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- PDB-7v0f: Structure of 6-carboxy-5,6,7,8-tetrahydropterin synthase paralog ... -

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Basic information

Entry
Database: PDB / ID: 7v0f
TitleStructure of 6-carboxy-5,6,7,8-tetrahydropterin synthase paralog QueD2 from Acinetobacter baumannii
Components6-carboxy-5,6,7,8-tetrahydropterin synthase
KeywordsLYASE / queuosine / transfer RNA / translation elongation / Zn metalloenzyme / nutritional immunity
Function / homology6-carboxytetrahydropterin synthase / 6-carboxy-5,6,7,8-tetrahydropterin synthase activity / 6-pyruvoyl tetrahydropterin synthase/QueD family / 6-pyruvoyl tetrahydropterin synthase/QueD superfamily / 6-pyruvoyl tetrahydropterin synthase / metal ion binding / DI(HYDROXYETHYL)ETHER / 6-carboxy-5,6,7,8-tetrahydropterin synthase
Function and homology information
Biological speciesAcinetobacter baumannii ATCC 17978 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsJordan, M.R. / Gonzalez-Gutierrez, G. / Giedroc, D.P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118157 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI110171 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM109825 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM131994 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Metal retention and replacement in QueD2 protect queuosine-tRNA biosynthesis in metal-starved Acinetobacter baumannii.
Authors: Jordan, M.R. / Gonzalez-Gutierrez, G. / Trinidad, J.C. / Giedroc, D.P.
History
DepositionMay 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6448
Polymers46,2142
Non-polymers4306
Water61334
1
A: 6-carboxy-5,6,7,8-tetrahydropterin synthase
B: 6-carboxy-5,6,7,8-tetrahydropterin synthase
hetero molecules

A: 6-carboxy-5,6,7,8-tetrahydropterin synthase
B: 6-carboxy-5,6,7,8-tetrahydropterin synthase
hetero molecules

A: 6-carboxy-5,6,7,8-tetrahydropterin synthase
B: 6-carboxy-5,6,7,8-tetrahydropterin synthase
hetero molecules

A: 6-carboxy-5,6,7,8-tetrahydropterin synthase
B: 6-carboxy-5,6,7,8-tetrahydropterin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,57632
Polymers184,8578
Non-polymers1,71924
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area29890 Å2
ΔGint-665 kcal/mol
Surface area51110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.060, 84.060, 122.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

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


Mass: 23107.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 17978 (bacteria)
Gene: A7M90_11685, AB945B12_03522, Aba9201_05020, ABCAM1_1682, ABKPCSM17A_00528, ABR2091_1604, ACX61_10285, APC21_11720, APD31_06340, AUO97_15390, B9X95_12070, C2U32_04285, CBE85_10595, DOL94_12095, ...Gene: A7M90_11685, AB945B12_03522, Aba9201_05020, ABCAM1_1682, ABKPCSM17A_00528, ABR2091_1604, ACX61_10285, APC21_11720, APD31_06340, AUO97_15390, B9X95_12070, C2U32_04285, CBE85_10595, DOL94_12095, E1A86_09590, E1A87_16305, EA706_07350, EA722_05115, EGM95_11990, EKS29_14165, EWO96_00585, F2P40_09185, FGL68_05460, FJU36_05345, FQK04_11425, FR761_08970, G3N53_00580, GSE42_09090, GUK62_05625, H0529_06425, HB367_04620, IMO23_08060, ITE13_09665, SAMEA104305318_01743, SAMEA104305385_02424, SI89_17865
Production host: Escherichia coli (E. coli)
References: UniProt: A0A081GYS3, 6-carboxytetrahydropterin synthase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Bis-Tris 0.1 M pH 6.5, 0.2 M NaF and 18-20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003,1.27819
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.000031
21.278191
ReflectionResolution: 2.35→42.64 Å / Num. obs: 17654 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 46.55 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Rrim(I) all: 0.102 / Rsym value: 0.095 / Net I/σ(I): 15.1
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 898 / CC1/2: 0.75 / Rpim(I) all: 0.598 / Rrim(I) all: 1.598 / Rsym value: 1.481 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→42.64 Å / SU ML: 0.376 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.274 2037 5.88 %
Rwork0.2372 32622 -
obs0.2394 17637 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.09 Å2
Refinement stepCycle: LAST / Resolution: 2.35→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 15 34 2916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852944
X-RAY DIFFRACTIONf_angle_d1.10143965
X-RAY DIFFRACTIONf_chiral_restr0.0593423
X-RAY DIFFRACTIONf_plane_restr0.0094507
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.45031240.36472172X-RAY DIFFRACTION99.18
2.41-2.470.42311450.35052152X-RAY DIFFRACTION99.52
2.47-2.530.41251300.33582224X-RAY DIFFRACTION99.66
2.53-2.610.33341230.32572197X-RAY DIFFRACTION99.44
2.61-2.690.35011530.30912150X-RAY DIFFRACTION99.48
2.69-2.790.30061320.30172162X-RAY DIFFRACTION99.7
2.79-2.90.30161400.2882194X-RAY DIFFRACTION99.74
2.9-3.030.3081680.29432181X-RAY DIFFRACTION99.87
3.03-3.190.29921330.26712165X-RAY DIFFRACTION99.61
3.19-3.390.30671530.24442159X-RAY DIFFRACTION99.66
3.39-3.650.3451830.2412211X-RAY DIFFRACTION97.7
3.65-4.020.28271280.2362120X-RAY DIFFRACTION97.11
4.02-4.60.23451580.18162161X-RAY DIFFRACTION99.66
4.6-5.790.20381260.18362182X-RAY DIFFRACTION99.91
5.8-42.640.19861410.19242192X-RAY DIFFRACTION99.19
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)
15.09115012465-2.818150261012.026606333587.45442410779-2.603382107624.294183903550.021915359167-0.257804894380.558337367062-0.0208470254975-0.209097314716-0.165785124619-0.07811260682170.1230247052250.1823066741650.248473231221-0.02771026692090.07996447099420.2887234963560.0527865091130.50812534277325.2594201019-44.1679975982-18.0732587875
29.512382630653.94649025278-2.201762095635.403280058231.203061590988.92178794454-0.4461590564620.3686750615230.6244520370330.2001218879470.3650592052182.66624250817-1.25062420595-0.90199695354-0.05867559617320.6092178130580.30259427560.06487358213050.846790679970.1287665305011.1199462358515.1498112024-16.3394705206-17.6705997626
33.55594927175-0.7290020714360.932707610527.74187838342-2.317637643723.06150436261-0.0649778979625-0.309424193381-0.6791291857590.4825095481310.3113690775720.9957636805740.116125733909-0.227808609511-0.2933784936960.2505435871630.02469840995070.1361659143190.4452059329990.05656488666110.60988018132324.7344095982-50.0266864564-15.9880429522
44.223634964320.485039852882-0.3855639239222.817519349571.285164660173.51287356397-0.0861641784434-0.1048710350430.1890035925480.100383072054-0.05690164167221.0383591763-0.294452025022-0.2037857280390.1225656197420.278120669434-0.01563821358580.1018818888890.3322202935830.01549311380760.67894692922413.2206338687-38.6044220694-17.9881396995
55.564230200951.071083775380.7529510649617.106423313790.3058133985145.072848635140.0073675714202-0.671679633638-0.1772734994880.948650216315-0.05728723486110.441115876685-0.127557267166-0.009630023890390.03275047158770.2783707910710.03012880812080.08260053699940.3836860250250.01869040776510.38087166972126.4338450511-42.3304228268-10.6178751507
63.271457872261.529304516990.4953225649515.6006906502-0.4957951756290.7795597423240.210143022227-0.763382036692-0.1762056434120.723247135093-0.2243842688391.097173821120.200997908136-0.2549920869680.007497877587850.387882908885-0.02109274918150.1956907742430.550902158729-0.02518450697310.8419244456759.56494007933-46.5819505203-12.8426493874
74.58734520306-0.111225772862-1.103724640884.4743927433-0.4155536861745.764150826420.3504966799860.8251254436060.130314652604-0.5247301831830.01683293773760.672476262208-0.143055364217-0.455440845165-0.1975879766610.465416306390.00766727721211-0.1375874468240.4982104846420.1520303780250.3772585189727.0522664607-31.6369406167-39.0090351249
83.16449529723-1.51536245165-4.946162457130.5441934033792.220435019257.512836913290.730220368380.5780334576591.08881187216-0.128263272557-0.0287534500649-0.00619251493993-1.49598186138-0.609571908419-0.6079211854971.19934551969-0.156535038031-0.03213954713771.194543866010.2462147761141.1297028193441.315652202-15.4016904637-44.589184586
93.67940969404-1.78885939383-0.01234370120632.65848864665-0.9192384335935.281809882980.3213312053010.9381780729720.997953343513-0.08665792944870.07615694768710.969089277965-0.399478902872-1.05207755522-0.3470001278530.6617024200040.171898655408-0.1106421210080.7178605233970.3160526650880.93903752659416.0539278309-24.5511955133-37.2598884767
103.96755883580.876545768579-1.224051463773.76499693072-1.522607548284.56593896384-0.1478091188720.9656902495120.897098942545-0.6447884779580.2363809460690.695263910301-0.931408603543-0.63305721544-0.1478275817780.8269419300690.0392225091595-0.2991818631610.712454524080.2840816849460.6180509977524.3424705034-24.4564166119-45.6216389875
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 15 )AA0 - 151 - 16
22chain 'A' and (resid 16 through 25 )AA16 - 2517 - 26
33chain 'A' and (resid 26 through 53 )AA26 - 5327 - 54
44chain 'A' and (resid 54 through 114 )AA54 - 11455 - 115
55chain 'A' and (resid 115 through 149 )AA115 - 149116 - 142
66chain 'A' and (resid 150 through 188 )AA150 - 188143 - 181
77chain 'B' and (resid 0 through 40 )BF0 - 401 - 34
88chain 'B' and (resid 41 through 54 )BF41 - 5435 - 48
99chain 'B' and (resid 55 through 99 )BF55 - 9949 - 93
1010chain 'B' and (resid 100 through 185 )BF100 - 18594 - 169

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