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- PDB-2zhy: Crystal structure of a pduO-type ATP:cobalamin adenosyltransferas... -

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Basic information

Entry
Database: PDB / ID: 2zhy
TitleCrystal structure of a pduO-type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis
ComponentsATP:cob(I)alamin adenosyltransferase, putative
KeywordsTRANSFERASE / helix bundle
Function / homology
Function and homology information


corrinoid adenosyltransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / cobalamin biosynthetic process / ATP binding / metal ion 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
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsMoon, J.H. / Park, A.K. / Jang, E.H. / Kim, H.S. / Chi, Y.M.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of a PduO-type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis.
Authors: Moon, J.H. / Park, A.K. / Jang, E.H. / Kim, H.S. / Chi, Y.M.
History
DepositionFeb 11, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 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:cob(I)alamin adenosyltransferase, putative
B: ATP:cob(I)alamin adenosyltransferase, putative
C: ATP:cob(I)alamin adenosyltransferase, putative


Theoretical massNumber of molelcules
Total (without water)58,5663
Polymers58,5663
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-18 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.583, 149.107, 157.354
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ATP:cob(I)alamin adenosyltransferase, putative / pduO-type adenosyltransferase


Mass: 19522.150 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: pduO / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SZ09, corrinoid adenosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1M Na Citrate, 22% Isopropanol, 12% PEG 4000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 2007 / Details: mirrors
RadiationMonochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 54263 / Num. obs: 54261 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 14.7 Å2 / Limit h max: 29 / Limit h min: 0 / Limit k max: 82 / Limit k min: 0 / Limit l max: 86 / Limit l min: 0 / Observed criterion F max: 54211.48 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.091 / Χ2: 1.713 / Net I/σ(I): 10.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.344 / Num. unique all: 3908 / Χ2: 0.524 / % possible all: 68.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 1.8→47.3 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2749 4.8 %RANDOM
Rwork0.229 ---
all0.239 57592 --
obs0.242 54261 93.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 64.305 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 67.45 Å2 / Biso mean: 28.473 Å2 / Biso min: 10.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å20 Å20 Å2
2--0.174 Å20 Å2
3----2.634 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.41 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 0 200 3803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg19.3
X-RAY DIFFRACTIONx_torsion_impr_deg0.84
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.4312665.30.41347610.0267120502770.6
1.88-1.980.3913034.70.3761840.0227108648791.3
1.98-2.110.3113515.10.29465630.0177148691496.7
2.11-2.270.2343605.10.22966500.0127153701098
2.27-2.50.2423394.80.20467360.0137171707598.7
2.5-2.860.2583745.30.20867470.0137201712198.9
2.86-3.60.2336050.19568430.0127261720399.2
3.6-47.30.213965.30.19970280.0117492742499.1
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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