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- PDB-1mgp: Hypothetical protein TM841 from Thermotoga maritima reveals fatty... -

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Basic information

Entry
Database: PDB / ID: 1mgp
TitleHypothetical protein TM841 from Thermotoga maritima reveals fatty acid binding function
ComponentsHypothetical protein TM841
KeywordsLIPID BINDING PROTEIN / two domain structure with mixed alpha/beta structures in both domains / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Rossmann fold - #10170 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / : / Rossmann fold / 2-Layer Sandwich ...Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Rossmann fold - #10170 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / : / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Fatty acid-binding protein TM_1468
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / single anomolous dispersion / Resolution: 2 Å
AuthorsSchulze-Gahmen, U. / Pelaschier, J. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2003
Title: Crystal structure of a hypothetical protein, TM841 of Thermotoga maritima, reveals its function as fatty acid binding protein
Authors: Schulze-Gahmen, U. / Pelaschier, J. / Yokota, H. / Kim, R. / Kim, S.-H.
History
DepositionAug 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein TM841
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1932
Polymers35,9371
Non-polymers2561
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.010, 115.010, 91.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Hypothetical protein TM841


Mass: 35937.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pSKB3? / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta/pLysS/Rare / References: UniProt: Q9X1H9
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: magnesium sulfate, PEG 3350, PEG 400, HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMHEPES1droppH7.5
31 mMEDTA1drop
41 mMdithiothreitol1drop
50.2 M1reservoirMg2SO4
620 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2001 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 45620 / Num. obs: 45541 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.096 / Net I/σ(I): 24
Reflection shellResolution: 2→2.06 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.357 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 417875 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: single anomolous dispersion / Resolution: 2→19.62 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3286 7.4 %RANDOM
Rwork0.202 ---
all-44468 --
obs-44468 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.1267 Å2 / ksol: 0.438493 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å22.43 Å20 Å2
2--2.43 Å20 Å2
3----4.87 Å2
Refine analyzeLuzzati coordinate error free: 0.25 Å / Luzzati sigma a free: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 18 224 2431
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 559 7.9 %
Rwork0.232 6521 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PLM.PARAMPLM.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 7.5 % / Rfactor Rfree: 0.2426 / Rfactor Rwork: 0.2204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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