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- PDB-1c9k: THE THREE DIMENSIONAL STRUCTURE OF ADENOSYLCOBINAMIDE KINASE/ ADE... -

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Basic information

Entry
Database: PDB / ID: 1c9k
TitleTHE THREE DIMENSIONAL STRUCTURE OF ADENOSYLCOBINAMIDE KINASE/ ADENOSYLCOBINAMIDE PHOSPHATE GUALYLYLTRANSFERASE (COBU) COMPLEXED WITH GMP: EVIDENCE FOR A SUBSTRATE INDUCED TRANSFERASE ACTIVE SITE
ComponentsADENOSYLCOBINAMIDE KINASE
KeywordsTRANSFERASE / ALPHA/BETA STRUCTURE ROSSMANN FOLD P-LOOP
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
GUANOSINE-5'-MONOPHOSPHATE / PHOSPHATE ION / PYROPHOSPHATE 2- / Bifunctional adenosylcobalamin biosynthesis protein CobU
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsThompson, T.B. / Thomas, M.G. / Esclante-Semerena, J.C. / Rayment, I.
Citation
Journal: Biochemistry / Year: 1999
Title: Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site.
Authors: Thompson, T.B. / Thomas, M.G. / Escalante-Semerena, J.C. / Rayment, I.
#1: Journal: Biochemistry / Year: 1998
Title: Three-Dimensional Structure of Adenosylcobinamide Kinase/Adenosylcobinamide Phosphate Guanylyltransferase from Salmonella typhimurium Determined to 2.3 A Resolution
History
DepositionAug 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 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_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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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: ADENOSYLCOBINAMIDE KINASE
B: ADENOSYLCOBINAMIDE KINASE
C: ADENOSYLCOBINAMIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,86410
Polymers59,3843
Non-polymers1,4807
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-65 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.380, 87.770, 101.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein ADENOSYLCOBINAMIDE KINASE / COBU


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) / References: UniProt: Q05599

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Non-polymers , 5 types, 343 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 277 K / Method: batch / pH: 9
Details: 16% PEG 4000 100 MM CACL2 50 MM CHES, pH 9.0, BATCH
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %(w/v)PEG400011
2100 mM11CaCl2
350 mMCHES11

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.072
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 27168 / Num. obs: 26435 / % possible obs: 97.3 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 5.6 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 27.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.227 / % possible all: 94.9
Reflection shell
*PLUS
% possible obs: 94.9 % / Mean I/σ(I) obs: 9.5

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Processing

Software
NameClassification
AMoREphasing
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→30 Å / σ(F): 1.5 / σ(I): 1.5 / Stereochemistry target values: TNT REFINEMENT SOFTWARE
Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE FROM TNT
RfactorNum. reflection% reflection
obs0.191 26435 97.3 %
all-27168 -
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 88 336 4253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg2.32
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.94
X-RAY DIFFRACTIONt_plane_restr0.009

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