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- PDB-6d5x: Structure of Human ATP:Cobalamin Adenosyltransferase bound to ATP... -

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Basic information

Entry
Database: PDB / ID: 6d5x
TitleStructure of Human ATP:Cobalamin Adenosyltransferase bound to ATP, Adenosylcobalamin, and Triphosphate
ComponentsCob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial
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 / 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
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
TRIPHOSPHATE / 5'-DEOXYADENOSINE / ADENOSINE-5'-TRIPHOSPHATE / COBALAMIN / Corrinoid adenosyltransferase MMAB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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 1.4Mar 13, 2024Group: 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_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)69,64417
Polymers65,1623
Non-polymers4,48214
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-98 kcal/mol
Surface area22590 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)139,28734
Polymers130,3246
Non-polymers8,96328
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area29760 Å2
ΔGint-273 kcal/mol
Surface area41630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.685, 112.685, 117.939
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
11(chain B and (resid 61 through 80 or resid 82 through 239))
21(chain C and (resid 61 through 80 or resid 82 through 239))

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
11LYSLYSASPASP(chain B and (resid 61 through 80 or resid 82 through 239))BB61 - 807 - 26
12VALVALMETMET(chain B and (resid 61 through 80 or resid 82 through 239))BB82 - 23928 - 185
21LYSLYSASPASP(chain C and (resid 61 through 80 or resid 82 through 239))CC61 - 807 - 26
22VALVALMETMET(chain C and (resid 61 through 80 or resid 82 through 239))CC82 - 23928 - 185

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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)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, 88 molecules

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


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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.32 Å3/Da / Density % sol: 62.92 %
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: 2.4→48.79 Å / Num. obs: 34408 / % possible obs: 99.8 % / Redundancy: 9.9 % / Biso Wilson estimate: 59.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.034 / Rrim(I) all: 0.108 / Net I/σ(I): 14.5 / Num. measured all: 339498 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.4910.11.40434850.7020.4611.47998
8.96-48.799.20.0457390.9980.0160.04899.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.4→48.79 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.37
RfactorNum. reflection% reflection
Rfree0.2121 2013 5.81 %
Rwork0.1839 --
obs0.1856 65432 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.93 Å2 / Biso mean: 69.7322 Å2 / Biso min: 34.71 Å2
Refinement stepCycle: final / Resolution: 2.4→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 290 74 4383
Biso mean--83.42 64.24 -
Num. residues----515
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B1623X-RAY DIFFRACTION18.248TORSIONAL
12C1623X-RAY DIFFRACTION18.248TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4001-2.43050.44471410.441222582399
2.4305-2.46250.43811400.392822782418
2.4625-2.49620.36251390.358122602399
2.4962-2.53190.30131420.306322862428
2.5319-2.56970.30611460.283723232469
2.5697-2.60980.26561380.285622532391
2.6098-2.65260.33831340.278722822416
2.6526-2.69830.28251400.266822582398
2.6983-2.74740.30151410.268223462487
2.7474-2.80020.32661440.275222392383
2.8002-2.85740.2891380.26222972435
2.8574-2.91950.27411400.246323092449
2.9195-2.98740.24521360.222722372373
2.9874-3.06210.22781360.206823302466
3.0621-3.14490.26211360.199922902426
3.1449-3.23740.27531380.20322822420
3.2374-3.34190.23271440.193622862430
3.3419-3.46130.20791420.198422602402
3.4613-3.59990.2361460.18522722418
3.5999-3.76360.22051340.170423122446
3.7636-3.9620.20121440.158822912435
3.962-4.21010.16651440.152622782422
4.2101-4.53490.17231480.131622962444
4.5349-4.99090.15081400.137822542394
4.9909-5.71210.16111440.157722832427
5.7121-7.1930.1941420.170122792421
7.193-48.80410.1511420.132922942436

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