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- PDB-2xdh: Non-cellulosomal cohesin from the hyperthermophilic archaeon Arch... -

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Basic information

Entry
Database: PDB / ID: 2xdh
TitleNon-cellulosomal cohesin from the hyperthermophilic archaeon Archaeoglobus fulgidus
ComponentsCOHESIN
KeywordsCELL ADHESION / ARCHAEAL PROTEIN
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding
Similarity search - Function
WD40-like beta propeller / WD40-like Beta Propeller Repeat / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-bladed beta-propeller, TolB-like ...WD40-like beta propeller / WD40-like Beta Propeller Repeat / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-bladed beta-propeller, TolB-like / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cohesin domain-containing protein
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsVoronov-Goldman, M. / Lamed, R. / Noach, I. / Borovok, I. / Kwiat, M. / Rosenheck, S. / Shimon, L.J.W. / Bayer, E.A. / Frolow, F.
Citation
Journal: Proteins / Year: 2011
Title: Non-Cellulosomal Cohesin from the Hyperthermophilic Archaeon Archaeoglobus Fulgidus
Authors: Voronov-Goldman, M. / Lamed, R. / Noach, I. / Borovok, I. / Kwiat, M. / Rosenheck, S. / Shimon, L.J.W. / Bayer, E.A. / Frolow, F.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and Preliminary X-Ray Analysis of a Cohesin-Like Module from Af2375 of the Archaeon Archaeoglobus Fulgidus.
Authors: Voronov-Goldman, M. / Noach, I. / Lamed, R. / Shimon, L.J.W. / Borovok, I. / Bayer, E.A. / Frolow, F.
History
DepositionMay 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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 / _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

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Assembly

Deposited unit
A: COHESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8275
Polymers17,6361
Non-polymers1914
Water2,126118
1
A: COHESIN
hetero molecules

A: COHESIN
hetero molecules

A: COHESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,48115
Polymers52,9073
Non-polymers57412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
Buried area2830 Å2
ΔGint-106.6 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.754, 101.754, 101.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-1669-

MG

21A-1670-

SO4

31A-1670-

SO4

41A-2104-

HOH

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Components

#1: Protein COHESIN /


Mass: 17635.570 Da / Num. of mol.: 1 / Fragment: ORF 2375, RESIDUES 278-433
Source method: isolated from a genetically manipulated source
Details: COHESIN MODULE OF ORF 2375 / Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: 4304 / Description: GERMAN COLLECTION OF MICROORGANISMS(DSM) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / Variant (production host): B834 / References: UniProt: O30295
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.83 Å3/Da / Density % sol: 56.53 % / Description: NONE
Crystal growDetails: 0.1 M TRIS HYDROCHLORIDE PH 8.5, 2 M MONO-AMMONIUM DIHYDROGEN PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.956
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 8, 2004
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 1.96→30 Å / Num. obs: 13584 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 18.5 % / Biso Wilson estimate: 37.67 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 46.6
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ANU, 1AOH, 1G1K, 1QZN, 1TYJ

1anu

1aoh

1g1k

1qzn

1tyj


Resolution: 1.96→25.438 Å / SU ML: 0.26 / σ(F): 0.05 / Phase error: 20.89 / Stereochemistry target values: ML / Details: DISORDERED REGION A97-A123 IS OMITTED
RfactorNum. reflection% reflection
Rfree0.2296 1257 10.17 %
Rwork0.189 --
obs0.1931 12483 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.152 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.96→25.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 8 118 1180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071125
X-RAY DIFFRACTIONf_angle_d1.0931537
X-RAY DIFFRACTIONf_dihedral_angle_d12.75403
X-RAY DIFFRACTIONf_chiral_restr0.078180
X-RAY DIFFRACTIONf_plane_restr0.003204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9575-2.03590.33881170.22641075X-RAY DIFFRACTION81
2.0359-2.12850.25651350.20621158X-RAY DIFFRACTION89
2.1285-2.24060.31461230.2061090X-RAY DIFFRACTION83
2.2406-2.38090.24111320.21631191X-RAY DIFFRACTION90
2.3809-2.56460.24811410.19451246X-RAY DIFFRACTION94
2.5646-2.82240.24231430.18681297X-RAY DIFFRACTION96
2.8224-3.23010.24751490.1841313X-RAY DIFFRACTION98
3.2301-4.06690.1981520.16661375X-RAY DIFFRACTION99
4.0669-25.44060.21741650.19531481X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 51.3317 Å / Origin y: 80.8691 Å / Origin z: 36.0372 Å
111213212223313233
T0.2715 Å2-0.0235 Å20.0383 Å2-0.14 Å20.0348 Å2--0.2931 Å2
L1.4201 °2-0.8316 °20.2964 °2-3.1768 °20.3977 °2--1.8708 °2
S-0.0905 Å °-0.1458 Å °-0.0642 Å °0.1949 Å °0.1484 Å °0.4991 Å °0.0058 Å °-0.1489 Å °-0.0276 Å °
Refinement TLS groupSelection details: CHAIN A

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