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- PDB-7ruu: Structure of Human ATP:Cobalamin Adenosyltransferase R190C bound ... -

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Basic information

Entry
Database: PDB / ID: 7ruu
TitleStructure of Human ATP:Cobalamin Adenosyltransferase R190C bound to adenosylcobalamin
ComponentsCorrinoid adenosyltransferase
KeywordsTRANSFERASE / ATP:cobalamin adenosyl transferase / cobalamin / vitamin B12 / patient mutation
Function / homology
Function and homology information


Defective MMAB causes MMA, cblB type / Cobalamin (Cbl) metabolism / cobalamin metabolic process / corrinoid adenosyltransferase activity / transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / cobalamin binding / mitochondrial matrix / mitochondrion / ATP binding
Similarity search - Function
Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily
Similarity search - Domain/homology
5'-DEOXYADENOSINE / ACETATE ION / COBALAMIN / : / Corrinoid adenosyltransferase MMAB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMascarenhas, R. / Gouda, H. / Koutmos, M. / Banerjee, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK45776 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Patient mutations in human ATP:cob(I)alamin adenosyltransferase differentially affect its catalytic versus chaperone functions.
Authors: Gouda, H. / Mascarenhas, R. / Pillay, S. / Ruetz, M. / Koutmos, M. / Banerjee, R.
History
DepositionAug 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Corrinoid adenosyltransferase
B: Corrinoid adenosyltransferase
C: Corrinoid adenosyltransferase
D: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,40520
Polymers86,6674
Non-polymers6,73916
Water4,468248
1
A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,15618
Polymers65,0003
Non-polymers5,15715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11520 Å2
ΔGint-36 kcal/mol
Surface area18270 Å2
MethodPISA
2
C: Corrinoid adenosyltransferase
D: Corrinoid adenosyltransferase
hetero molecules

B: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,02014
Polymers65,0003
Non-polymers5,02011
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_544-x+y+1/3,-x-1/3,z-1/31
Buried area11730 Å2
ΔGint-36 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.807, 121.807, 171.629
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-302-

K

21A-303-

K

31D-463-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Corrinoid adenosyltransferase / Cob(II)alamin adenosyltransferase / Cob(II)yrinic acid a / c-diamide adenosyltransferase / ...Cob(II)alamin adenosyltransferase / Cob(II)yrinic acid a / c-diamide adenosyltransferase / Cobinamide/cobalamin adenosyltransferase / Methylmalonic aciduria type B protein


Mass: 21666.643 Da / Num. of mol.: 4 / Mutation: R190C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMAB / Production host: Escherichia coli (E. coli) / References: UniProt: Q96EY8, corrinoid adenosyltransferase

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Non-polymers , 5 types, 264 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% (v/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate pH 4.6, 20 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.85→39.75 Å / Num. obs: 80886 / % possible obs: 99.8 % / Redundancy: 10.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.1
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.11 / Num. unique obs: 4590 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IDX

2idx


Resolution: 1.85→36.159 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 4077 5.04 %
Rwork0.1772 76786 -
obs0.1785 80863 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.2 Å2 / Biso mean: 42.0263 Å2 / Biso min: 20.02 Å2
Refinement stepCycle: final / Resolution: 1.85→36.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 459 248 5248
Biso mean--41.09 46.87 -
Num. residues----593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8501-1.87180.3641330.3213261299
1.8718-1.89470.30321300.28932645100
1.8947-1.91860.28551370.26792664100
1.9186-1.94390.25451090.25382669100
1.9439-1.97050.27811020.23622762100
1.9705-1.99870.29161350.22312617100
1.9987-2.02850.23461510.2162650100
2.0285-2.06020.22781410.20932689100
2.0602-2.0940.24081510.21082616100
2.094-2.13010.2261250.20682629100
2.1301-2.16880.21131310.1972680100
2.1688-2.21050.22781580.19222664100
2.2105-2.25560.22631500.18542623100
2.2556-2.30460.21071280.17572653100
2.3046-2.35820.18741550.17382616100
2.3582-2.41720.20091840.18152612100
2.4172-2.48260.19121330.18092686100
2.4826-2.55560.19091260.17962617100
2.5556-2.6380.20821600.1807262799
2.638-2.73230.2251360.18542648100
2.7323-2.84170.20591190.19032670100
2.8417-2.97090.19981830.18362616100
2.9709-3.12750.19451450.17872668100
3.1275-3.32330.21071240.17692632100
3.3233-3.57970.17921630.17262653100
3.5797-3.93950.15921280.16042678100
3.9395-4.50870.19351510.13972630100
4.5087-5.67690.20031440.1672262299
5.6769-36.10.19421450.1642638100

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