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- PDB-6pd1: PntC-AEPT: fusion protein of phosphonate-specific cytidylyltransf... -

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Basic information

Entry
Database: PDB / ID: 6pd1
TitlePntC-AEPT: fusion protein of phosphonate-specific cytidylyltransferase and 2-aminoethylphosphonate (AEP) transaminase from Treponema denticola
ComponentsNucleotidyl transferase/aminotransferase, class V
KeywordsBIOSYNTHETIC PROTEIN / Phosphonate / Cytidylyltransferase / Cytidine monophosphate- 2-aminoethylphosphonate (CMP-AEP)
Function / homology
Function and homology information


(2-aminoethyl)phosphonate cytidylyltransferase / 2-aminoethylphosphonate-pyruvate transaminase / 2-aminoethylphosphonate-pyruvate transaminase activity / organic phosphonate biosynthetic process / organic phosphonate catabolic process / nucleotidyltransferase activity / metal ion binding
Similarity search - Function
2-aminoethylphosphonate--pyruvate transaminase / MobA-like NTP transferase / MobA-like NTP transferase domain / Aminotransferase class V domain / Aminotransferase class-V / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...2-aminoethylphosphonate--pyruvate transaminase / MobA-like NTP transferase / MobA-like NTP transferase domain / Aminotransferase class V domain / Aminotransferase class-V / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Bifunctional 2-aminoethylphosphonate cytidylyltransferase/aminotransferase
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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 1.2Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 / software / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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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)282,27227
Polymers280,5954
Non-polymers1,67723
Water3,099172
1
A: Nucleotidyl transferase/aminotransferase, class V
C: Nucleotidyl transferase/aminotransferase, class V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,22515
Polymers140,2972
Non-polymers92813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-143 kcal/mol
Surface area47110 Å2
MethodPISA
2
B: Nucleotidyl transferase/aminotransferase, class V
D: Nucleotidyl transferase/aminotransferase, class V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,04612
Polymers140,2972
Non-polymers74910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-151 kcal/mol
Surface area45250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.053, 129.012, 135.797
Angle α, β, γ (deg.)90.00, 92.99, 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 , 6 types, 195 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#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: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.01 M nickel II chloride hexahydrate, 0.1 M Tris-HCl, pH 8.5, 1.0 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→38 Å / Num. obs: 82344 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC1/2: 0.996 / Net I/σ(I): 13
Reflection shellResolution: 2.72→2.77 Å / Num. unique obs: 4114

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JYK, 1VJO

1jyk

1vjo


Resolution: 2.72→38 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.33
RfactorNum. reflection% reflection
Rfree0.2329 4101 4.98 %
Rwork0.1989 --
obs0.2006 82314 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.72→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19241 0 90 172 19503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00519689
X-RAY DIFFRACTIONf_angle_d0.94826603
X-RAY DIFFRACTIONf_dihedral_angle_d7.5211897
X-RAY DIFFRACTIONf_chiral_restr0.0553003
X-RAY DIFFRACTIONf_plane_restr0.0053368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7184-2.75040.34461340.28842701X-RAY DIFFRACTION100
2.7504-2.78390.33141580.27152687X-RAY DIFFRACTION100
2.7839-2.81920.30011390.26492637X-RAY DIFFRACTION100
2.8192-2.85630.29531540.24822691X-RAY DIFFRACTION100
2.8563-2.89540.29181320.24212710X-RAY DIFFRACTION100
2.8954-2.93680.31351290.252692X-RAY DIFFRACTION100
2.9368-2.98060.3261390.24232685X-RAY DIFFRACTION100
2.9806-3.02720.28561330.23652715X-RAY DIFFRACTION100
3.0272-3.07680.29721440.22512700X-RAY DIFFRACTION100
3.0768-3.12990.26971330.21412674X-RAY DIFFRACTION100
3.1299-3.18680.24571580.22512696X-RAY DIFFRACTION100
3.1868-3.24810.27751380.21482663X-RAY DIFFRACTION100
3.2481-3.31440.25871480.21562694X-RAY DIFFRACTION100
3.3144-3.38650.23611470.21342682X-RAY DIFFRACTION100
3.3865-3.46520.27281450.21742689X-RAY DIFFRACTION100
3.4652-3.55190.28511520.20132693X-RAY DIFFRACTION100
3.5519-3.64790.22431310.19422708X-RAY DIFFRACTION100
3.6479-3.75530.22051600.18422678X-RAY DIFFRACTION100
3.7553-3.87650.23921640.19162684X-RAY DIFFRACTION100
3.8765-4.0150.21681540.19272687X-RAY DIFFRACTION100
4.015-4.17580.22341500.1832690X-RAY DIFFRACTION100
4.1758-4.36580.22291280.17082720X-RAY DIFFRACTION100
4.3658-4.5960.19791600.16992650X-RAY DIFFRACTION99
4.596-4.88390.2121400.17232722X-RAY DIFFRACTION100
4.8839-5.2610.19641600.18612684X-RAY DIFFRACTION100
5.261-5.79030.21411080.19492736X-RAY DIFFRACTION100
5.7903-6.6280.22171260.19332734X-RAY DIFFRACTION100
6.628-8.34960.18681090.18072778X-RAY DIFFRACTION100
8.3496-88.97910.15511280.1822733X-RAY DIFFRACTION97

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