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

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Basic information

Entry
Database: PDB / ID: 2zhz
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
ADENOSINE-5'-TRIPHOSPHATE / 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 12, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,90610
Polymers58,5663
Non-polymers1,3397
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-19 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.907, 148.174, 158.096
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.7 Å3/Da / Density % sol: 54.36 %
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: 6C1 / Wavelength: 1.23986 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2008 / Details: mirrors
RadiationMonochromator: Double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23986 Å / Relative weight: 1
ReflectionResolution: 1.8→42.94 Å / Num. all: 57721 / Num. obs: 57707 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Redundancy: 6 % / Biso Wilson estimate: 22.2 Å2 / Limit h max: 29 / Limit h min: 0 / Limit k max: 82 / Limit k min: 0 / Limit l max: 87 / Limit l min: 0 / Observed criterion F max: 63856.65 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.052 / Χ2: 0.965 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.249 / Num. unique all: 5155 / Χ2: 0.576 / % possible all: 88.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementResolution: 1.8→42.94 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 63858.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2918 5.1 %RANDOM
Rwork0.201 ---
all0.212 59041 --
obs0.211 57697 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.679 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 69.83 Å2 / Biso mean: 23.9 Å2 / Biso min: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1-7.77 Å20 Å20 Å2
2---2.71 Å20 Å2
3----5.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 82 283 4038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg19.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.87
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 (%)
1.8-1.880.2993445.30.27661180.0167263646289
1.88-1.980.2563585.10.24166760.0147305703496.3
1.98-2.110.2573454.80.20668630.0147334720898.3
2.11-2.270.2433404.70.19368940.0137326723498.7
2.27-2.50.2193805.20.18969190.0117357729999.2
2.5-2.860.2363765.10.269920.0127393736899.7
2.86-3.60.2463845.20.20470470.0137444743199.8
3.6-42.940.1933915.10.18772700.017672766199.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4atp2_gly.paramatp2_gly.top

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