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- PDB-1l1s: Structure of Protein of Unknown Function MTH1491 from Methanobact... -

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Basic information

Entry
Database: PDB / ID: 1l1s
TitleStructure of Protein of Unknown Function MTH1491 from Methanobacterium thermoautotrophicum
Componentshypothetical protein MTH1491
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical Protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologySulphur relay, DsrE/F-like / DsrE/DsrF-like family / DsrEFH-like / DsrEFH-like / Hypothetical Protein Ychn; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsChristendat, D. / Saridakis, V. / Kim, Y. / Kumar, P.A. / Xu, X. / Semesi, A. / Joachimiak, A. / Arrowsmith, C.H. / Edwards, A.M. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2002
Title: The crystal structure of hypothetical protein MTH1491 from Methanobacterium thermoautotrophicum.
Authors: Christendat, D. / Saridakis, V. / Kim, Y. / Kumar, P.A. / Xu, X. / Semesi, A. / Joachimiak, A. / Arrowsmith, C.H. / Edwards, A.M.
History
DepositionFeb 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 30, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein MTH1491


Theoretical massNumber of molelcules
Total (without water)12,7541
Polymers12,7541
Non-polymers00
Water34219
1
A: hypothetical protein MTH1491

A: hypothetical protein MTH1491

A: hypothetical protein MTH1491


Theoretical massNumber of molelcules
Total (without water)38,2613
Polymers38,2613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area3950 Å2
ΔGint-18 kcal/mol
Surface area13610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.440, 82.440, 37.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein hypothetical protein MTH1491


Mass: 12753.667 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: ORF1491 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O27535
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30 % MPD, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 57.3 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %MPD11
2100 mMHEPES11pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.93927 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 14, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.3→27.55 Å / Num. all: 12028 / Num. obs: 12028 / % possible obs: 92.2 % / Redundancy: 12 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.064 / Net I/σ(I): 32.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 7.6 / Num. unique all: 652 / Rsym value: 0.25 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 6492 / % possible obs: 98.4 % / Num. measured all: 77390
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 12.3

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Processing

Software
NameClassification
d*TREKdata scaling
SCALEPACKdata scaling
CNSrefinement
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→27.55 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1761771.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.226 579 5 %RANDOM
Rwork0.202 ---
obs0.202 11538 92.2 %-
all-12028 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.2413 Å2 / ksol: 0.371473 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å26.27 Å20 Å2
2---0.24 Å20 Å2
3---0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.3→27.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 0 19 881
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.228 72 4.4 %
Rwork0.203 1561 -
obs--78.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
LS refinement shell
*PLUS
Rfactor obs: 0.203

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