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- PDB-4ntn: E.coli QueD, SeMet protein, 2A resolution -

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Basic information

Entry
Database: PDB / ID: 4ntn
TitleE.coli QueD, SeMet protein, 2A resolution
Components6-carboxy-5,6,7,8-tetrahydropterin synthase
KeywordsLYASE / T-fold / 6-PTPS / queuosine biosynthesis enzyme / sepiapterin
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
FORMIC ACID / 6-carboxy-5,6,7,8-tetrahydropterin synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 / Item: _software.name
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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.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_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)84,32113
Polymers83,8836
Non-polymers4387
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13710 Å2
ΔGint-293 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.080, 111.760, 161.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 13980.462 Da / Num. of mol.: 6
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 5% MPD, 50 mM sodium acetate, 40 mM CaCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.99→55.8 Å / Num. all: 66155 / Num. obs: 66142 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.4
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.2 / Num. unique all: 9592 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
REFMAC5.7.0032refinement
CrystalCleardata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→55.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.803 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.159 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22219 3360 5.1 %RANDOM
Rwork0.20312 ---
obs0.2041 62782 99.83 %-
all-62782 --
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: 39.506 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2---2.78 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.99→55.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 9 127 5826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195900
X-RAY DIFFRACTIONr_bond_other_d0.0020.025541
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.958034
X-RAY DIFFRACTIONr_angle_other_deg0.716312799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39723.13262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59615906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8861530
X-RAY DIFFRACTIONr_chiral_restr0.0690.2875
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021370
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_it0.962.5892849
X-RAY DIFFRACTIONr_mcbond_other0.962.5912850
X-RAY DIFFRACTIONr_mcangle_it1.5713.8723556
X-RAY DIFFRACTIONr_mcangle_other1.5713.8733557
X-RAY DIFFRACTIONr_scbond_it1.2332.7153051
X-RAY DIFFRACTIONr_scbond_other1.2322.7163052
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.884.0144479
X-RAY DIFFRACTIONr_long_range_B_refined3.40420.8836420
X-RAY DIFFRACTIONr_long_range_B_other3.40420.8896421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 255 -
Rwork0.303 4584 -
obs--99.9 %
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)
13.82571.6621-1.63551.5776-1.42411.44270.13840.01650.19310.08120.00770.14440.02560.0545-0.14610.1223-0.01760.02920.1331-0.0050.0887-10.31719.80331.97
23.56881.40820.13532.22820.11571.2145-0.01720.1349-0.19120.12620.014-0.17350.03450.09250.00330.0431-0.0168-0.01420.08350.04570.0815-7.69914.9732.146
30.87080.00150.16690.99880.78642.6394-0.02610.08620.16270.0707-0.0672-0.0227-0.04590.0220.09330.0471-0.00730.04930.15390.01890.1316-2.07141.9321.823
416.86237.81069.51018.94963.89247.8060.0416-0.4487-0.23490.0910.2319-0.3137-0.0801-0.1641-0.27360.07240.03690.05990.10430.00130.0738-1.59533.13424.855
53.0037-2.46150.17034.88150.31960.1920.05240.07880.05630.0483-0.12550.03420.0848-0.08610.07310.0712-0.04380.0520.12480.01490.0849-33.58122.7326.987
62.9157-1.87070.98991.9186-0.23821.5514-0.0729-0.05520.063-0.05060.07110.1295-0.1138-0.02860.00180.0657-0.04670.03810.13660.02330.1697-38.3320.99529.12
73.12273.1821-0.46853.4564-0.74991.13890.06880.13930.10770.0645-0.00890.1641-0.0551-0.0793-0.05990.03890.03840.05020.2029-0.02320.0978-22.49629.7219.242
84.45531.5286-0.26112.303-0.01561.3812-0.04930.1678-0.1874-0.10020.05190.03060.0452-0.1119-0.00260.0454-0.00090.02970.1518-0.0090.0405-22.1226.9714.224
91.043-1.05480.5863.6414-0.11630.4470.0889-0.11660.05570.0159-0.0956-0.01960.0462-0.06010.00670.0616-0.02240.06640.1358-0.01370.0767-15.71138.14341.472
102.967-1.58810.62213.5696-0.91151.2523-0.047-0.2667-0.03030.27740.11750.04160.0403-0.0734-0.07050.1085-0.02380.05010.0923-0.03210.0487-17.29640.17646.578
111.024-0.5155-0.36210.50570.99925.03190.07620.060.14410.0106-0.04440.07050.0301-0.2194-0.03190.06450.01530.0630.0965-0.00340.2129-31.03344.89322.785
121.62780.37941.09662.38181.10075.0127-0.05990.0770.1049-0.2462-0.0840.1605-0.2888-0.0080.14380.07240.0360.02260.0542-0.01220.1151-33.34349.5721.251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 52
2X-RAY DIFFRACTION2A53 - 120
3X-RAY DIFFRACTION3B3 - 107
4X-RAY DIFFRACTION4B108 - 121
5X-RAY DIFFRACTION5C4 - 51
6X-RAY DIFFRACTION6C52 - 120
7X-RAY DIFFRACTION7D3 - 51
8X-RAY DIFFRACTION8D52 - 121
9X-RAY DIFFRACTION9E2 - 52
10X-RAY DIFFRACTION10E53 - 120
11X-RAY DIFFRACTION11F4 - 52
12X-RAY DIFFRACTION12F53 - 121

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