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- PDB-1g64: THE THREE-DIMENSIONAL STRUCTURE OF ATP:CORRINOID ADENOSYLTRANSFER... -

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Basic information

Entry
Database: PDB / ID: 1g64
TitleTHE THREE-DIMENSIONAL STRUCTURE OF ATP:CORRINOID ADENOSYLTRANSFERASE FROM SALMONELLA TYPHIMURIUM. COBALAMIN/ATP TERNARY COMPLEX
ComponentsCOB(I)ALAMIN ADENOSYLTRANSFERASE
KeywordsTRANSFERASE / P-loop protein / Cobalamin biosynthesis / RecA fold
Function / homology
Function and homology information


corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / porphyrin-containing compound biosynthetic process / cobalamin biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
ATP:cob(I)alamin adenosyltransferase CobA/CobO/BtuR / ATP:corrinoid adenosyltransferase BtuR/CobO/CobP / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / COBALAMIN / Corrinoid adenosyltransferase CobA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, Molecular replacement / Resolution: 2.1 Å
AuthorsRayment, I. / Escalante-Semerena, J.C. / Bauer, C.B.
CitationJournal: Biochemistry / Year: 2001
Title: Three-dimensional structure of ATP:corrinoid adenosyltransferase from Salmonella typhimurium in its free state, complexed with MgATP, or complexed with hydroxycobalamin and MgATP.
Authors: Bauer, C.B. / Fonseca, M.V. / Holden, H.M. / Thoden, J.B. / Thompson, T.B. / Escalante-Semerena, J.C. / Rayment, I.
History
DepositionNov 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 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: COB(I)ALAMIN ADENOSYLTRANSFERASE
B: COB(I)ALAMIN ADENOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9017
Polymers43,5072
Non-polymers2,3935
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-50 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.000, 80.000, 142.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein COB(I)ALAMIN ADENOSYLTRANSFERASE / CORRINOID ADENOSYLTRANSFERASE


Mass: 21753.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: COBA / Production host: Salmonella typhimurium (bacteria) / References: UniProt: P31570, 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-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 278 K / Method: microbatch / pH: 7
Details: 5-9% Peg 3350, 300 mM NaCl, 1 mM MgATP, 1 mM hydroxycobalamin, pH 7.0, microbatch, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
25-9 %PEG335011
3300 mM11NaCl
4imidazole11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923, 0.97947, 0.98325, 0.908
Detector
TypeIDDetectorDate
APS-11CCDJul 1, 1999
MARRESEARCH2IMAGE PLATEJul 1, 1998
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)MADMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.979471
30.983251
40.9081
ReflectionResolution: 2.05→30 Å / Num. all: 29134 / Num. obs: 29134 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 24.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.281 / % possible all: 97.1
Reflection shell
*PLUS
% possible obs: 97.1 % / Num. unique obs: 2803 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
TNTrefinement
CNSrefinement
DMmodel building
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
DMphasing
RefinementMethod to determine structure: MAD, Molecular replacement / Resolution: 2.1→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.288 2943 randomm
Rwork0.206 --
all0.206 29095 -
obs0.206 29095 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 155 292 3216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_dihedral_angle_d0.008
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.7
X-RAY DIFFRACTIONt_plane_restr0.013

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