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- PDB-3qn0: Structure of 6-pyruvoyltetrahydropterin synthase -

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Basic information

Entry
Database: PDB / ID: 3qn0
TitleStructure of 6-pyruvoyltetrahydropterin synthase
Components6-carboxy-5,6,7,8-tetrahydropterin synthase
KeywordsLYASE / 6-pyruvoyltetrahydropterin synthase / BH4 synthase / sepiapterin
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 / 6-carboxy-5,6,7,8-tetrahydropterin synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsSeo, K.H. / Zhuang, N.N. / Lee, K.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural basis of a novel activity of bacterial 6-pyruvoyltetrahydropterin synthase homologues distinct from mammalian 6-pyruvoyltetrahydropterin synthase activity.
Authors: Seo, K.H. / Zhuang, N. / Park, Y.S. / Park, K.H. / Lee, K.H.
History
DepositionFeb 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Experimental preparation
Revision 1.2Dec 25, 2013Group: Structure summary
Revision 1.3May 28, 2014Group: Database references
Revision 1.4Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.5Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-carboxy-5,6,7,8-tetrahydropterin synthase
B: 6-carboxy-5,6,7,8-tetrahydropterin synthase
C: 6-carboxy-5,6,7,8-tetrahydropterin synthase
D: 6-carboxy-5,6,7,8-tetrahydropterin synthase
E: 6-carboxy-5,6,7,8-tetrahydropterin synthase
F: 6-carboxy-5,6,7,8-tetrahydropterin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,17812
Polymers95,7856
Non-polymers3926
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-63 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.853, 117.680, 153.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
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: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 2 - 118 / Label seq-ID: 23 - 139

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
6-carboxy-5,6,7,8-tetrahydropterin synthase / 6-carboxyterahydropterin synthase / PTPS


Mass: 15964.247 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Gene: EcDH1_0923 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C6EJA7, UniProt: A0A140N8U9*PLUS, 6-carboxytetrahydropterin 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.: 22 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.16M tri-ammonium citrate pH 7.0, 16 % PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→93.47 Å / Num. all: 43356 / Num. obs: 43356 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.094 / Rsym value: 0.108
Reflection shellHighest resolution: 2.343 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.094 / Num. unique all: 43356 / Rsym value: 0.108 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QN9

3qn9


Resolution: 2.34→36.571 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 22.168 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26659 2172 5 %RANDOM
Rwork0.22207 ---
all0.23 43356 --
obs0.2244 41012 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.988 Å2
Baniso -1Baniso -2Baniso -3
1--3.21 Å20 Å20 Å2
2--3.12 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.34→36.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5640 0 6 22 5668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0215826
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.9427938
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1985696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61923.023258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44315936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6581530
X-RAY DIFFRACTIONr_chiral_restr0.130.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214446
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9471.53516
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69525724
X-RAY DIFFRACTIONr_scbond_it2.78132310
X-RAY DIFFRACTIONr_scangle_it3.9584.52214
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 941 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.330.5
Bmedium positional0.320.5
Cmedium positional0.330.5
Dmedium positional0.330.5
Emedium positional0.320.5
Fmedium positional0.610.5
Amedium thermal1.952
Bmedium thermal1.152
Cmedium thermal1.312
Dmedium thermal1.272
Emedium thermal1.282
Fmedium thermal1.332
LS refinement shellResolution: 2.343→2.404 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 144 -
Rwork0.361 2949 -
obs--97.36 %
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)
12.29671.0022-2.70651.3348-0.57334.3436-0.05390.25280.2561-0.0747-0.01950.17450.0232-0.12650.07350.29860.03140.0110.74130.66270.642420.351455.646221.3293
21.5047-1.56840.53263.6709-1.11781.28040.0417-0.00760.144-0.127-0.0046-0.17770.00530.0922-0.03710.2583-0.0109-0.04160.48540.42420.426744.251147.552631.8952
34.04840.98610.37251.09960.31910.688-0.0635-0.1388-0.05420.16040.0567-0.0081-0.0117-0.00110.00670.2831-0.0010.0310.40470.38940.399220.758439.081242.9845
43.0494-2.34450.75693.8953-0.53391.9750.02250.34920.1763-0.2276-0.0405-0.26360.09840.07380.0180.3878-0.02850.02190.63880.51650.471633.249136.42044.6415
51.11860.3408-1.5041.4776-0.28035.7060.01710.2556-0.0206-0.10560.01410.1106-0.0073-0.3165-0.03120.2663-0.04350.01020.430.37020.451713.050225.277219.2872
65.03631.99281.1262.47680.55251.60840.0911-0.1905-0.28350.0329-0.1351-0.09540.22760.01030.04390.31730.0467-0.01970.31880.33580.412439.130520.292725.7804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 118
2X-RAY DIFFRACTION2B2 - 118
3X-RAY DIFFRACTION3C2 - 118
4X-RAY DIFFRACTION4D2 - 118
5X-RAY DIFFRACTION5E2 - 118
6X-RAY DIFFRACTION6F2 - 118

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