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- PDB-6npb: X-ray crystal structure of TmpA, 2-trimethylaminoethylphosphonate... -

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Basic information

Entry
Database: PDB / ID: 6npb
TitleX-ray crystal structure of TmpA, 2-trimethylaminoethylphosphonate hydroxylase, with Fe and 2OG
ComponentsTmpA, 2-trimethylaminoethylphosphonate hydroxylase
KeywordsOXIDOREDUCTASE / organophosphonate / iron oxygenase / HD-domain / gene annotation / enzyme
Function / homology
Function and homology information


[2-(trimethylamino)ethyl]phosphonate dioxygenase / gamma-butyrobetaine dioxygenase activity / carnitine biosynthetic process / iron ion binding
Similarity search - Function
Gamma-butyrobetaine hydroxylase / Gamma-butyrobetaine hydroxylase-like, N-terminal / GBBH-like, N-terminal domain superfamily / Gamma-butyrobetaine hydroxylase-like, N-terminal / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / [2-(trimethylamino)ethyl]phosphonate dioxygenase
Similarity search - Component
Biological speciesLeisingera caerulea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsRajakovich, L.J. / Mitchell, A.J. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1330784 United States
CitationJournal: Biochemistry / Year: 2019
Title: A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases.
Authors: Rajakovich, L.J. / Pandelia, M.E. / Mitchell, A.J. / Chang, W.C. / Zhang, B. / Boal, A.K. / Krebs, C. / Bollinger Jr., J.M.
History
DepositionJan 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: 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

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Assembly

Deposited unit
A: TmpA, 2-trimethylaminoethylphosphonate hydroxylase
B: TmpA, 2-trimethylaminoethylphosphonate hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4269
Polymers84,7842
Non-polymers6427
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-110 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.051, 87.051, 220.696
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TmpA, 2-trimethylaminoethylphosphonate hydroxylase


Mass: 42391.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leisingera caerulea (bacteria) / Plasmid: pET-28a(+) / Details (production host): NdeI/XhoI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V8H042*PLUS, Oxidoreductases
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 15 mg/mL TmpA, 1.0-1.4 M lithium sulfate, 1.6-1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 88259 / % possible obs: 98.8 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.024 / Rrim(I) all: 0.07 / Χ2: 0.869 / Net I/σ(I): 10.2 / Num. measured all: 721833
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.767.90.8710.7760.3230.9310.7599.9
1.76-1.798.10.7140.8410.2610.7620.74299.9
1.79-1.838.10.6230.8790.2270.6640.76299.8
1.83-1.868.20.5170.9070.1890.5520.79599.8
1.86-1.98.20.4040.9390.1470.4310.82499.7
1.9-1.958.20.3350.960.1230.3580.85399.8
1.95-28.20.270.9720.0980.2870.87799.6
2-2.058.20.2180.9780.080.2320.89699.5
2.05-2.118.20.1810.9820.0660.1930.91299.5
2.11-2.188.20.1460.9880.0530.1550.94699.4
2.18-2.268.30.1280.9890.0470.1361.01699.2
2.26-2.358.30.1170.990.0430.1251.06599.1
2.35-2.458.30.10.9920.0370.1071.02799
2.45-2.588.30.0820.9940.030.0870.92198.9
2.58-2.758.30.0660.9950.0240.0710.84198.7
2.75-2.968.30.0570.9960.0210.0610.8498.4
2.96-3.268.20.0560.9960.020.061.10297.9
3.26-3.738.20.0450.9970.0160.0481.02197.5
3.73-4.698.10.0320.9980.0120.0350.68896.6
4.69-507.90.0280.9990.010.0290.48894.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O2G

3o2g


Resolution: 1.73→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.274 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.104
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 4424 5 %RANDOM
Rwork0.1931 ---
obs0.194 83209 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.8 Å2 / Biso mean: 21.138 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5886 0 32 464 6382
Biso mean--33.35 24.74 -
Num. residues----755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196055
X-RAY DIFFRACTIONr_bond_other_d0.0010.025513
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.9578222
X-RAY DIFFRACTIONr_angle_other_deg0.694312689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86623.51302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24315936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1341554
X-RAY DIFFRACTIONr_chiral_restr0.0620.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216983
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021435
LS refinement shellResolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 288 -
Rwork0.243 5619 -
all-5907 -
obs--90.71 %

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