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- PDB-3zqw: Structure of CBM3b of major scaffoldin subunit ScaA from Acetivib... -

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Basic information

Entry
Database: PDB / ID: 3zqw
TitleStructure of CBM3b of major scaffoldin subunit ScaA from Acetivibrio cellulolyticus
ComponentsCELLULOSOMAL SCAFFOLDIN
KeywordsCARBOHYDRATE-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: 1.07 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
DepositionJun 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Other
Revision 1.2Apr 29, 2015Group: Data collection
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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 SCAFFOLDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1875
Polymers16,7881
Non-polymers3994
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.506, 52.506, 193.978
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-2296-

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, 298 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.: 294 / 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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID2910.97622
SYNCHROTRONESRF BM1421.48395
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDFeb 23, 2011MIRRORS
ADSC CCD2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATORSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.976221
21.483951
ReflectionResolution: 1.08→50 Å / Num. obs: 69264 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 17.57 % / Biso Wilson estimate: 6.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.4
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / % possible all: 97.2

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Processing

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

Resolution: 1.07→19.616 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 10.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1352 3709 2.8 %
Rwork0.1215 --
obs0.1219 130568 98.98 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.567 Å2 / ksol: 0.49 e/Å3
Displacement parametersBiso mean: 7.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.145 Å20 Å20 Å2
2---1.145 Å20 Å2
3---2.2901 Å2
Refinement stepCycle: LAST / Resolution: 1.07→19.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 22 294 1503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111325
X-RAY DIFFRACTIONf_angle_d1.4031813
X-RAY DIFFRACTIONf_dihedral_angle_d14.994459
X-RAY DIFFRACTIONf_chiral_restr0.098191
X-RAY DIFFRACTIONf_plane_restr0.009236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.08410.2631330.27734561X-RAY DIFFRACTION94
1.0841-1.0990.20741370.2244857X-RAY DIFFRACTION98
1.099-1.11470.19621440.18594809X-RAY DIFFRACTION98
1.1147-1.13130.17351390.15254811X-RAY DIFFRACTION98
1.1313-1.1490.14541400.14014859X-RAY DIFFRACTION98
1.149-1.16780.14941450.1294890X-RAY DIFFRACTION98
1.1678-1.18790.15581410.1244792X-RAY DIFFRACTION98
1.1879-1.20950.13141410.11894866X-RAY DIFFRACTION99
1.2095-1.23280.1431420.11134852X-RAY DIFFRACTION99
1.2328-1.2580.11631420.10964880X-RAY DIFFRACTION99
1.258-1.28530.14541400.11154909X-RAY DIFFRACTION99
1.2853-1.31520.13761440.114916X-RAY DIFFRACTION99
1.3152-1.34810.13581420.10954881X-RAY DIFFRACTION99
1.3481-1.38450.14021450.10564890X-RAY DIFFRACTION99
1.3845-1.42520.11341430.10394903X-RAY DIFFRACTION100
1.4252-1.47120.13611400.09684913X-RAY DIFFRACTION100
1.4712-1.52380.09471500.0944877X-RAY DIFFRACTION100
1.5238-1.58480.12541450.09274970X-RAY DIFFRACTION100
1.5848-1.65690.11471420.0864914X-RAY DIFFRACTION100
1.6569-1.74420.09661460.09334946X-RAY DIFFRACTION100
1.7442-1.85340.10761450.09114920X-RAY DIFFRACTION100
1.8534-1.99640.13251450.10434894X-RAY DIFFRACTION100
1.9964-2.1970.121430.10724947X-RAY DIFFRACTION100
2.197-2.51440.14111480.12894942X-RAY DIFFRACTION100
2.5144-3.16570.1541440.13484918X-RAY DIFFRACTION100
3.1657-19.61880.13351430.14574942X-RAY DIFFRACTION100

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