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- PDB-3u2g: Crystal structure of the C-terminal DUF1608 domain of the Methano... -

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Basic information

Entry
Database: PDB / ID: 3u2g
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
CITRIC ACID / AMMONIUM ION / Major S-layer protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: S-layer protein MA0829
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7845
Polymers32,3901
Non-polymers3944
Water3,027168
1
A: S-layer protein MA0829
hetero molecules

A: S-layer protein MA0829
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,56910
Polymers64,7802
Non-polymers7898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area3200 Å2
ΔGint-5 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.995, 120.995, 88.978
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
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: 32389.953 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.4 M ammonium citrate, 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: 0.979028 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2010
RadiationMonochromator: Si(111) double crystal monochromator (Kohzu HLD8-24 Monochromator)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979028 Å / Relative weight: 1
ReflectionResolution: 2.3→90 Å / Num. obs: 17588 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rsym value: 0.092 / Net I/σ(I): 21.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 1715 / Rsym value: 0.494 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→90 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.602 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 921 5.2 %RANDOM
Rwork0.178 ---
obs0.1802 17584 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.78 Å2 / Biso mean: 27.182 Å2 / Biso min: 8.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0.59 Å20 Å2
2---1.18 Å20 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 26 168 2356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222236
X-RAY DIFFRACTIONr_bond_other_d0.0010.021398
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.9553046
X-RAY DIFFRACTIONr_angle_other_deg0.77133432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43426.557122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65615349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.904154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022558
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
X-RAY DIFFRACTIONr_mcbond_it0.6351.51358
X-RAY DIFFRACTIONr_mcbond_other0.1061.5562
X-RAY DIFFRACTIONr_mcangle_it1.28722198
X-RAY DIFFRACTIONr_scbond_it2.2643878
X-RAY DIFFRACTIONr_scangle_it3.3994.5847
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 78 -
Rwork0.204 1169 -
all-1247 -
obs--98.97 %
Refinement TLS params.Method: refined / Origin x: 12.7909 Å / Origin y: 45.2377 Å / Origin z: 19.8265 Å
111213212223313233
T0.0304 Å20.0254 Å2-0.0135 Å2-0.0244 Å2-0.0051 Å2--0.0541 Å2
L0.3346 °20.5451 °2-0.1844 °2-1.3346 °2-0.6096 °2--0.3984 °2
S-0.0065 Å °-0.0282 Å °-0.0122 Å °0.0607 Å °0.0271 Å °-0.0631 Å °-0.0195 Å °-0.0231 Å °-0.0205 Å °

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