-0.2431-0.0055-0.09130.09190.01320.0516-0.01450.0450.0023-0.02330.0352-0.04150.055122.164754.332513.0856
20.8007-0.0073-0.09110.4235-0.05870.5054-0.0470.0439-0.0901-0.01410.0243-0.0087-0.0282-0.02730.02270.02470.0061-0.00370.0078-0.01080.025818.51353.285511.4178
31.9902-0.4138-0.55560.9561-0.10771.4321-0.07710.0217-0.2013-0.03180.01720.02450.08120.15950.05980.01120.0044-0.00250.0232-0.01050.040927.884347.16818.426
42.87712.20930.15323.4517-0.30891.8967-0.05460.2144-0.0493-0.07850.0561-0.1514-0.18270.1752-0.00150.0281-0.00390.00470.03920.01370.043327.210142.47127.0469
57.06361.8912-1.23081.7076-1.18190.8775-0.0607-0.0986-0.26990.02290.0172-0.01120.07380.03820.04350.05930.01090.01530.0279-0.0120.072820.999333.720934.3085
62.02590.18650.49630.54960.12760.7948-0.0237-0.05430.08980.05120.02930.0179-0.0208-0.0058-0.00560.0294-0.00330.00630.00310.00280.030822.179940.529633.1146
73.22341.69561.63492.04061.12171.6887-0.14830.02730.1391-0.03390.10430.0203-0.13970.11990.0440.0185-0.00420.00870.0135-0.01430.046532.001747.865633.8561
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 42
2X-RAY DIFFRACTION2A43 - 135
3X-RAY DIFFRACTION3A136 - 174
4X-RAY DIFFRACTION4B0 - 26
5X-RAY DIFFRACTION5B27 - 44
6X-RAY DIFFRACTION6B45 - 135
7X-RAY DIFFRACTION7B136 - 173

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