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- PDB-1kjn: Structure of MT0777 -

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Basic information

Entry
Database: PDB / ID: 1kjn
TitleStructure of MT0777
ComponentsMTH0777
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypotethical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyMTH777-like / Uncharacterised conserved protein UCP006600 / MTH777-like superfamily / Domain of unknown function (DUF1890) / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Conserved protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsChristendat, D. / Edwards, A. / Joachimiak, A. / Korolev, S. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be published
Title: Crystal structure of MT0777
Authors: Christendat, D. / Edwards, A. / Joachimiak, A. / Korolev, S.
History
DepositionDec 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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: MTH0777
B: MTH0777


Theoretical massNumber of molelcules
Total (without water)34,9592
Polymers34,9592
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-19 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.590, 62.280, 68.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MTH0777


Mass: 17479.367 Da / Num. of mol.: 2 / Fragment: hypothetical protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Production host: Escherichia coli (E. coli) / Strain (production host): pET15B / References: UniProt: O26871
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97938, 0.97916, 0.97779
DetectorType: SBC-1 / Detector: CCD / Date: Jul 8, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979381
20.979161
30.977791
ReflectionResolution: 2→50 Å / Num. all: 42424 / Num. obs: 37502 / % possible obs: 88.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16
Reflection shellResolution: 2→2.07 Å / Redundancy: 1 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.4 / % possible all: 40.3

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Processing

Software
NameVersionClassification
d*TREKdata scaling
HKL-2000data reduction
SnBphasing
SHARPphasing
ARP/wARPmodel building
CNS1.1refinement
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→48.07 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1858443.3 / Data cutoff high rms absF: 1858443.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 836 5.1 %RANDOM
Rwork0.217 ---
all-17092 --
obs-16544 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.0748 Å2 / ksol: 0.344549 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.26 Å20 Å20 Å2
2--2.56 Å20 Å2
3----8.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 0 173 2515
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.42
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.942.5
X-RAY DIFFRACTIONc_mcangle_it4.083
X-RAY DIFFRACTIONc_scbond_it4.313
X-RAY DIFFRACTIONc_scangle_it6.153.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2865 55 4.5 %
Rwork0.2143 2224 -
obs-1355 79.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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