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- PDB-1nog: Crystal Structure of Conserved Protein 0546 from Thermoplasma Aci... -

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Basic information

Entry
Database: PDB / ID: 1nog
TitleCrystal Structure of Conserved Protein 0546 from Thermoplasma Acidophilum
Componentsconserved hypothetical protein TA0546
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


corrinoid adenosyltransferase activity / ATP binding
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
Cobalamin adenosyltransferase-like domain-containing protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsSaridakis, V. / Sanishvili, R. / Iakounine, A. / Xu, X. / Pennycooke, M. / Gu, J. / Joachimiak, A. / Arrowsmith, C.H. / Edwards, A.M. / Christendat, D. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The structural basis for methylmalonic aciduria. The crystal structure of archaeal ATP:cobalamin adenosyltransferase.
Authors: Saridakis, V. / Yakunin, A. / Xu, X. / Anandakumar, P. / Pennycooke, M. / Gu, J. / Cheung, F. / Lew, J.M. / Sanishvili, R. / Joachimiak, A. / Arrowsmith, C.H. / Christendat, D. / Edwards, A.M.
History
DepositionJan 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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
Remark 999SEQUENCE The authors state that According to the density, the residue at position 110 is valine and ...SEQUENCE The authors state that According to the density, the residue at position 110 is valine and the residue at position 159 is ile.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein TA0546


Theoretical massNumber of molelcules
Total (without water)20,0291
Polymers20,0291
Non-polymers00
Water3,063170
1
A: conserved hypothetical protein TA0546

A: conserved hypothetical protein TA0546

A: conserved hypothetical protein TA0546


Theoretical massNumber of molelcules
Total (without water)60,0873
Polymers60,0873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area5180 Å2
ΔGint-32 kcal/mol
Surface area18770 Å2
MethodPISA
2
A: conserved hypothetical protein TA0546
x 12


Theoretical massNumber of molelcules
Total (without water)240,34912
Polymers240,34912
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
MethodPQS
Unit cell
Length a, b, c (Å)89.080, 89.080, 89.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by crystallographic symmetry.

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Components

#1: Protein conserved hypothetical protein TA0546


Mass: 20029.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: TA1434 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HIA7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.4 M ammonium phosphate, 6 % methylpentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop / Details: Christendat, D., (2000) J.Biol.Chem., 275, 24608.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG40001reservoir
2100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 14, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 34479 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 21.1
Reflection shellResolution: 1.55→1.6 Å / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3233 / % possible all: 100
Reflection
*PLUS
Num. obs: 62540 / % possible obs: 99 % / Num. measured all: 341835 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.47

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→29.69 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1309 3.9 %RANDOM
Rwork0.197 ---
obs0.197 33491 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.7177 Å2 / ksol: 0.378784 e/Å3
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.17 Å20 Å2
3---0.17 Å2
Refine analyzeLuzzati coordinate error free: 0.19 Å / Luzzati sigma a free: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.55→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 0 170 1354
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.215 200 3.8 %
Rwork0.214 5093 -
obs-3233 92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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