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- PDB-6npa: X-ray crystal structure of TmpB, (R)-1-hydroxy-2-trimethylaminoet... -

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Basic information

Entry
Database: PDB / ID: 6npa
TitleX-ray crystal structure of TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase, with (R)-1-hydroxy-2-trimethylaminoethylphosphonate
ComponentsTmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
KeywordsOXIDOREDUCTASE / organophosphonate / iron oxygenase / HD-domain / gene annotation / enzyme
Function / homologyHD domain / Oxidoreductases / HD domain / HD/PDEase domain / : / : / Chem-KVP / TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
Function and homology information
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_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: TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
B: TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
C: TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
D: TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,15816
Polymers92,2324
Non-polymers92712
Water4,702261
1
A: TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1703
Polymers23,0581
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2815
Polymers23,0581
Non-polymers2234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3544
Polymers23,0581
Non-polymers2963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3544
Polymers23,0581
Non-polymers2963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.110, 151.322, 135.833
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase


Mass: 23057.904 Da / Num. of mol.: 4
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: A0A4V8H040*PLUS, Oxidoreductases
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-KVP / (2R)-2-hydroxy-N,N,N-trimethyl-2-phosphonoethan-1-aminium


Mass: 184.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H15NO4P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.1 Å3/Da / Density % sol: 37.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mg/mL TmpB, 0.2 M calcium chloride, 0.1 M HEPES, pH 7.5, 27-33% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(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: 76571 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Χ2: 0.902 / Net I/σ(I): 7.6 / Num. measured all: 568175
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.767.40.9570.8740.381.030.719100
1.76-1.797.40.8230.9010.3260.8860.755100
1.79-1.837.40.6770.9280.2670.7280.785100
1.83-1.867.40.5220.9580.2060.5620.796100
1.86-1.97.50.4480.970.1760.4820.848100
1.9-1.957.50.3750.9780.1470.4030.861100
1.95-27.50.3130.9830.1230.3360.912100
2-2.057.50.2630.9870.1030.2830.942100
2.05-2.117.50.2210.9890.0870.2381.003100
2.11-2.187.50.1810.9920.0710.1941.035100
2.18-2.267.50.1510.9940.0590.1621.047100
2.26-2.357.50.1310.9940.0520.1411.05999.9
2.35-2.457.50.1070.9960.0420.1151.023100
2.45-2.587.50.0910.9960.0360.0980.967100
2.58-2.757.50.0790.9970.0310.0850.98599.9
2.75-2.967.40.0730.9970.0290.0781.04499.9
2.96-3.267.40.0650.9970.0250.071.07799.9
3.26-3.737.40.0520.9980.020.0560.93599.8
3.73-4.697.20.0360.9990.0140.0390.7399.6
4.69-506.90.0320.9990.0130.0350.48899.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MLM

4mlm


Resolution: 1.73→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.853 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.129
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 3773 5 %RANDOM
Rwork0.2224 ---
obs0.2238 71844 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.85 Å2 / Biso mean: 23.865 Å2 / Biso min: 8.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 32 261 6175
Biso mean--20.99 26.72 -
Num. residues----737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196036
X-RAY DIFFRACTIONr_bond_other_d0.0010.025593
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.9518143
X-RAY DIFFRACTIONr_angle_other_deg0.774312887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.08624.41322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.794151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1051538
X-RAY DIFFRACTIONr_chiral_restr0.0610.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021419
LS refinement shellResolution: 1.718→1.763 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 242 -
Rwork0.295 4372 -
all-4614 -
obs--81.63 %

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