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- PDB-1ihn: MT938 -

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Basic information

Entry
Database: PDB / ID: 1ihn
TitleMT938
Componentshypothetical protein MTH938
KeywordsSTRUCTURAL GENOMICS / unknown function / Methanobacterium thermoautotrophicum / Northeast Structural Genomics Consortium / MTH938 / MT938 / PSI / Protein Structure Initiative / NESG
Function / homology
Function and homology information


Mth938 domain-containing protein / Hypothetical Protein Mth938; Chain: A, / MTH938-like / NDUFAF3/Mth938 domain-containing protein / MTH938-like superfamily / Protein of unknown function (DUF498/DUF598) / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsDas, K. / Montelione, G.T. / Arnold, E. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2001
Title: X-ray crystal structure of MTH938 from Methanobacterium thermoautotrophicum at 2.2 A resolution reveals a novel tertiary protein fold.
Authors: Das, K. / Xiao, R. / Wahlberg, E. / Hsu, F. / Arrowsmith, C.H. / Montelione, G.T. / Arnold, E.
History
DepositionApr 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
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 / 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein MTH938
B: hypothetical protein MTH938
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8607
Polymers25,6822
Non-polymers1775
Water1,44180
1
A: hypothetical protein MTH938
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9123
Polymers12,8411
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein MTH938
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9484
Polymers12,8411
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.630, 63.630, 116.800
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 hypothetical protein MTH938


Mass: 12841.159 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: O27021
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% PEG 3350, 0.1 M ammonium sulphate, 0.1M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
3100 mM1dropNaCl
45 mMbeta-mercaptoethanol1drop
520 %PEG33501reservoir
60.2 M1reservoirNH4Cl
70.1 Msodium cacodylate1reservoirpH6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9789, 0.9792, 0.9537
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97921
30.95371
ReflectionResolution: 2.2→40 Å / Num. all: 234960 / Num. obs: 23544 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.27 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 234960
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 100 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 93

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnB& SOLVEphasing
CNS1refinement
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / σ(F): 0 / σ(I): -3 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 651 5 %Random
Rwork0.228 ---
all0.228 12671 --
obs0.229 12020 99.3 %-
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 5 80 1846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

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