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- PDB-1nxh: X-RAY STRUCTURE: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TT87 -

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Basic information

Entry
Database: PDB / ID: 1nxh
TitleX-RAY STRUCTURE: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TT87
ComponentsMTH396 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / Disulfide bonds / Homodimer / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyHypothetical protein MTH393 / EhaM-like / [NiFe]-hydrogenase-3-type complex Eha, subunit EhaM / EhaM-like superfamily / Domain of unknown function (DUF1959) / Orthogonal Bundle / Mainly Alpha / : / Conserved protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsKhayat, R. / Savchenko, A. / Edwards, A. / Arowsmith, C. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-RAY STRUCTURE OF MTH396
Authors: Khayat, R. / Savchenko, A. / Edwards, A. / Arowsmith, C. / Tong, L.
History
DepositionFeb 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 13, 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: MTH396 protein
B: MTH396 protein


Theoretical massNumber of molelcules
Total (without water)30,4272
Polymers30,4272
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-26 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.223, 80.223, 106.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MTH396 protein / conserved protein


Mass: 15213.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: MTH396 / Production host: Escherichia coli (E. coli) / References: UniProt: O26496, GenBank: 15678424
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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 0.1M Tris-HCl 9.2, 0.2M Sodium Acetate, 30% PEG 4000, 2% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 19, 2001
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 8995 / Num. obs: 8628 / % possible obs: 96 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 48.3 Å2
Reflection shellResolution: 2.8→2.97 Å / % possible all: 78

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.9 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1947897.47 / Data cutoff high rms absF: 1947897.47 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.319 605 7.4 %RANDOM
Rwork0.226 ---
obs0.226 8205 91.2 %-
all-8995 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9687 Å2 / ksol: 0.314755 e/Å3
Displacement parametersBiso mean: 59.5 Å2
Baniso -1Baniso -2Baniso -3
1--6 Å20 Å20 Å2
2---6 Å20 Å2
3---12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 0 0 2012
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d0.77
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 79 6.9 %
Rwork0.325 1059 -
obs--78 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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