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- PDB-3zu8: STRUCTURE OF CBM3B OF MAJOR SCAFFOLDIN SUBUNIT SCAA FROM ACETIVIB... -

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Basic information

Entry
Database: PDB / ID: 3zu8
TitleSTRUCTURE OF CBM3B OF MAJOR SCAFFOLDIN SUBUNIT SCAA FROM ACETIVIBRIO CELLULOLYTICUS DETERMINED ON THE NIKEL ABSORPTION EDGE
ComponentsCELLULOSOMAL SCAFFOLDIN
KeywordsSUGAR BINDING PROTEIN / CELLULOSOME
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Endoglucanase-like / CarboxypepD_reg-like domain / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Carboxypeptidase-like, regulatory domain superfamily / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 ...Endoglucanase-like / CarboxypepD_reg-like domain / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Carboxypeptidase-like, regulatory domain superfamily / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Dockerin domain / Dockerin domain profile. / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Endoglucanase
Similarity search - Component
Biological speciesACETIVIBRIO CELLULOLYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsYaniv, O. / Halfon, Y. / Lamed, R. / Frolow, F.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of Cbm3B of the Major Scaffoldin Subunit Scaa from Acetivibrio Cellulolyticus
Authors: Yaniv, O. / Halfon, Y. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.
History
DepositionJul 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Other
Revision 1.2May 8, 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.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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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 SCAFFOLDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1875
Polymers16,7881
Non-polymers3994
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.263, 52.263, 192.938
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2021-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CELLULOSOMAL SCAFFOLDIN / FAMILY 3B CARBOHYDRATE BINDING MODULE


Mass: 16788.248 Da / Num. of mol.: 1 / Fragment: RESIDUES 973-1121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACETIVIBRIO CELLULOLYTICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: Q9RPL0

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Non-polymers , 5 types, 178 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.24 Å3/Da / Density % sol: 45.2 % / Description: NONE
Crystal growpH: 7.5
Details: 1.9 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5, 0.5% (W/V) POLYETHYLENE GLYCOL 400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.48395
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2011 / Details: BENT COLLIMATING MIRROR AND TOROID
RadiationMonochromator: SI(111) MONOCHROMATOR. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48395 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 15471 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 43.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.96 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
SHELXC D Ephasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.801→45.261 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 15.21 / Stereochemistry target values: ML
Details: 27239 REFLECTIONS USED IN REFINEMENT USIN SEPARATED FRIEDEL PAIRS.
RfactorNum. reflection% reflection
Rfree0.1819 1360 5 %
Rwork0.154 --
obs0.1554 27239 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.117 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 11.05 Å2
Baniso -1Baniso -2Baniso -3
1-2.262 Å20 Å20 Å2
2--2.262 Å20 Å2
3----4.5239 Å2
Refinement stepCycle: LAST / Resolution: 1.801→45.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 22 174 1383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071333
X-RAY DIFFRACTIONf_angle_d1.1091826
X-RAY DIFFRACTIONf_dihedral_angle_d14.209462
X-RAY DIFFRACTIONf_chiral_restr0.091193
X-RAY DIFFRACTIONf_plane_restr0.004238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8005-1.86490.221410.22012578X-RAY DIFFRACTION99
1.8649-1.93950.20141360.16082585X-RAY DIFFRACTION100
1.9395-2.02780.16991370.13732579X-RAY DIFFRACTION100
2.0278-2.13470.1571400.13392565X-RAY DIFFRACTION100
2.1347-2.26850.20251340.14692639X-RAY DIFFRACTION100
2.2685-2.44360.18951330.15132575X-RAY DIFFRACTION100
2.4436-2.68950.20851360.15822588X-RAY DIFFRACTION100
2.6895-3.07860.17791360.16462606X-RAY DIFFRACTION100
3.0786-3.87840.15071340.14432575X-RAY DIFFRACTION100
3.8784-45.27540.19261330.15542589X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8122-0.0618-0.27480.1382-0.08790.11890.11650.52360.1201-0.26940.07270.1776-0.0271-0.05980.05380.28710.015-0.04910.1647-0.01190.1602-16.937327.7094-5.0219
20.5578-0.34830.22260.4881-0.2180.17380.0130.0635-0.0202-0.09580.08730.07280.16750.07610.08030.1935-0.0004-0.00060.1203-0.01720.1211-14.65926.91175.5785
30.6531-0.24630.03810.9306-0.02760.7712-0.00930.0038-0.0238-0.07650.0227-0.04670.07560.10950.00050.1210.0175-0.00170.1038-0.0090.1111-14.405932.77787.7297
40.24110.02310.12330.12890.07990.09180.1108-0.04720.0824-0.103-0.07420.07950.04770.03810.01050.13960.0161-0.0060.1036-0.00880.1298-20.207136.3885-3.0785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:12)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 13:37)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 38:137)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 138:153)

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