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- PDB-4ntk: QueD from E. coli -

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Basic information

Entry
Database: PDB / ID: 4ntk
TitleQueD from E. coli
Components6-carboxy-5,6,7,8-tetrahydropterin synthase
KeywordsLYASE / T-fold / 6-PTPS / queuosine biosynthesis enzyme / sepiapterin / C27A
Function / homology
Function and homology information


6-carboxytetrahydropterin synthase / 6-carboxytetrahydropterin synthase activity / tRNA queuosine(34) biosynthetic process / zinc ion binding / identical protein 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
ACETATE ION / Chem-ZSP / 6-carboxy-5,6,7,8-tetrahydropterin synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBandarian, V. / Roberts, S.A. / Miles, Z.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Biochemical and Structural Studies of 6-Carboxy-5,6,7,8-tetrahydropterin Synthase Reveal the Molecular Basis of Catalytic Promiscuity within the Tunnel-fold Superfamily.
Authors: Miles, Z.D. / Roberts, S.A. / McCarty, R.M. / Bandarian, V.
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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 / _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)84,67623
Polymers82,5656
Non-polymers2,11117
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-97 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.070, 112.595, 115.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
6-carboxy-5,6,7,8-tetrahydropterin synthase / CPH4 synthase / Queuosine biosynthesis protein QueD


Mass: 13760.816 Da / Num. of mol.: 6 / Mutation: C27A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2765, JW2735, queD, ygcM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P65870, 6-carboxytetrahydropterin synthase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ZSP / 2-amino-6-[(1Z)-1,2-dihydroxyprop-1-en-1-yl]-7,8-dihydropteridin-4(3H)-one / Sepiapterin (enol-form)


Mass: 237.215 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H11N5O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE MOLECULE BOUND TO THE ZINC IS THE ENOL-FORM OF SEPIAPTERIN

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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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Crystals grown in 3% PEG4000, 0.1 M sodium acetate, pH 4.6. Crystal transfered to 35% PEG8000 and soaked for 1 hour with 7 mM sepiapterin, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9796 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 6, 2011
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.6→38.4 Å / Num. all: 99956 / Num. obs: 98203 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.1 / Num. unique all: 13940 / % possible all: 97

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→36.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.742 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21743 4925 5 %RANDOM
Rwork0.18495 ---
all0.1866 93200 --
obs0.1866 93200 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.55 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5732 0 128 499 6359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196178
X-RAY DIFFRACTIONr_bond_other_d0.0020.025741
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9628428
X-RAY DIFFRACTIONr_angle_other_deg0.837313252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2285743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6423.068264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56615976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5721531
X-RAY DIFFRACTIONr_chiral_restr0.1060.2898
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216918
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021447
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_it1.712.2112947
X-RAY DIFFRACTIONr_mcbond_other1.6982.2072941
X-RAY DIFFRACTIONr_mcangle_it2.4373.3063695
X-RAY DIFFRACTIONr_mcangle_other2.4373.3073696
X-RAY DIFFRACTIONr_scbond_it2.5392.4733231
X-RAY DIFFRACTIONr_scbond_other2.5382.4743232
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6413.6154734
X-RAY DIFFRACTIONr_long_range_B_refined5.12119.2627396
X-RAY DIFFRACTIONr_long_range_B_other5.00518.9157196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 341 -
Rwork0.267 6494 -
obs--93.82 %

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