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

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Basic information

Entry
Database: PDB / ID: 7rut
TitleStructure of Human ATP:Cobalamin Adenosyltransferase R190C bound to ATP
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 metabolic process / Cobalamin (Cbl) metabolism / 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 / ATP binding
Similarity search - Function
Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Corrinoid adenosyltransferase MMAB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
E: Corrinoid adenosyltransferase
C: Corrinoid adenosyltransferase
F: Corrinoid adenosyltransferase
B: Corrinoid adenosyltransferase
A: Corrinoid adenosyltransferase
D: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,78433
Polymers130,0006
Non-polymers3,78427
Water12,917717
1
E: Corrinoid adenosyltransferase
D: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,94517
Polymers65,0003
Non-polymers1,94514
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area13210 Å2
ΔGint-81 kcal/mol
Surface area21370 Å2
MethodPISA
2
C: Corrinoid adenosyltransferase
F: Corrinoid adenosyltransferase
B: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,83816
Polymers65,0003
Non-polymers1,83913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-93 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.151, 75.769, 95.844
Angle α, β, γ (deg.)90.000, 91.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ECFBAD

#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.: 6 / 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, 744 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% (v/v) 2-propanol, 100 mM Tris pH 8.5, and 30% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→47.9 Å / Num. obs: 176322 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 1.072 / Num. unique obs: 8753 / CC1/2: 0.66

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Processing

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

2idx


Resolution: 1.5→40.494 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 8845 5.02 %
Rwork0.1499 167435 -
obs0.1516 176280 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.32 Å2 / Biso mean: 31.7175 Å2 / Biso min: 13.06 Å2
Refinement stepCycle: final / Resolution: 1.5→40.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8498 0 212 717 9427
Biso mean--23.14 41.58 -
Num. residues----1117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.5-1.5170.29882860.25315645
1.517-1.53490.26432710.2285499
1.5349-1.55360.2562530.2155590
1.5536-1.57330.24952570.20585660
1.5733-1.5940.25132860.20715509
1.594-1.61580.25242700.1935591
1.6158-1.63890.25572730.18445595
1.6389-1.66340.23173080.1725527
1.6634-1.68940.21592770.17135610
1.6894-1.71710.20692500.16035625
1.7171-1.74670.21652850.15325521
1.7467-1.77840.19833340.14965501
1.7784-1.81260.2123160.14915552
1.8126-1.84960.20023210.14675540
1.8496-1.88990.19553730.1445506
1.8899-1.93380.18253330.14345525
1.9338-1.98220.18053120.14535531
1.9822-2.03580.18452790.13325619
2.0358-2.09570.18143200.14075512
2.0957-2.16330.1773200.1385579
2.1633-2.24060.18742900.14025585
2.2406-2.33030.17242550.13735600
2.3303-2.43640.17592990.14085582
2.4364-2.56480.19232930.14275595
2.5648-2.72550.17812720.14745615
2.7255-2.93580.19292730.15275626
2.9358-3.23120.18143320.15155571
3.2312-3.69840.18023320.14795611
3.6984-4.65860.15932850.13325641
4.6586-40.490.16122900.15785772

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