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- PDB-6sl4: The unique CBM-Cthe_0271 of Ruminiclostridium thermocellum -

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Basic information

Entry
Database: PDB / ID: 6sl4
TitleThe unique CBM-Cthe_0271 of Ruminiclostridium thermocellum
ComponentsType 3a cellulose-binding domain protein
KeywordsCELL ADHESION / CBM3 / highly-expressed / xylan-binding / lack of salt bridge
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process / membrane / metal ion binding
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
Type 3a cellulose-binding domain protein
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 CBM-Cthe_0271 of Ruminiclostridium thermocellum
Authors: Milana, M.V. / Almog, R. / Yaniv, O. / Oded, L. / Inna, R.G. / Felix, F. / Edward, A.B. / Raphael, L.
History
DepositionAug 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type 3a cellulose-binding domain protein
B: Type 3a cellulose-binding domain protein
C: Type 3a cellulose-binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2848
Polymers52,0843
Non-polymers2005
Water3,387188
1
A: Type 3a cellulose-binding domain protein
B: Type 3a cellulose-binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8435
Polymers34,7232
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-13 kcal/mol
Surface area13790 Å2
MethodPISA
2
C: Type 3a cellulose-binding domain protein
hetero molecules

C: Type 3a cellulose-binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8836
Polymers34,7232
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1480 Å2
ΔGint-17 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.990, 77.990, 288.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11C-145-

ARG

21C-202-

CA

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Components

#1: Protein Type 3a cellulose-binding domain protein


Mass: 17361.357 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_0271 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DC31
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes buffer ph7.5, 4.3M sodium cloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9184 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: May 7, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→67.541 Å / Num. obs: 46318 / % possible obs: 99 % / Redundancy: 5.9 % / CC1/2: 0.999 / Net I/σ(I): 17.7
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2494 / CC1/2: 0.398

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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 / Resolution: 1.8→67.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.578 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.134
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 2471 5.1 %RANDOM
Rwork0.2082 ---
obs0.2105 46318 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.23 Å2 / Biso mean: 34.946 Å2 / Biso min: 19.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.8→67.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 5 188 3869
Biso mean--30.04 35.18 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.023803
X-RAY DIFFRACTIONr_bond_other_d0.0010.023459
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.935155
X-RAY DIFFRACTIONr_angle_other_deg0.83337974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2925456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65224.667195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93415644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4321513
X-RAY DIFFRACTIONr_chiral_restr0.1140.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
LS refinement shellResolution: 1.802→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 182 -
Rwork0.378 3307 -
all-3489 -
obs--98.03 %

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