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- PDB-1nbc: BACTERIAL TYPE 3A CELLULOSE-BINDING DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1nbc
TitleBACTERIAL TYPE 3A CELLULOSE-BINDING DOMAIN
ComponentsCELLULOSOMAL SCAFFOLDING PROTEIN A
KeywordsCELLULOSE DEGRADATION / CELLULOSE-BINDING DOMAIN / CELLULOSOME / SCAFOLDIN
Function / homology
Function and homology information


cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / extracellular region
Similarity search - Function
Endoglucanase-like / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Carboxypeptidase-like, regulatory domain superfamily / Clostridium cellulosome enzymes repeated domain signature. ...Endoglucanase-like / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Carboxypeptidase-like, regulatory domain superfamily / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cellulosomal-scaffolding protein A
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.75 Å
AuthorsTormo, J. / Lamed, R. / Steitz, T.A.
Citation
Journal: EMBO J. / Year: 1996
Title: Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose.
Authors: Tormo, J. / Lamed, R. / Chirino, A.J. / Morag, E. / Bayer, E.A. / Shoham, Y. / Steitz, T.A.
#1: Journal: Appl.Environ.Microbiol. / Year: 1995
Title: Expression, Purification, and Characterization of the Cellulose-Binding Domain of the Scaffoldin Subunit from the Cellulosome of Clostridium Thermocellum
Authors: Morag, E. / Lapidot, A. / Govorko, D. / Lamed, R. / Wilchek, M. / Bayer, E.A. / Shoham, Y.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Analysis of the Major Cellulose-Binding Domain of the Cellulosome from Clostridium Thermocellum
Authors: Lamed, R. / Tormo, J. / Chirino, A.J. / Morag, E. / Bayer, E.A.
History
DepositionSep 10, 1996Processing site: BNL
Revision 1.0Sep 26, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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_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 / _struct_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: CELLULOSOMAL SCAFFOLDING PROTEIN A
B: CELLULOSOMAL SCAFFOLDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5384
Polymers34,4572
Non-polymers802
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.570, 50.320, 95.960
Angle α, β, γ (deg.)90.00, 99.47, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999769, -0.006031, -0.020615), (-0.006081, 0.999979, 0.002351), (0.0206, 0.002476, -0.999785)
Vector: 25.0368, -3.1047, 47.327)
DetailsTHE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS TWO COPIES OF THE PROTEIN MOLECULE. CHAIN IDENTIFIER A: PROTOMER 1, CHAIN IDENTIFIER B: PROTOMER 2.

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Components

#1: Protein CELLULOSOMAL SCAFFOLDING PROTEIN A / SCAFOLDIN SUBUNIT


Mass: 17228.727 Da / Num. of mol.: 2 / Fragment: CELLULOSE-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: YS / Gene: CIPB / Plasmid: PCBD / Gene (production host): CIPB / Production host: Escherichia coli (E. coli) / References: UniProt: Q06851
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41 %
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein11
225 mMMES11
350 mMsodium acetate11
412.5 %PEG335011
550 mMMES12
6100 mMsodium acetate12
725 %PEG335012

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: YALE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→10 Å / Num. obs: 26267 / % possible obs: 87.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.082
Reflection
*PLUS
Num. measured all: 113902
Reflection shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 7.83 Å / % possible obs: 51 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.75→10 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.25 -10 %RANDOM
Rwork0.193 ---
obs0.193 26090 86.5 %-
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1-15.2465 Å20 Å2-1.1087 Å2
2--15.5469 Å20 Å2
3---10.9537 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 2 280 2718
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.67
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5631.5
X-RAY DIFFRACTIONx_mcangle_it2.4232
X-RAY DIFFRACTIONx_scbond_it3.092
X-RAY DIFFRACTIONx_scangle_it4.4812.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.67
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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