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- PDB-2g2d: Crystal structure of a putative pduO-type ATP:cobalamin adenosylt... -

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Basic information

Entry
Database: PDB / ID: 2g2d
TitleCrystal structure of a putative pduO-type ATP:cobalamin adenosyltransferase from Mycobacterium tuberculosis
ComponentsATP:cobalamin adenosyltransferase
KeywordsTRANSFERASE / helix bundle / trimer / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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
Hypothetical Protein Ta1238; Chain: A; / Cobalamin adenosyltransferase-like / Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Corrinoid adenosyltransferase / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMoon, J.H. / Kaviratne, A. / Yu, M. / Bursey, E.H. / Hung, L.-W. / Lekin, T.P. / Segelke, B.W. / Terwilliger, T.C. / Kim, C.-Y. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal structure of a putative pduO-type ATP:cobalamin adenosyltransferase from Mycobacterium tuberculosis.
Authors: Moon, J.H. / Kaviratne, A. / Yu, M. / Bursey, E.H. / Hung, L.-W. / Lekin, T.P. / Segelke, B.W. / Terwilliger, T.C. / Kim, C.-Y.
History
DepositionFeb 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP:cobalamin adenosyltransferase


Theoretical massNumber of molelcules
Total (without water)20,7181
Polymers20,7181
Non-polymers00
Water1,42379
1
A: ATP:cobalamin adenosyltransferase

A: ATP:cobalamin adenosyltransferase

A: ATP:cobalamin adenosyltransferase


Theoretical massNumber of molelcules
Total (without water)62,1553
Polymers62,1553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5160 Å2
ΔGint-29 kcal/mol
Surface area20840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.318, 131.318, 131.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
DetailsThe biological assembly is a trimer generated by the operations: z, y, x and y, z, x.

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Components

#1: Protein ATP:cobalamin adenosyltransferase


Mass: 20718.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P64803, UniProt: P9WP99*PLUS, corrinoid adenosyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 1.6M Ammonium Sulfate, 10% Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.211
SYNCHROTRONALS 5.0.220.91970, 0.91989, 0.8984
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDAug 4, 2005
ADSC QUANTUM 42CCDAug 4, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 Double CrystalSINGLE WAVELENGTHMx-ray1
2Si 111 Double CrystalMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.91971
30.919891
40.89841
ReflectionResolution: 2→30 Å / Num. all: 13272 / Num. obs: 13238 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.1 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 91.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 5552242.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 673 5.1 %RANDOM
Rwork0.194 ---
all0.213 13238 --
obs0.194 13238 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.7764 Å2 / ksol: 0.356097 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 0 79 1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it3.211.5
X-RAY DIFFRACTIONc_mcangle_it4.212
X-RAY DIFFRACTIONc_scbond_it4.722
X-RAY DIFFRACTIONc_scangle_it6.272.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 103 5 %
Rwork0.22 1953 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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