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- PDB-1g5t: THE THREE-DIMENSIONAL STRUCTURE OF ATP:CORRINOID ADENOSYLTRANSFER... -

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Basic information

Entry
Database: PDB / ID: 1g5t
TitleTHE THREE-DIMENSIONAL STRUCTURE OF ATP:CORRINOID ADENOSYLTRANSFERASE FROM SALMONELLA TYPHIMURIUM. APO-ATP FORM
ComponentsCOB(I)ALAMIN ADENOSYLTRANSFERASE
KeywordsTRANSFERASE / P-loop protein / Cobalamin biosynthesis / RecA fold
Function / homologyATP:cob(I)alamin adenosyltransferase CobA/CobO/ButR / P-loop containing nucleoside triphosphate hydrolase / ATP:corrinoid adenosyltransferase BtuR/CobO/CobP / corrinoid adenosyltransferase / cob(I)yrinic acid a,c-diamide adenosyltransferase activity / porphyrin-containing compound biosynthetic process / cobalamin biosynthetic process / ATP binding / cytoplasm / Corrinoid adenosyltransferase
Function and homology information
Specimen sourceSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.8 Å resolution
AuthorsRayment, I. / Escalante-Semerena, J.C. / Bauer, C.B.
CitationJournal: Biochemistry / Year: 2001
Title: Three-dimensional structure of ATP:corrinoid adenosyltransferase from Salmonella typhimurium in its free state, complexed with MgATP, or complexed with hydroxycobalamin and MgATP.
Authors: Bauer, C.B. / Fonseca, M.V. / Holden, H.M. / Thoden, J.B. / Thompson, T.B. / Escalante-Semerena, J.C. / Rayment, I.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 2, 2000 / Release: Nov 22, 2000
RevisionDateData content typeGroupProviderType
1.0Nov 22, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COB(I)ALAMIN ADENOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2853
Polyers21,7541
Non-polymers5312
Water2,378132
1
A: COB(I)ALAMIN ADENOSYLTRANSFERASE
hetero molecules

A: COB(I)ALAMIN ADENOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5706
Polyers43,5072
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
2
A: COB(I)ALAMIN ADENOSYLTRANSFERASE
hetero molecules

A: COB(I)ALAMIN ADENOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5706
Polyers43,5072
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area (Å2)4600
ΔGint (kcal/M)-44
Surface area (Å2)13540
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)49.500, 49.500, 249.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP 65 2 2

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Components

#1: Protein/peptide COB(I)ALAMIN ADENOSYLTRANSFERASE / CORRINOID ADENOSYLTRANSFERASE


Mass: 21753.719 Da / Num. of mol.: 1 / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Genus: Salmonella / Gene: COBA / Genus (production host): Salmonella / Production host: Salmonella typhimurium (bacteria) / References: UniProt: P31570, corrinoid adenosyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Formula: H2O / Water

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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: 2.03 / Density percent sol: 39.38 %
Crystal growTemp: 298 K / Method: batch / pH: 5.5
Details: 13% me-peg 350, 100 mM NaCl, 50 mM MES, pH 5.5, batch, temperature 298K
Crystal grow
*PLUS
Temp: 4 ℃ / Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
113 %methyl ether-polyethylene glycol 35011
2100 mM11NaCl
350 mM MES11
45 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 19-ID / Synchrotron site: APS / Beamline: 19-ID / Wavelength: 0.7009
DetectorType: APS-1 / Detector: CCD / Collection date: Jul 1, 1999
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7009 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 3 Å / Number all: 17014 / Number obs: 17014 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.061 / NetI over sigmaI: 31.6 / Redundancy: 8.3 % / Percent possible obs: 93.3
Reflection shellRmerge I obs: 0.31 / Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / Redundancy: 4.7 % / Percent possible all: 63
Reflection shell
*PLUS
Number unique obs: 1357 / Percent possible obs: 63

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Processing

Software
NameClassification
AMoREphasing
TNTrefinement
d*TREKdata reduction
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT / R Free selection details: random / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.267 / R factor R work: 0.192 / R factor all: 0.192 / R factor obs: 0.192 / Highest resolution: 1.8 Å / Lowest resolution: 3 Å / Number reflection R free: 1435 / Number reflection all: 14575 / Number reflection obs: 14575
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 1207 / Nucleic acid: 0 / Ligand: 32 / Solvent: 132 / Total: 1371
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.73
X-RAY DIFFRACTIONt_dihedral_angle_d0.007
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.8
X-RAY DIFFRACTIONt_plane_restr0.007

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