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- PDB-4hut: Structure of ATP:co(I)rrinoid adenosyltransferase (CobA) from Sal... -

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Basic information

Entry
Database: PDB / ID: 4hut
TitleStructure of ATP:co(I)rrinoid adenosyltransferase (CobA) from Salmonella enterica in complex with four and five-coordinate cob(II)alamin and ATP
ComponentsCob(I)yrinic acid a,c-diamide adenosyltransferase
KeywordsTRANSFERASE
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 enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMoore, T.C. / Newmister, S.A. / Rayment, I. / Escalante-Semerena, J.C.
CitationJournal: Biochemistry / Year: 2012
Title: Structural Insights into the Mechanism of Four-Coordinate Cob(II)alamin Formation in the Active Site of the Salmonella enterica ATP:Co(I)rrinoid Adenosyltransferase Enzyme: Critical Role of ...Title: Structural Insights into the Mechanism of Four-Coordinate Cob(II)alamin Formation in the Active Site of the Salmonella enterica ATP:Co(I)rrinoid Adenosyltransferase Enzyme: Critical Role of Residues Phe91 and Trp93.
Authors: Moore, T.C. / Newmister, S.A. / Rayment, I. / Escalante-Semerena, J.C.
History
DepositionNov 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_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

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Assembly

Deposited unit
A: Cob(I)yrinic acid a,c-diamide adenosyltransferase
B: Cob(I)yrinic acid a,c-diamide adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,11610
Polymers42,2682
Non-polymers3,8488
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-25 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.862, 74.223, 92.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cob(I)yrinic acid a,c-diamide adenosyltransferase / Cob(I)alamin adenosyltransferase / Corrinoid adenosyltransferase


Mass: 21134.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: btuR, cobA, STM1718 / Plasmid: pCOBA15
Production host: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain (production host): JE2884 / References: UniProt: P31570, corrinoid adenosyltransferase

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Non-polymers , 5 types, 331 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 19.6% PEG4000, 320 mM NaCl, pH 6.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: SBC-3 / Detector: CCD / Date: Apr 25, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 30567 / Num. obs: 30078 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.091 / Χ2: 2.469 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.984.80.73214971.779199.8
1.98-2.024.80.53914801.766199.7
2.02-2.064.80.46814991.781199.5
2.06-2.14.80.415001.783199.6
2.1-2.154.80.34814931.805199.7
2.15-2.24.80.31714931.856199.6
2.2-2.254.80.29515171.931199.1
2.25-2.314.90.25414851.883198.9
2.31-2.384.90.22615092.056199.1
2.38-2.464.80.21614922.106199.1
2.46-2.544.80.17915002.122199.2
2.54-2.654.80.14915042.234198.5
2.65-2.774.80.1314992.309199.1
2.77-2.914.80.11114902.635198.3
2.91-3.14.80.09415202.804198.4
3.1-3.334.70.07715183.235198.3
3.33-3.674.60.06515033.706197.6
3.67-4.24.40.05815144.058197.1
4.2-5.294.30.05515264.25196.2
5.29-503.80.05315394.166191.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G5R

1g5r


Resolution: 1.95→29.87 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.975 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 1514 5.1 %RANDOM
Rwork0.1752 ---
all0.178 30679 --
obs0.178 29962 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.34 Å2 / Biso mean: 34.4362 Å2 / Biso min: 18.74 Å2
Baniso -1Baniso -2Baniso -3
1-3.49 Å20 Å2-0 Å2
2---0.41 Å20 Å2
3----3.08 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 227 323 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193069
X-RAY DIFFRACTIONr_angle_refined_deg2.2081.9974207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04123.798129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74515464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9461521
X-RAY DIFFRACTIONr_chiral_restr0.1470.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212425
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 115 -
Rwork0.239 1962 -
all-2077 -
obs--92.64 %

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