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- PDB-6pd2: PntC-AEPT: fusion protein of phosphonate-specific cytidylyltransf... -

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Basic information

Entry
Database: PDB / ID: 6pd2
TitlePntC-AEPT: fusion protein of phosphonate-specific cytidylyltransferase and 2-aminoethylphosphonate (AEP) transaminase from Treponema denticola in complex with cytidine monophosphate-AEP
ComponentsNucleotidyl transferase/aminotransferase, class V
KeywordsBIOSYNTHETIC PROTEIN / Phosphonate / Cytidylyltransferase / Cytidine monophosphate- 2-aminoethylphosphonate (CMP-AEP)
Function / homology
Function and homology information


2-aminoethylphosphonate-pyruvate transaminase activity / organic phosphonate catabolic process
Similarity search - Function
2-aminoethylphosphonate--pyruvate transaminase / MobA-like NTP transferase / MobA-like NTP transferase domain / Aminotransferase class V domain / Aminotransferase class-V / Nucleotide-diphospho-sugar transferases / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-0RC / ACETATE ION / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Nucleotidyl transferase/aminotransferase, class V
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSuits, M.D.L. / Whiteside, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2014-05018 Canada
CitationJournal: Nat Commun / Year: 2019
Title: The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis.
Authors: Rice, K. / Batul, K. / Whiteside, J. / Kelso, J. / Papinski, M. / Schmidt, E. / Pratasouskaya, A. / Wang, D. / Sullivan, R. / Bartlett, C. / Weadge, J.T. / Van der Kamp, M.W. / Moreno- ...Authors: Rice, K. / Batul, K. / Whiteside, J. / Kelso, J. / Papinski, M. / Schmidt, E. / Pratasouskaya, A. / Wang, D. / Sullivan, R. / Bartlett, C. / Weadge, J.T. / Van der Kamp, M.W. / Moreno-Hagelsieb, G. / Suits, M.D. / Horsman, G.P.
History
DepositionJun 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleotidyl transferase/aminotransferase, class V
B: Nucleotidyl transferase/aminotransferase, class V
C: Nucleotidyl transferase/aminotransferase, class V
D: Nucleotidyl transferase/aminotransferase, class V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,58163
Polymers280,5954
Non-polymers5,98659
Water26,0681447
1
A: Nucleotidyl transferase/aminotransferase, class V
C: Nucleotidyl transferase/aminotransferase, class V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,45635
Polymers140,2972
Non-polymers3,15933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14710 Å2
ΔGint-75 kcal/mol
Surface area43590 Å2
MethodPISA
2
B: Nucleotidyl transferase/aminotransferase, class V
D: Nucleotidyl transferase/aminotransferase, class V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,12428
Polymers140,2972
Non-polymers2,82726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13430 Å2
ΔGint-97 kcal/mol
Surface area43520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.450, 154.050, 134.580
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Nucleotidyl transferase/aminotransferase, class V


Mass: 70148.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (strain ATCC 35405 / CIP 103919 / DSM 14222) (bacteria)
Strain: ATCC 35405 / CIP 103919 / DSM 14222 / Gene: TDE_1415 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73MU2

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Non-polymers , 8 types, 1506 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-0RC / 5'-O-[(S)-{[(R)-(2-aminoethyl)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine


Mass: 430.245 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H20N4O10P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1447 / 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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate pH 6.5, 20% (w/v) polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.95→48 Å / Num. obs: 221625 / % possible obs: 98.2 % / Redundancy: 6.8 % / CC1/2: 0.989 / Net I/σ(I): 9.8
Reflection shellResolution: 1.95→2.06 Å / Num. unique obs: 31932

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
AutoProcessdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JYK, 1VJO

1jyk

1vjo


Resolution: 1.95→47.976 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.23
RfactorNum. reflection% reflection
Rfree0.254 10985 4.96 %
Rwork0.2204 --
obs0.2221 221487 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→47.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19276 0 367 1447 21090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01119972
X-RAY DIFFRACTIONf_angle_d1.1426955
X-RAY DIFFRACTIONf_dihedral_angle_d9.15412125
X-RAY DIFFRACTIONf_chiral_restr0.0623011
X-RAY DIFFRACTIONf_plane_restr0.0073382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.31933630.28916901X-RAY DIFFRACTION97
1.9722-1.99540.32834050.27086855X-RAY DIFFRACTION97
1.9954-2.01970.30253660.25626941X-RAY DIFFRACTION97
2.0197-2.04530.30273360.25236949X-RAY DIFFRACTION97
2.0453-2.07220.29643700.24836955X-RAY DIFFRACTION97
2.0722-2.10060.31813370.25436914X-RAY DIFFRACTION97
2.1006-2.13060.31423890.25356970X-RAY DIFFRACTION97
2.1306-2.16240.27133770.2396879X-RAY DIFFRACTION98
2.1624-2.19620.29653510.24447020X-RAY DIFFRACTION97
2.1962-2.23220.29363590.24026990X-RAY DIFFRACTION98
2.2322-2.27070.29172830.23967020X-RAY DIFFRACTION98
2.2707-2.31190.28793720.23326982X-RAY DIFFRACTION98
2.3119-2.35640.2923430.23197006X-RAY DIFFRACTION98
2.3564-2.40450.2843700.23897008X-RAY DIFFRACTION98
2.4045-2.45680.30113700.23076975X-RAY DIFFRACTION98
2.4568-2.51390.28283410.23237021X-RAY DIFFRACTION98
2.5139-2.57680.29424030.23386979X-RAY DIFFRACTION98
2.5768-2.64650.2923730.23937072X-RAY DIFFRACTION98
2.6465-2.72430.27683770.24356972X-RAY DIFFRACTION98
2.7243-2.81230.26863890.23547031X-RAY DIFFRACTION98
2.8123-2.91280.27614020.23367014X-RAY DIFFRACTION99
2.9128-3.02940.27523560.24367065X-RAY DIFFRACTION99
3.0294-3.16720.29893440.24257094X-RAY DIFFRACTION99
3.1672-3.33420.2583890.23227080X-RAY DIFFRACTION99
3.3342-3.5430.24023700.23477056X-RAY DIFFRACTION99
3.543-3.81640.24773560.22147149X-RAY DIFFRACTION99
3.8164-4.20030.22023860.19927093X-RAY DIFFRACTION99
4.2003-4.80760.19363700.187127X-RAY DIFFRACTION99
4.8076-6.05520.18773550.17257143X-RAY DIFFRACTION99
6.0552-47.990.15393830.14257241X-RAY DIFFRACTION99

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