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- PDB-3u2h: Crystal structure of the C-terminal DUF1608 domain of the Methano... -

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Basic information

Entry
Database: PDB / ID: 3u2h
TitleCrystal structure of the C-terminal DUF1608 domain of the Methanosarcina acetivorans S-layer (MA0829) protein
ComponentsS-layer protein MA0829
KeywordsSTRUCTURAL PROTEIN / DUF1608 domain / cell envelop / surface layer / S-layer / UNKNOWN FUNCTION
Function / homology
Function and homology information


S-layer / cell wall organization / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Immunoglobulin-like - #4190 / DU1608 C-terminal domain / S-layer family duplication domain / S-layer protein / PGF-CTERM archaeal protein-sorting signal / PGF-CTERM motif / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major S-layer protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsChan, S. / Phan, T. / Ahn, C.J. / Shin, A. / Rohlin, L. / Gunsalus, R.P. / Arbing, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the surface layer of the methanogenic archaean Methanosarcina acetivorans.
Authors: Arbing, M.A. / Chan, S. / Shin, A. / Phan, T. / Ahn, C.J. / Rohlin, L. / Gunsalus, R.P.
History
DepositionOct 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: S-layer protein MA0829
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2012
Polymers32,1091
Non-polymers921
Water1,20767
1
A: S-layer protein MA0829
hetero molecules

A: S-layer protein MA0829
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4014
Polymers64,2172
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2230 Å2
ΔGint-5 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.675, 49.582, 84.952
Angle α, β, γ (deg.)90.000, 106.150, 90.000
Int Tables number5
Space group name H-MC121
Detailsthe full-length natural protein consists of a tandem repeats of two DUF1608 domains of highly similar sequences

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Components

#1: Protein S-layer protein MA0829


Mass: 32108.582 Da / Num. of mol.: 1 / Fragment: C-terminal DUF1608 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: MA0829, MA_0829 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) / References: UniProt: Q8TSG7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2M sodium sulfate, 20% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2009
RadiationMonochromator: Si(111) double crystal monochromator (Kohzu HLD8-24 Monochromator)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.36→90 Å / Num. obs: 12345 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rsym value: 0.096 / Χ2: 1.01 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.36-2.4470.3926.811951.051100
2.44-2.5470.30710.212260.976100
2.54-2.667.10.23912.712421.015100
2.66-2.870.19514.712391.016100
2.8-2.9770.1471512321.00999.9
2.97-3.26.90.1241512311.011100
3.2-3.536.70.1031512281.007100
3.53-4.046.50.08515.812421.00499.8
4.04-5.0860.06718.512301.00798.6
5.08-906.50.06421.612801.00598.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3U2G

3u2g


Resolution: 2.36→81.6 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.332 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 570 4.6 %RANDOM
Rwork0.2087 ---
obs0.2108 12333 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.71 Å2 / Biso mean: 30.983 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å2-0.05 Å2
2--1.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.36→81.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 6 67 2056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222037
X-RAY DIFFRACTIONr_bond_other_d0.0020.021263
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9472777
X-RAY DIFFRACTIONr_angle_other_deg0.833098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13726.214103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75615307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.355153
X-RAY DIFFRACTIONr_chiral_restr0.0740.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02405
X-RAY DIFFRACTIONr_mcbond_it0.5521.51267
X-RAY DIFFRACTIONr_mcbond_other0.0871.5525
X-RAY DIFFRACTIONr_mcangle_it1.09422035
X-RAY DIFFRACTIONr_scbond_it1.6563770
X-RAY DIFFRACTIONr_scangle_it2.7154.5741
LS refinement shellResolution: 2.361→2.422 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 32 -
Rwork0.2 785 -
all-817 -
obs--93.69 %
Refinement TLS params.Method: refined / Origin x: 10.0717 Å / Origin y: -22.4895 Å / Origin z: 15.607 Å
111213212223313233
T0.0525 Å20.0296 Å2-0.0097 Å2-0.1256 Å2-0.0308 Å2--0.0598 Å2
L1.007 °20.2464 °2-0.3079 °2-0.4119 °2-0.6962 °2--1.6813 °2
S-0.0708 Å °-0.2842 Å °-0.0013 Å °-0.0239 Å °0.0479 Å °-0.0727 Å °0.0242 Å °-0.0801 Å °0.0229 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 154
2X-RAY DIFFRACTION1A164 - 191
3X-RAY DIFFRACTION1A197 - 274

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