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

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Basic information

Entry
Database: PDB / ID: 3zuc
TitleStructure of CBM3b of major scaffoldin subunit ScaA from Acetivibrio cellulolyticus determined from the crystals grown in the presence of Nickel
ComponentsCELLULOSOMAL SCAFFOLDIN
KeywordsCRYSTALLINE CELLULOSE-BINDING PROTEIN / SUGAR 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 / MOLECULAR REPLACEMENT / Resolution: 1.001 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 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Other
Revision 1.2Mar 29, 2017Group: Structure summary
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.697, 52.697, 194.159
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-2101-

HOH

21A-2311-

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, 315 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 / Ethylene glycol


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


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


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


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsNICKEL (II) ION (NI): CRYSTALS WERE GROWN IN THE PRESENCE OF NICKEL IONS

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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 0.2M NICKEL CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2011 / Details: MIRRORS
RadiationMonochromator: SI(311) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 87445 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 8.24 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.2
Reflection shellResolution: 1→1.02 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.6 / % possible all: 82.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZQW

3zqw


Resolution: 1.001→44.426 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 10.62 / Stereochemistry target values: ML
Details: 159400 REFLECTIONS USED IN REFINEMENT USING SEPARATED FRIEDEL PAIRS
RfactorNum. reflection% reflection
Rfree0.136 3719 2.3 %
Rwork0.1249 --
obs0.1251 159400 98.08 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.45 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.879 Å2 / ksol: 0.498 e/Å3
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2---1.41 Å20 Å2
3---2.82 Å2
Refinement stepCycle: LAST / Resolution: 1.001→44.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 22 311 1520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111369
X-RAY DIFFRACTIONf_angle_d1.4021877
X-RAY DIFFRACTIONf_dihedral_angle_d14.715479
X-RAY DIFFRACTIONf_chiral_restr0.101195
X-RAY DIFFRACTIONf_plane_restr0.009249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0011-1.01370.35911120.34674611X-RAY DIFFRACTION77
1.0137-1.02710.2731210.29815144X-RAY DIFFRACTION88
1.0271-1.04110.28181340.25695454X-RAY DIFFRACTION93
1.0411-1.0560.24391350.22065677X-RAY DIFFRACTION96
1.056-1.07180.18121410.18785816X-RAY DIFFRACTION99
1.0718-1.08850.16981380.14835796X-RAY DIFFRACTION99
1.0885-1.10640.14261370.13065806X-RAY DIFFRACTION99
1.1064-1.12550.14711360.12115852X-RAY DIFFRACTION99
1.1255-1.14590.13571350.10885866X-RAY DIFFRACTION99
1.1459-1.1680.12041420.10665839X-RAY DIFFRACTION100
1.168-1.19180.13071440.10165844X-RAY DIFFRACTION100
1.1918-1.21770.11991440.10255854X-RAY DIFFRACTION100
1.2177-1.24610.11721400.10045850X-RAY DIFFRACTION100
1.2461-1.27720.10541430.1015857X-RAY DIFFRACTION100
1.2772-1.31180.12651410.10015886X-RAY DIFFRACTION100
1.3118-1.35040.11641440.09885904X-RAY DIFFRACTION100
1.3504-1.3940.10441380.09755850X-RAY DIFFRACTION100
1.394-1.44380.10431370.09565848X-RAY DIFFRACTION100
1.4438-1.50160.1111390.09285942X-RAY DIFFRACTION100
1.5016-1.56990.11881390.09385823X-RAY DIFFRACTION100
1.5699-1.65270.12121380.09295911X-RAY DIFFRACTION100
1.6527-1.75630.10531430.15883X-RAY DIFFRACTION100
1.7563-1.89190.11591400.10315850X-RAY DIFFRACTION100
1.8919-2.08220.1311360.10495890X-RAY DIFFRACTION100
2.0822-2.38350.11031350.11745871X-RAY DIFFRACTION100
2.3835-3.00290.16211460.13755861X-RAY DIFFRACTION100
3.0029-44.470.14931410.1595896X-RAY DIFFRACTION100

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