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- PDB-1zv9: Crystal structure analysis of a type II cohesin domain from the c... -

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Basic information

Entry
Database: PDB / ID: 1zv9
TitleCrystal structure analysis of a type II cohesin domain from the cellulosome of Acetivibrio cellulolyticus- SeMet derivative
ComponentsCellulosomal scaffoldin adaptor protein B
Keywordscellulosome / cohesins II
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like ...Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / FORMIC ACID / NITRATE ION / 1,3-PROPANDIOL / : / Cellulosomal scaffoldin adaptor protein B
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsNoach, I. / Rosenheck, S. / Lamed, R. / Shimon, L. / Bayer, E. / Frolow, F.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Intermodular linker flexibility revealed from crystal structures of adjacent cellulosomal cohesins of Acetivibrio cellulolyticus.
Authors: Noach, I. / Frolow, F. / Alber, O. / Lamed, R. / Shimon, L.J. / Bayer, E.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Preliminary X-ray characterisation and phasing of a type II cohesin domain from the cellulosome of Acetivibrio cellulolyticus
Authors: Noach, I. / Lamed, R. / Xu, Q. / Rosenheck, S. / Shimon, L.J.W. / Bayer, E. / Frolow, F.
History
DepositionJun 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,26813
Polymers18,5291
Non-polymers73912
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.858, 53.858, 111.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cellulosomal scaffoldin adaptor protein B / ScaB


Mass: 18529.287 Da / Num. of mol.: 1 / Fragment: cohesin II domain from cellulosome assembly / Mutation: MET41MSE,MET63MSE,MET139MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: ScaB / Plasmid: pet28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 31540575, UniProt: Q7WYN3*PLUS

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Non-polymers , 6 types, 307 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.5 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: Ammonium sulfate, pH 6, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 16, 2003 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. all: 49349 / Num. obs: 48796 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Χ2: 1.23 / Net I/σ(I): 24.2
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2340 / Rsym value: 0.49 / Χ2: 0.841 / % possible all: 97.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.401data extraction
ProDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZN

1qzn


Resolution: 1.28→46.63 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.182 / SU ML: 0.023 / SU R Cruickshank DPI: 0.035 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.039 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.158 2462 5.1 %RANDOM
Rwork0.116 ---
all0.118 48796 --
obs0.118 48747 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.28→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 32 316 1676
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01513940.022
X-RAY DIFFRACTIONr_bond_other_d0.0019280.02
X-RAY DIFFRACTIONr_angle_refined_deg1.47218821.986
X-RAY DIFFRACTIONr_angle_other_deg0.98923043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5051845
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0555226.538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.84924115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.027315
X-RAY DIFFRACTIONr_chiral_restr0.0872260.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00715280.02
X-RAY DIFFRACTIONr_gen_planes_other0.0012380.02
X-RAY DIFFRACTIONr_nbd_refined0.2362160.2
X-RAY DIFFRACTIONr_nbd_other0.1989500.2
X-RAY DIFFRACTIONr_nbtor_refined0.1646760.2
X-RAY DIFFRACTIONr_nbtor_other0.0837230.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1741940.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3100.2
X-RAY DIFFRACTIONr_symmetry_vdw_other0.278280.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.155380.2
X-RAY DIFFRACTIONr_mcbond_it6.83210903
X-RAY DIFFRACTIONr_mcbond_other3.4183543
X-RAY DIFFRACTIONr_mcangle_it7.38914435
X-RAY DIFFRACTIONr_scbond_it11.1965587
X-RAY DIFFRACTIONr_scangle_it13.03743210
X-RAY DIFFRACTIONr_rigid_bond_restr5.6627013
X-RAY DIFFRACTIONr_sphericity_free29731.928
X-RAY DIFFRACTIONr_sphericity_bonded230910.211
LS refinement shellResolution: 1.28→1.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 187 -
Rwork0.168 3230 -
obs-3230 94.68 %

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