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- PDB-1g64: THE THREE-DIMENSIONAL STRUCTURE OF ATP:CORRINOID ADENOSYLTRANSFER... -

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Basic information

Entry
Database: PDB / ID: 1g64
TitleTHE THREE-DIMENSIONAL STRUCTURE OF ATP:CORRINOID ADENOSYLTRANSFERASE FROM SALMONELLA TYPHIMURIUM. COBALAMIN/ATP TERNARY COMPLEX
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 / MAD, Molecular replacement / 2.1 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 3, 2000 / Release: Dec 20, 2000
RevisionDateData content typeGroupProviderType
1.0Dec 20, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Oct 24, 2012Structure modelNon-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,9017
Polyers43,5072
Non-polymers2,3935
Water5,260292
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)6590
ΔGint (kcal/M)-50
Surface area (Å2)15420
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)80.000, 80.000, 142.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP 41 21 2

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Components

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


Mass: 21753.719 Da / Num. of mol.: 2 / 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.: 2 / Formula: Mg / Magnesium
#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Formula: C62H89CoN13O14P / Vitamin B12
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.61 / Density percent sol: 52.88 %
Crystal growTemp: 278 K / Method: microbatch / pH: 7
Details: 5-9% Peg 3350, 300 mM NaCl, 1 mM MgATP, 1 mM hydroxycobalamin, pH 7.0, microbatch, temperature 278K
Crystal grow
*PLUS
Temp: 4 ℃ / Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
110 mg/mlprotein11
25-9 %PEG335011
3300 mM11NaCl
4imidazole11

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Data collection

Diffraction
IDMean temperatureCrystal ID
11001
21001
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 19-ID / Synchrotron site: APS / Beamline: 19-ID / Wavelength: 0.97923, 0.97947, 0.98325, 0.908
Detector
TypeIdDetectorCollection date
APS-11CCD1999-07-01
MARRESEARCH2IMAGE PLATE1998-07-01
Radiation
IdMonochromatorDiffraction protocolMonochromatic or laue m lScattering typeWavelength ID
1SAGITALLY FOCUSED Si(111)MADMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelengthRelative weight
10.979231.0
20.979471.0
30.983251.0
40.9081.0
ReflectionD resolution high: 2.05 Å / D resolution low: 3 Å / Number all: 29134 / Number obs: 29134 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.055 / NetI over sigmaI: 24.3 / Redundancy: 4.6 % / Percent possible obs: 98.1
Reflection shellRmerge I obs: 0.281 / Highest resolution: 2.05 Å / Lowest resolution: 2.12 Å / Redundancy: 3.9 % / Percent possible all: 97.1
Reflection shell
*PLUS
Number unique obs: 2803 / Percent possible obs: 97.1 / MeanI over sigI obs: 3.6

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DMmodel building
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
DMphasing
RefineMethod to determine structure: MAD, Molecular replacement / R Free selection details: randomm / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.288 / R factor R work: 0.206 / R factor all: 0.206 / R factor obs: 0.206 / Highest resolution: 2.1 Å / Lowest resolution: 3 Å / Number reflection R free: 2943 / Number reflection all: 29095 / Number reflection obs: 29095
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 2769 / Nucleic acid: 0 / Ligand: 155 / Solvent: 292 / Total: 3216
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.60
X-RAY DIFFRACTIONt_dihedral_angle_d0.008
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.7
X-RAY DIFFRACTIONt_plane_restr0.013

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