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- PDB-4ums: The crystal structure of the seventh ScaB type I cohesin from Pse... -

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Basic information

Entry
Database: PDB / ID: 4ums
TitleThe crystal structure of the seventh ScaB type I cohesin from Pseudobacteroides cellulosolvens
ComponentsCELLULOSOMAL ANCHORING SCAFFOLDIN B
KeywordsSTRUCTURAL PROTEIN / CELLULOSOME / COHESINS / DOCKERINS / TYPE I BINDING SCAFFOLDIN SCAB
Function / homology
Function and homology information


S-layer / polysaccharide catabolic process / hormone activity / carbohydrate binding / extracellular region
Similarity search - Function
Large cysteine-rich periplasmic protein OmcB-like, DUF11 domain / Domain of unknown function DUF11 / Natriuretic peptide / Natriuretic peptide / : / Immunoglobulin-like - #680 / S-layer homology domain / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain ...Large cysteine-rich periplasmic protein OmcB-like, DUF11 domain / Domain of unknown function DUF11 / Natriuretic peptide / Natriuretic peptide / : / Immunoglobulin-like - #680 / S-layer homology domain / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology (SLH) domain profile. / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cellulosomal anchoring scaffoldin B
Similarity search - Component
Biological speciesBACTEROIDES CELLULOSOLVENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsCameron, K. / Alves, V.D. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Combined Crystal Structure of a Type-I Cohesin, Mutation and Affinity-Binding Studies Reveal Structural Determinants of Cohesin-Dockerin Specificity
Authors: Cameron, K. / Alves, V.D. / Bayer, E.A. / Gilbert, H.J. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionMay 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jul 8, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELLULOSOMAL ANCHORING SCAFFOLDIN B


Theoretical massNumber of molelcules
Total (without water)16,9581
Polymers16,9581
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.382, 52.767, 90.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CELLULOSOMAL ANCHORING SCAFFOLDIN B / SCABCOH7


Mass: 16958.141 Da / Num. of mol.: 1
Fragment: SEVENTH COHESIN MODULE OF SCAB, RESIDUES 1039-1186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES CELLULOSOLVENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: Q6A564
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHAS A C-TERMINAL HIS TAG.

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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: 2.13 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7
Details: 0.2 M SODIUM CHLORIDE AND 20 % W/V PEG 3350. 30% GLYCEROL ADDED AS CRYOPROTECTANT., pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93929
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93929 Å / Relative weight: 1
ReflectionResolution: 1.84→45.58 Å / Num. obs: 13249 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.9
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.3 / % possible all: 9.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CCL

2ccl


Resolution: 1.84→45.58 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.037 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE LAST 2 HISTIDINES ARE DISORDERED. ISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25647 648 4.9 %RANDOM
Rwork0.1898 ---
obs0.19304 12510 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---0.79 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.84→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 0 167 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191251
X-RAY DIFFRACTIONr_bond_other_d0.0010.021185
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.9371701
X-RAY DIFFRACTIONr_angle_other_deg0.84232741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6075167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.8126.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97515216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg33.511151
X-RAY DIFFRACTIONr_chiral_restr0.110.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021467
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02286
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.541.607641
X-RAY DIFFRACTIONr_mcbond_other1.5361.605640
X-RAY DIFFRACTIONr_mcangle_it2.4742.397808
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1981.869610
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 58 -
Rwork0.274 902 -
obs--98.46 %
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)
120.1288-13.89347.49518.09813.723512.0941-0.5334-0.625-0.2650.53861.6773-0.817-0.01731.0623-1.14390.33080.0916-0.22580.2073-0.17180.266921.9022-19.5024-12.7526
20.49290.15740.74390.39670.83082.4215-0.069-0.0279-0.01760.0212-0.019-0.0121-0.0372-0.10820.08810.10210.0262-0.05010.0587-0.0010.10728.0584-10.0843-23.9674
31.1163-0.31290.95521.10240.45362.2066-0.2539-0.07540.15950.04130.1154-0.001-0.2446-0.07290.13850.1410.0223-0.06820.0298-0.02180.085710.029-0.9894-20.1722
40.90220.15561.56080.90920.34553.6841-0.1019-0.00820.01670.09870.04420.0153-0.1381-0.06910.05770.08520.0297-0.05110.0585-0.00990.09510.5617-7.764-22.0974
53.1844-0.36324.04680.0486-0.44966.4545-0.3813-0.3465-0.11420.0740.07340.0035-0.4158-0.32310.3080.23680.1488-0.05250.12180.00450.202416.0256-14.0258-17.1332
618.17944.30153.53972.79522.61382.97150.07280.7638-0.9469-0.03880.0092-0.44810.03540.0448-0.0820.1060.02490.0280.1859-0.01940.3032-21.9082-18.5647-41.1034
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1039 - 1042
2X-RAY DIFFRACTION2A1043 - 1090
3X-RAY DIFFRACTION3A1091 - 1112
4X-RAY DIFFRACTION4A1113 - 1161
5X-RAY DIFFRACTION5A1162 - 1183
6X-RAY DIFFRACTION6A1184 - 1192

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