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- PDB-1g5r: THE THREE-DIMENSIONAL STRUCTURE OF ATP:CORRINOID ADENOSYLTRANSFER... -

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Basic information

Entry
Database: PDB / ID: 1g5r
TitleTHE THREE-DIMENSIONAL STRUCTURE OF ATP:CORRINOID ADENOSYLTRANSFERASE FROM SALMONELLA TYPHIMURIUM. APO FORM
ComponentsCOB(I)ALAMIN ADENOSYLTRANSFERASE
KeywordsTRANSFERASE / P-loop protein / Cobalamin biosynthesis / RecA fold
Function / homology
Function and homology information


corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / porphyrin-containing compound biosynthetic process / cobalamin biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
ATP:cob(I)alamin adenosyltransferase CobA/CobO/BtuR / ATP:corrinoid adenosyltransferase BtuR/CobO/CobP / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Corrinoid adenosyltransferase CobA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
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.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,1172
Polymers22,0821
Non-polymers351
Water2,450136
1
A: COB(I)ALAMIN ADENOSYLTRANSFERASE
hetero molecules

A: COB(I)ALAMIN ADENOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2354
Polymers44,1642
Non-polymers712
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)44,2354
Polymers44,1642
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3240 Å2
ΔGint-41 kcal/mol
Surface area14130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.400, 49.400, 249.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 22081.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: COBA / Production host: Salmonella typhimurium (bacteria) / References: UniProt: P31570, corrinoid adenosyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 278 K / Method: batch / pH: 5.5
Details: 13% me-peg 350, 100 mM NaCl, 50 mM MES, pH 5.5, Batch, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common 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 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.94290, 0.97939, 0.97960, 1.0205
DetectorType: APS-1 / Detector: CCD / Date: Dec 1, 1998
RadiationMonochromator: ID-19 optics / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94291
20.979391
30.97961
41.02051
ReflectionResolution: 2.1→100 Å / Num. all: 10494 / Num. obs: 10494 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 35.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.177 / % possible all: 63
Reflection shell
*PLUS
% possible obs: 63.2 % / Num. unique obs: 698 / Mean I/σ(I) obs: 7.2

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Processing

Software
NameClassification
SOLVEphasing
TNTrefinement
d*TREKdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 1033 random
Rwork0.178 --
all0.178 10482 -
obs0.178 10482 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 1 136 1344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.58
X-RAY DIFFRACTIONt_dihedral_angle_d0.007
LS refinement shellHighest resolution: 2.1 Å
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.6
X-RAY DIFFRACTIONt_plane_restr0.009

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