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- PDB-1cbu: ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTR... -

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Basic information

Entry
Database: PDB / ID: 1cbu
TitleADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE (COBU) FROM SALMONELLA TYPHIMURIUM
ComponentsADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE
KeywordsCOBALAMIN BIOSYNTHESIS / ADENOSYLCOBINAMIDE / KINASE / ATPASE / GUANYLYLTRANSFERASE / SALMONELLA TYPHIMURIUM / TRANSFERASE / COENZYME B12
Function / homology
Function and homology information


adenosylcobinamide kinase activity / adenosylcobinamide kinase / adenosylcobinamide-phosphate guanylyltransferase / cobinamide phosphate guanylyltransferase activity / cobalamin biosynthetic process / GTP binding / ATP binding
Similarity search - Function
Cobinamide kinase/cobinamide phosphate guanyltransferase / Cobinamide kinase / cobinamide phosphate guanyltransferase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional adenosylcobalamin biosynthesis protein CobU
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsThompson, T.B. / Thomas, M.G. / Escalante-Semerena, J.C. / Rayment, I.
Citation
Journal: Biochemistry / Year: 1998
Title: Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 A resolution,.
Authors: Thompson, T.B. / Thomas, M.G. / Escalante-Semerena, J.C. / Rayment, I.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Purification and Characterization of the Bifunctional Cobu Enzyme of Salmonella Typhimurium Lt2. Evidence for a Cobu-Gmp Intermediate
Authors: O'Toole, G.A. / Escalante-Semerena, J.C.
History
DepositionMar 12, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE
B: ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE
C: ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6726
Polymers59,3843
Non-polymers2883
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-93 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.400, 114.400, 106.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.34327, 0.56648, 0.74918), (-0.55671, -0.51971, 0.64805), (0.75647, -0.63953, 0.13697)-43.18497, 15.23066, 49.20813
2given(0.35818, -0.56417, 0.74392), (0.59147, -0.47939, -0.64834), (0.72241, 0.67223, 0.16198)-13.33835, 62.20041, 14.04711

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Components

#1: Protein ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE


Mass: 19794.711 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): LT2 / References: UniProt: Q05599
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 50 %
Crystal growMethod: microbatch / pH: 5.5
Details: PROTEIN WAS CRYSTALLIZED BY MICRO BATCH FROM 6% PEG 3350, 200 MM NACL AND 50 MM SUCCINATE, PH 5.5 AT 4 C., micro batch
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 %PEG335011
2200 mM11NaCl
350 mMsuccinate11
45-8 mg/mlprotein11

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 1, 1997 / Details: SIEMENS GOBEL FOCUSING OPTICS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 24136 / % possible obs: 88.5 % / Observed criterion σ(I): 0.33 / Redundancy: 3 % / Biso Wilson estimate: 46.9 Å2 / Rsym value: 0.043 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.21 / % possible all: 64.4
Reflection
*PLUS
Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 64.4 % / Rmerge(I) obs: 0.21

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Processing

Software
NameVersionClassification
HEAVYmodel building
TNT4Crefinement
XDSdata reduction
XCALIBREdata scaling
HEAVYphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.198 26109 -
obs-24136 88.5 %
Solvent computationSolvent model: TNT / Bsol: 740 Å2 / ksol: 0.97 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 15 202 4334
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01563711
X-RAY DIFFRACTIONt_angle_deg2.0784152
X-RAY DIFFRACTIONt_dihedral_angle_d18.541470
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle00
X-RAY DIFFRACTIONt_trig_c_planes0.0041118
X-RAY DIFFRACTIONt_gen_planes0.005115316
X-RAY DIFFRACTIONt_it042250
X-RAY DIFFRACTIONt_nbd0.0414610
Software
*PLUS
Name: TNT / Version: 4C / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.50
X-RAY DIFFRACTIONt_plane_restr0.00516

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