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

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Basic information

Entry
Database: PDB / ID: 6npc
TitleX-ray crystal structure of TmpA, 2-trimethylaminoethylphosphonate hydroxylase, with Fe, 2OG, and 2-trimethylaminoethylphosphonate
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 / : / N,N,N-trimethyl-2-phosphonoethan-1-aminium / [2-(trimethylamino)ethyl]phosphonate dioxygenase
Similarity search - Component
Biological speciesLeisingera caerulea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: TmpA, 2-trimethylaminoethylphosphonate hydroxylase
B: TmpA, 2-trimethylaminoethylphosphonate hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3067
Polymers84,7842
Non-polymers5225
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-66 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.901, 86.901, 220.613
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 526 molecules

#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-KVV / N,N,N-trimethyl-2-phosphonoethan-1-aminium


Mass: 168.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO3P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
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-F / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 16, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 93533 / % possible obs: 99.6 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.019 / Rrim(I) all: 0.055 / Χ2: 0.906 / Net I/σ(I): 11.3 / Num. measured all: 760196
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.737.20.6330.8510.250.6820.814100
1.73-1.7680.550.8950.2050.5880.813100
1.76-1.798.20.4580.930.1670.4880.825100
1.79-1.838.20.3870.9450.1420.4130.827100
1.83-1.878.20.3110.9610.1140.3320.854100
1.87-1.918.20.2560.9730.0940.2730.876100
1.91-1.968.20.2050.9830.0750.2180.882100
1.96-2.028.20.1650.9880.060.1760.882100
2.02-2.078.20.1350.9910.0490.1440.869100
2.07-2.148.20.1120.9940.0410.1190.881100
2.14-2.228.30.0960.9940.0350.1030.96199.9
2.22-2.318.20.090.9940.0330.0961.0899.9
2.31-2.418.30.0830.9950.030.0881.08499.9
2.41-2.548.30.0680.9960.0250.0730.99299.7
2.54-2.78.20.0560.9970.020.060.86999.7
2.7-2.918.20.0490.9980.0180.0520.87699.5
2.91-3.28.20.0510.9970.0190.0541.24799.3
3.2-3.668.20.0410.9980.0150.0441.17399.1
3.66-4.618.10.0280.9990.010.030.73398.5
4.61-507.70.0240.9990.0090.0260.55497

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NPB

6npb


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.023 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.102
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 4543 4.9 %RANDOM
Rwork0.2005 ---
obs0.2014 88905 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 51.23 Å2 / Biso mean: 15.529 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5852 0 27 521 6400
Biso mean--11.16 21.1 -
Num. residues----750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196017
X-RAY DIFFRACTIONr_bond_other_d0.0020.025490
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9558168
X-RAY DIFFRACTIONr_angle_other_deg0.868312634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85423.51302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37115931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7591554
X-RAY DIFFRACTIONr_chiral_restr0.0690.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216939
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021429
LS refinement shellResolution: 1.699→1.743 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 337 -
Rwork0.245 6445 -
all-6782 -
obs--99.3 %

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