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- PDB-2oba: Pseudomonas aeruginosa 6-pyruvoyl tetrahydrobiopterin synthase -

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Basic information

Entry
Database: PDB / ID: 2oba
TitlePseudomonas aeruginosa 6-pyruvoyl tetrahydrobiopterin synthase
ComponentsProbable 6-pyruvoyl tetrahydrobiopterin synthase
KeywordsLYASE / Tetrahydrobiopterin biosynthesis / PTP synthase / PTPS
Function / homology
Function and homology information


6-carboxy-5,6,7,8-tetrahydropterin synthase activity / Lyases / queuosine biosynthetic process / metal ion binding
Similarity search - Function
6-pyruvoyl tetrahydropterin synthase/QueD / 6-pyruvoyl tetrahydropterin synthase/QueD family / 6-pyruvoyl tetrahydropterin synthase/QueD superfamily / 6-pyruvoyl tetrahydropterin synthase / Tetrahydropterin Synthase; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
6-carboxy-5,6,7,8-tetrahydropterin synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsMcGrath, T.E. / Kisselman, G. / Battaile, K. / Romanov, V. / Wu-Brown, J. / Guthrie, J. / Virag, C. / Mansoury, K. / Edwards, A.M. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: TO BE PUBLISHED
Title: Pseudomonas aeruginosa 6-pyruvoyl tetrahydrobiopterin synthase
Authors: McGrath, T.E. / Kisselman, G. / Battaile, K. / Romanov, V. / Wu-Brown, J. / Guthrie, J. / Virag, C. / Mansoury, K. / Edwards, A.M. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionDec 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_asym_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.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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 999SEQUENCE Residue MSE 19 is a cloning artifact and a modified residue

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 6-pyruvoyl tetrahydrobiopterin synthase
B: Probable 6-pyruvoyl tetrahydrobiopterin synthase
C: Probable 6-pyruvoyl tetrahydrobiopterin synthase
D: Probable 6-pyruvoyl tetrahydrobiopterin synthase
E: Probable 6-pyruvoyl tetrahydrobiopterin synthase
F: Probable 6-pyruvoyl tetrahydrobiopterin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,84712
Polymers96,4556
Non-polymers3926
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14240 Å2
ΔGint-297 kcal/mol
Surface area29200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.082, 87.521, 124.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 6 / Auth seq-ID: 1 - 118 / Label seq-ID: 21 - 138

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsThe biological assembly is the hexamer contained in the asymmetric unit

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Components

#1: Protein
Probable 6-pyruvoyl tetrahydrobiopterin synthase


Mass: 16075.805 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: 633 / Gene: PA2666 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9I0H2, 6-pyruvoyltetrahydropterin synthase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.2M lithium sulphate, 0.1M Tris HCl, 30% PEG3000 frozen in 70%paratone/30% mineral oil, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 7, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→42.22 Å / Num. all: 35610 / Num. obs: 33806 / % possible obs: 98.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Χ2: 1.025 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.32-2.43.20.25133720.893194.8
2.4-2.53.30.21534750.878197.3
2.5-2.613.30.16135550.847199.9
2.61-2.753.30.1335670.914199.9
2.75-2.923.30.08335900.893199.9
2.92-3.153.30.05735870.983199.8
3.15-3.473.30.04335881.162199.6
3.47-3.973.30.03336151.283199.2
3.97-53.30.02536271.12198.9
5-503.20.02536341.268194.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
JDirectordata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B66

1b66


Resolution: 2.33→42.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.375 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.371 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1769 5 %RANDOM
Rwork0.186 ---
obs0.189 33806 97.7 %-
all-35610 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.765 Å2
Baniso -1Baniso -2Baniso -3
1-4.14 Å20 Å20 Å2
2---1.47 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 2.33→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 6 259 6215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216157
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.938347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83423.292325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.421151019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3641543
X-RAY DIFFRACTIONr_chiral_restr0.1110.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024823
X-RAY DIFFRACTIONr_nbd_refined0.2030.22684
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23949
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.211
X-RAY DIFFRACTIONr_mcbond_it0.7231.53744
X-RAY DIFFRACTIONr_mcangle_it1.16225859
X-RAY DIFFRACTIONr_scbond_it1.91732776
X-RAY DIFFRACTIONr_scangle_it3.0674.52486
Refine LS restraints NCS

Ens-ID: 1 / Number: 960 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.445
2BLOOSE POSITIONAL0.455
3CLOOSE POSITIONAL0.435
4DLOOSE POSITIONAL0.445
5ELOOSE POSITIONAL0.485
6FLOOSE POSITIONAL0.595
1ALOOSE THERMAL2.3510
2BLOOSE THERMAL2.4410
3CLOOSE THERMAL2.1410
4DLOOSE THERMAL1.9210
5ELOOSE THERMAL1.9710
6FLOOSE THERMAL1.9810
LS refinement shellResolution: 2.327→2.387 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 110 -
Rwork0.211 2122 -
obs-2232 85.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.87070.5341-0.8684.8311-1.35323.79090.02420.17610.0251-0.0991-0.0176-0.219-0.22820.2494-0.0066-0.17290.04030.0032-0.2355-0.0137-0.19165.27711.917227.1761
23.17750.98152.09671.43030.84544.39850.05210.02810.2850.0051-0.1229-0.0193-0.50540.28260.0707-0.0355-0.06870.0758-0.08380.0235-0.091922.549314.06166.9805
31.403-1.6843-2.25862.7412.73624.9623-0.08890.235-0.0381-0.037-0.05820.18740.0501-0.31620.1471-0.0684-0.06730.0152-0.0892-0.02-0.11441.6998-2.79094.9119
41.9386-0.4878-0.85784.63161.37552.54440.00810.1354-0.0922-0.11270.0035-0.26920.03650.1959-0.0116-0.1830.0149-0.0069-0.2180.0214-0.153511.8557-15.754931.3406
55.37990.16951.9341.63180.1383.6927-0.23380.0783-0.0839-0.0990.066-0.31560.20810.4460.1678-0.01110.07770.1001-0.0939-0.0315-0.036426.5705-17.02468.9142
61.88781.9476-2.51993.0761-3.08645.5747-0.01980.091-0.26170.0911-0.1626-0.4603-0.12040.63290.1824-0.1442-0.0591-0.04290.0817-0.0079-0.032133.9427-0.622628.8266
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 118 / Label seq-ID: 21 - 138

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD
55EE
66FF

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