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- PDB-6xx1: The unique CBM3-Clocl_1192 of Hungateiclostridium clariflavum -

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Basic information

Entry
Database: PDB / ID: 6xx1
TitleThe unique CBM3-Clocl_1192 of Hungateiclostridium clariflavum
Components(Cellulose binding domain-containing protein) x 2
KeywordsCELL ADHESION / CBM3 / xylan-binding / lack cellulose-binding capabilities / lack of salt bridge / no calcium ion in the structure
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process / membrane
Similarity search - Function
Endoglucanase-like / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cellulose binding domain-containing protein
Similarity search - Component
Biological speciesHungateiclostridium clariflavum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsMilana, M.V. / Almog, R. / Yaniv, O. / Oded, L. / Inna, R.G. / Felix, F. / Edward, A.B. / Raphael, L.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation24/11 Israel
CitationJournal: To Be Published
Title: The unique CBM3-Cthe_0271 from Ruminoclostridium thermocellum and CBM3-Clocl_1192 from Hungateiclostridium clariflavum
Authors: Milana, M.V. / Almog, R. / Yaniv, O. / Oded, L. / Inna, R.G. / Felix, F. / Edward, A.B. / Raphael, L.
History
DepositionJan 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellulose binding domain-containing protein
B: Cellulose binding domain-containing protein
C: Cellulose binding domain-containing protein
D: Cellulose binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)67,6414
Polymers67,6414
Non-polymers00
Water5,531307
1
A: Cellulose binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)16,7761
Polymers16,7761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulose binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)16,7761
Polymers16,7761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cellulose binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,0451
Polymers17,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cellulose binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,0451
Polymers17,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.090, 157.740, 46.560
Angle α, β, γ (deg.)90.000, 94.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cellulose binding domain-containing protein


Mass: 16775.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hungateiclostridium clariflavum (strain DSM 19732 / NBRC 101661 / EBR45) (bacteria)
Gene: Clocl_1192 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): lambda-DE3 / References: UniProt: G8LYV1
#2: Protein Cellulose binding domain-containing protein


Mass: 17044.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hungateiclostridium clariflavum (strain DSM 19732 / NBRC 101661 / EBR45) (bacteria)
Gene: Clocl_1192 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): lambda-DE3 / References: UniProt: G8LYV1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: May 7, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.61→78.87 Å / Num. obs: 85011 / % possible obs: 99.2 % / Redundancy: 3.7 % / CC1/2: 0.996 / Net I/σ(I): 7.9
Reflection shellResolution: 1.61→1.67 Å / Num. unique obs: 4251 / CC1/2: 0.396

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SL4

6sl4


Resolution: 1.61→78.87 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.538 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 4212 5 %RANDOM
Rwork0.1826 ---
obs0.1841 80128 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.65 Å2 / Biso mean: 22.258 Å2 / Biso min: 12.13 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å20 Å21.41 Å2
2---3.5 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 1.61→78.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4731 0 0 307 5038
Biso mean---26.6 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.024857
X-RAY DIFFRACTIONr_bond_other_d0.0010.024407
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9276558
X-RAY DIFFRACTIONr_angle_other_deg0.858310164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1315588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03425.319235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07215833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.832158
X-RAY DIFFRACTIONr_chiral_restr0.1230.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021198
LS refinement shellResolution: 1.612→1.654 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 292 -
Rwork0.315 5619 -
all-5911 -
obs--93.75 %

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