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- PDB-4jo5: CBM3a-L domain with flanking linkers from scaffoldin cipA of cell... -

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Basic information

Entry
Database: PDB / ID: 4jo5
TitleCBM3a-L domain with flanking linkers from scaffoldin cipA of cellulosome of Clostridium thermocellum
ComponentsCellulosome anchoring protein cohesin region
KeywordsCELLULOSE BINDING PROTEIN / CBM / scaffolding / cellulose binding / beta sandwich / thermophile / CipA module
Function / homologyEndoglucanase-like / Immunoglobulin-like / Sandwich / Mainly Beta / 1-METHYLIMIDAZOLE / :
Function and homology information
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsShimon, L.J.W. / Frolow, F. / Bayer, E.A. / Yaniv, O. / Lamed, R. / Morag, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of a family 3a carbohydrate-binding module from the cellulosomal scaffoldin CipA of Clostridium thermocellum with flanking linkers: implications for cellulosome structure.
Authors: Yaniv, O. / Morag, E. / Borovok, I. / Bayer, E.A. / Lamed, R. / Frolow, F. / Shimon, L.J.
History
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellulosome anchoring protein cohesin region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0719
Polymers20,5571
Non-polymers5148
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.005, 109.005, 109.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-208-

1MZ

21A-208-

1MZ

31A-405-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cellulosome anchoring protein cohesin region / CBM3a-L


Mass: 20557.324 Da / Num. of mol.: 1 / Fragment: UNP residues 351-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: YS / Gene: CIPA, YSBL_2973 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: H8ERY3

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Non-polymers , 6 types, 169 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-1MZ / 1-METHYLIMIDAZOLE


Mass: 83.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.275 M ammonium sulfate, 0.085 M Tris, pH 8.5, 25.2% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9725 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2006
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 1.98→77.078 Å / Num. all: 16044 / Num. obs: 16044 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 25 % / Biso Wilson estimate: 28.41 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 34.51

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Processing

Software
NameVersionClassification
QUBEdata collection
MOLREPphasing
PHENIXdev_1389refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NCB

1ncb


Resolution: 1.98→29.133 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 790 5 %
Rwork0.172 --
obs0.1743 15806 98.84 %
all-16044 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→29.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 26 161 1500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011380
X-RAY DIFFRACTIONf_angle_d1.3371880
X-RAY DIFFRACTIONf_dihedral_angle_d14.535474
X-RAY DIFFRACTIONf_chiral_restr0.092202
X-RAY DIFFRACTIONf_plane_restr0.005244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.10360.34521160.2472342X-RAY DIFFRACTION95
2.1036-2.2660.27471310.20342453X-RAY DIFFRACTION100
2.266-2.49390.25491130.17332487X-RAY DIFFRACTION99
2.4939-2.85450.2261450.16022488X-RAY DIFFRACTION100
2.8545-3.59530.18991460.14852531X-RAY DIFFRACTION100
3.5953-29.1360.18911390.1712715X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -16.2353 Å / Origin y: 10.6183 Å / Origin z: -0.9061 Å
111213212223313233
T0.1666 Å2-0.0149 Å2-0.0438 Å2-0.2739 Å2-0.0333 Å2--0.2301 Å2
L1.3478 °2-0.2373 °2-0.6505 °2-1.0147 °2-0.3227 °2--0.5794 °2
S-0.0284 Å °0.1056 Å °-0.0161 Å °-0.0066 Å °0.0826 Å °0.103 Å °0.0678 Å °-0.0968 Å °0.0037 Å °
Refinement TLS groupSelection details: all

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