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- PDB-6d5k: Structure of Human ATP:Cobalamin Adenosyltransferase bound to ATP... -

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Basic information

Entry
Database: PDB / ID: 6d5k
TitleStructure of Human ATP:Cobalamin Adenosyltransferase bound to ATP, and Adenosylcobalamin
ComponentsCob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrialCob(I)yrinic acid a,c-diamide adenosyltransferase
KeywordsTRANSFERASE / B12 / metabolism / adenosyltransferase
Function / homology
Function and homology information


Defective MMAB causes MMA, cblB type / cobalamin metabolic process / Cobalamin (Cbl) metabolism / corrinoid adenosyltransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / cobalamin binding / transferase activity, transferring alkyl or aryl (other than methyl) groups / mitochondrial matrix / ATP binding
Similarity search - Function
Hypothetical Protein Ta1238; Chain: A; / Cobalamin adenosyltransferase-like / Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
5'-DEOXYADENOSINE / ADENOSINE-5'-TRIPHOSPHATE / COBALAMIN / Corrinoid adenosyltransferase MMAB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsDodge, G.J. / Campanello, G. / Smith, J.L. / 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. Am. Chem. Soc. / Year: 2018
Title: Sacrificial Cobalt-Carbon Bond Homolysis in Coenzyme B12as a Cofactor Conservation Strategy.
Authors: Campanello, G.C. / Ruetz, M. / Dodge, G.J. / Gouda, H. / Gupta, A. / Twahir, U.T. / Killian, M.M. / Watkins, D. / Rosenblatt, D.S. / Brunold, T.C. / Warncke, K. / Smith, J.L. / Banerjee, R.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.formula_weight
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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_ncs_dom_lim
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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,69617
Polymers65,1623
Non-polymers4,53414
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-89 kcal/mol
Surface area22400 Å2
MethodPISA
2
A: Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial
B: Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial
C: Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)139,39134
Polymers130,3246
Non-polymers9,06728
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area21780 Å2
ΔGint-227 kcal/mol
Surface area42910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.252, 112.252, 117.993
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain C and (resid 79 through 130 or resid 141 through 240))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYSchain AAA79 - 24025 - 186
21ASPASPTHRTHR(chain C and (resid 79 through 130 or resid 141 through 240))CC79 - 13025 - 76
22LYSLYSLYSLYS(chain C and (resid 79 through 130 or resid 141 through 240))CC141 - 24087 - 186

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial / Cob(I)yrinic acid a,c-diamide adenosyltransferase / Cob(I)alamin adenosyltransferase / Methylmalonic aciduria type B protein


Mass: 21720.693 Da / Num. of mol.: 3
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 , 7 types, 32 molecules

#2: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 19% PEG 3350, 0.2 M MgSO4, 10 % glycerol

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.5498 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2017
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.68→48.61 Å / Num. obs: 24504 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.074 / Rrim(I) all: 0.232 / Net I/σ(I): 7.6 / Num. measured all: 242325 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.68-2.819.65.16432140.1881.7525.45899.5
8.9-48.619.40.0537540.9980.0180.05699.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.31 Å28.36 Å
Translation6.31 Å28.36 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimless3.24data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2idx

2idx


Resolution: 2.85→48.607 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.56
RfactorNum. reflection% reflection
Rfree0.2394 1705 8.21 %
Rwork0.192 --
obs0.1957 38745 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 203.75 Å2 / Biso mean: 83.9279 Å2 / Biso min: 46.04 Å2
Refinement stepCycle: final / Resolution: 2.85→48.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 296 18 4314
Biso mean--103.62 75.2 -
Num. residues----512
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1392X-RAY DIFFRACTION16.916TORSIONAL
12C1392X-RAY DIFFRACTION16.916TORSIONAL

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