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- PDB-4b9f: High resolution structure for family 3a carbohydrate binding modu... -

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Basic information

Entry
Database: PDB / ID: 4b9f
TitleHigh resolution structure for family 3a carbohydrate binding module from the cipA scaffolding of clostridium thermocellum
ComponentsCELLULOSOMAL-SCAFFOLDING PROTEIN A
KeywordsSUGAR BINDING PROTEIN / CELLULOSOME
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 / Carboxypeptidase-like, regulatory domain superfamily / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Clostridium cellulosome enzymes repeated domain signature. ...Endoglucanase-like / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Carboxypeptidase-like, regulatory domain superfamily / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 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 ATCC 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsYaniv, O. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.
CitationJournal: To be Published
Title: High Resolution Structure of the Family 3A Carbohydrate-Binding Module from the Mafor Scaffoldin Subunit Cipa of Clostridium Thermocellum
Authors: Yaniv, O. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.
History
DepositionSep 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_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)34,2118
Polymers33,7472
Non-polymers4646
Water7,710428
1
A: CELLULOSOMAL-SCAFFOLDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0093
Polymers16,8731
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELLULOSOMAL-SCAFFOLDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2025
Polymers16,8731
Non-polymers3284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.939, 58.868, 87.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-2031-

HOH

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Components

#1: Protein CELLULOSOMAL-SCAFFOLDING PROTEIN A / CELLULOSE-INTEGRATING PROTEIN A / CELLULOSOMAL GLYCOPROTEIN S1/SL / COHESIN


Mass: 16873.316 Da / Num. of mol.: 2 / Fragment: RESIDUES 368-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM ATCC 27405 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: Q06851
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.04 Å3/Da / Density % sol: 39.81 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.85 M AMMONIUM SULFATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2010 / Details: MIRRORS
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. obs: 91467 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 11.11 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.2
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NBC

1nbc


Resolution: 1.19→40.165 Å / SU ML: 0.12 / σ(F): 1.02 / Phase error: 16.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1592 8837 5 %
Rwork0.1513 --
obs0.1517 91330 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.9992 Å2 / ksol: 0.9659 e/Å3
Displacement parametersBiso mean: 16.233 Å2
Baniso -1Baniso -2Baniso -3
1-0.8804 Å20.0379 Å2-0.2746 Å2
2---0.3092 Å2-0.1191 Å2
3----0.0741 Å2
Refinement stepCycle: LAST / Resolution: 1.19→40.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 22 428 2836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062560
X-RAY DIFFRACTIONf_angle_d1.1183506
X-RAY DIFFRACTIONf_dihedral_angle_d13.004882
X-RAY DIFFRACTIONf_chiral_restr0.09374
X-RAY DIFFRACTIONf_plane_restr0.006461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1903-1.20390.29233000.28795285X-RAY DIFFRACTION96
1.2039-1.2180.30472960.28835629X-RAY DIFFRACTION100
1.218-1.23290.30163100.27635513X-RAY DIFFRACTION100
1.2329-1.24850.28072820.2695600X-RAY DIFFRACTION100
1.2485-1.26490.28182980.26755515X-RAY DIFFRACTION100
1.2649-1.28220.25393210.26345571X-RAY DIFFRACTION100
1.2822-1.30060.2743230.24625500X-RAY DIFFRACTION100
1.3006-1.320.24022990.23735611X-RAY DIFFRACTION100
1.32-1.34060.2333100.22535530X-RAY DIFFRACTION100
1.3406-1.36260.22183190.20875519X-RAY DIFFRACTION100
1.3626-1.38610.19832550.20485620X-RAY DIFFRACTION100
1.3861-1.41130.20742830.19345570X-RAY DIFFRACTION100
1.4113-1.43840.19012690.18495601X-RAY DIFFRACTION100
1.4384-1.46780.17722900.17425569X-RAY DIFFRACTION100
1.4678-1.49970.20253040.16625492X-RAY DIFFRACTION100
1.4997-1.53460.14733140.14245576X-RAY DIFFRACTION100
1.5346-1.5730.142920.1345558X-RAY DIFFRACTION100
1.573-1.61550.13742820.12765612X-RAY DIFFRACTION100
1.6155-1.66310.1272840.1195568X-RAY DIFFRACTION100
1.6631-1.71670.15062550.11915610X-RAY DIFFRACTION100
1.7167-1.77810.11893050.11565558X-RAY DIFFRACTION100
1.7781-1.84930.11332630.11585555X-RAY DIFFRACTION100
1.8493-1.93340.1282760.11675556X-RAY DIFFRACTION100
1.9334-2.03540.11622920.11345629X-RAY DIFFRACTION100
2.0354-2.16290.13173250.11555506X-RAY DIFFRACTION100
2.1629-2.32990.1212950.12585542X-RAY DIFFRACTION100
2.3299-2.56430.16482900.13895573X-RAY DIFFRACTION100
2.5643-2.93530.16233040.14565553X-RAY DIFFRACTION100
2.9353-3.69770.14322670.1385604X-RAY DIFFRACTION100
3.6977-40.18780.13933340.14465489X-RAY DIFFRACTION99

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