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- PDB-7pxx: The crystal structure of Leishmania major Pteridine Reductase 1 i... -

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Basic information

Entry
Database: PDB / ID: 7pxx
TitleThe crystal structure of Leishmania major Pteridine Reductase 1 in complex with substrate folic acid
Components(Pteridine reductase ...) x 2
KeywordsOXIDOREDUCTASE / Enzyme-Substrate complex / Rossmann fold / cofactor
Function / homology
Function and homology information


pteridine reductase / 6,7-dihydropteridine reductase activity / pteridine reductase activity / tetrahydrobiopterin biosynthetic process / response to methotrexate / oxidoreductase activity / cytosol
Similarity search - Function
Pteridine reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FOLIC ACID / Chem-NDP / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Pteridine reductase 1
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsDi Pisa, F. / Dello Iacono, L. / Mangani, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)603240European Union
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure of the ternary complex of Leishmania major pteridine reductase 1 with the cofactor NADP + /NADPH and the substrate folic acid.
Authors: Dello Iacono, L. / Di Pisa, F. / Mangani, S.
History
DepositionOct 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pteridine reductase 1
B: Pteridine reductase 1
C: Pteridine reductase 1
D: Pteridine reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,34819
Polymers121,8264
Non-polymers5,52215
Water11,205622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25890 Å2
ΔGint-107 kcal/mol
Surface area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.900, 103.750, 136.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Pteridine reductase ... , 2 types, 4 molecules ABCD

#1: Protein Pteridine reductase 1 / / H region methotrexate resistance protein


Mass: 30456.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: PTR1, HMTXR, L1063.01, LmjF23.0270, LmjF_23_0270 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01782, pteridine reductase
#2: Protein Pteridine reductase 1 / / H region methotrexate resistance protein


Mass: 30456.580 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: PTR1, HMTXR, L1063.01, LmjF23.0270, LmjF_23_0270 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01782, pteridine reductase

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Non-polymers , 6 types, 637 molecules

#3: Chemical
ChemComp-FOL / FOLIC ACID / Folate


Mass: 441.397 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H19N7O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein solution: 12.5 mg/mL in 20 mM Sodium Acetate pH 5.3 and 10 mM DTT; Crystallization buffer: 12% PEG4600, 100 mM Sodium Acetate pH 5.5 and 120-160 mM Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→32.88 Å / Num. obs: 123220 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 18.9 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.4
Reflection shellResolution: 1.81→1.91 Å / Num. unique obs: 17721 / CC1/2: 0.706

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RXC

6rxc


Resolution: 1.81→32.493 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 6123 4.97 %
Rwork0.2271 116974 -
obs0.2291 123097 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.81 Å2 / Biso mean: 23.3248 Å2 / Biso min: 8.21 Å2
Refinement stepCycle: final / Resolution: 1.81→32.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7580 0 371 622 8573
Biso mean--30.32 28.28 -
Num. residues----1034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.81-1.83060.32751750.2924381498
1.8306-1.85210.33042250.28683839100
1.8521-1.87470.31861980.27833838100
1.8747-1.89840.34951940.27853913100
1.8984-1.92340.3172030.26913842100
1.9234-1.94970.29481930.27053857100
1.9497-1.97760.33532240.26013866100
1.9776-2.00710.32132340.2643814100
2.0071-2.03850.28911900.24973892100
2.0385-2.07190.27452070.24683879100
2.0719-2.10760.28491990.23813861100
2.1076-2.14590.26462140.23973854100
2.1459-2.18720.28632100.23983859100
2.1872-2.23180.27862020.23323892100
2.2318-2.28030.2652070.22313877100
2.2803-2.33340.28872120.22983839100
2.3334-2.39170.28322020.23593917100
2.3917-2.45630.31571970.23563883100
2.4563-2.52860.28561940.23313890100
2.5286-2.61020.27631950.22993912100
2.6102-2.70340.28192180.22933908100
2.7034-2.81160.25471920.23083917100
2.8116-2.93950.27652060.22843876100
2.9395-3.09430.2541970.2233933100
3.0943-3.2880.2662040.22433940100
3.288-3.54160.26882080.21183933100
3.5416-3.89750.23911930.20213973100
3.8975-4.46030.19851910.18973987100
4.4603-5.61470.23011940.19324039100
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)
11.2056-0.0251-0.28890.65860.05961.8503-0.018-0.10210.19870.01460.00960.0618-0.0881-0.07630.01970.15370.04450.00860.1255-0.03270.1648-46.922428.033721.0027
21.13590.06450.53480.58910.11611.2879-0.0221-0.01860.1486-0.09940.0321-0.0468-0.1020.00240.04680.1489-0.00130.02920.0837-0.00240.1746-38.452928.597711.6368
30.48540.3416-0.04740.53130.09540.3185-0.05870.03340.0123-0.05270.01520.0501-0.02880.00220.02460.14570.01970.03040.10460.00660.1369-43.711913.36439.7369
41.0906-0.1587-0.97820.8784-0.26621.07490.0070.37670.0415-0.1979-0.0269-0.1168-0.0929-0.1105-0.03410.2795-0.11280.0870.39510.06590.1993-24.297224.5008-22.435
50.76190.1574-0.41940.0401-0.13831.0265-0.08630.39270.191-0.0862-0.0134-0.0979-0.24650.1634-0.22870.3453-0.17870.05530.3390.13080.272-24.777833.3724-21.438
60.8269-0.03520.22750.8324-0.4011.7185-0.09530.31690.2434-0.22730.01840.0857-0.1734-0.0731-0.00280.2684-0.08090.02780.18990.07770.1911-31.063929.1953-14.4254
73.98132.98081.48247.78283.31212.47370.103-0.30850.17370.2704-0.15770.07730.06420.03920.00110.2304-0.04150.07250.14950.02670.2027-28.36331.1096-0.5005
82.01930.21351.36111.37460.90112.3651-0.13510.40260.2269-0.419-0.12180.0355-0.2199-0.36370.21210.2038-0.02620.00760.28630.04650.1629-42.357125.271-21.4685
90.1702-0.29770.07170.8026-0.5840.8621-0.05480.1136-0.0613-0.01040.04170.03030.2172-0.13910.0130.192-0.01260.07710.1857-0.02220.2017-27.170715.8242-4.2113
102.83250.88732.5430.47280.92012.5180.0050.0796-0.0666-0.06360.00270.02530.0628-0.0854-0.01740.1454-0.03080.04610.1230.00370.1142-37.430719.0147-7.0658
110.5392-0.5735-0.0750.7965-0.27650.7366-0.24680.34730.1337-0.06710.0918-0.1845-0.14010.26430.14840.2001-0.0360.06850.1633-0.00330.1822-23.812315.7947-11.1528
121.66480.4860.23070.8881-0.51410.4850.02140.08470.02120.1148-0.1146-0.0953-0.140.06620.03090.1771-0.05470.09480.1816-0.00180.2834-11.15128.754-6.1719
130.5663-0.17580.34270.2562-0.11510.4826-0.06830.2554-0.1398-0.12860.0471-0.14590.010.0107-0.00390.2323-0.04830.09260.1951-0.02750.1608-28.08328.6584-14.3604
141.19350.2029-0.22150.6596-0.41071.0386-0.0021-0.105-0.25260.0444-0.0228-0.10680.1011-0.00120.02890.1653-0.0060.04570.13060.04110.205-39.7803-17.535419.107
152.9805-0.8661-0.31961.74820.57771.62170.01770.19-0.1987-0.1486-0.0817-0.05820.2085-0.15250.06680.1981-0.0250.05450.09740.02290.1773-46.5001-15.57739.0058
161.0325-0.1343-0.00340.29260.08070.35940.0172-0.0114-0.1082-0.0242-0.0074-0.0101-0.03730.0084-0.02560.16990.00080.05930.1175-0.00410.1562-37.555-6.11575.1574
170.03740.233-0.15642.1787-0.04071.6536-0.1555-0.1125-0.24880.04580.0286-0.23890.02240.29140.12430.14320.0240.04760.15050.02680.1674-32.484-1.948514.4118
180.66620.07210.13910.5104-0.01810.4257-0.01-0.0323-0.1429-0.01150.0032-0.1007-0.03950.04930.01180.15970.01380.03890.11610.01250.1305-34.71723.244615.5578
190.265-0.2403-0.31380.50070.21630.78670.07990.0913-0.0285-0.1002-0.01270.0082-0.0794-0.05820.24320.2071-0.05880.13760.3644-0.17430.201-32.0442-13.2682-27.871
201.04620.1224-1.2330.2631-0.49023.8447-0.11530.0406-0.27290.03120.00550.0660.2648-0.20260.32850.2802-0.05840.1460.2224-0.11530.3304-30.2968-22.7964-20.0606
211.2005-0.4362-0.35640.71660.22780.8633-0.00790.1391-0.05590.00030.0422-0.10940.06570.0421-0.01650.2238-0.02850.09140.1916-0.080.2242-30.3572-13.8521-12.6176
224.04840.9615-0.47860.3806-0.29040.25970.00840.00770.0327-0.09090.0479-0.08390.0310.0519-0.02840.194-0.01880.09210.1621-0.04050.1769-30.053-7.219-5.4599
230.0636-0.3252-0.15871.94080.23011.4589-0.09840.1655-0.2832-0.13550.03450.2560.0833-0.25510.10880.228-0.080.07780.3042-0.11890.235-39.6079-1.3624-16.3784
240.616-0.262-0.28220.39160.01660.37370.01320.2293-0.0757-0.19430.0169-0.0591-0.13440.00950.0120.2184-0.05910.06420.2295-0.04370.1469-36.71823.9189-17.4528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 84 )A5 - 84
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 164 )A85 - 164
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 288 )A165 - 288
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 40 )B5 - 40
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 84 )B41 - 84
6X-RAY DIFFRACTION6chain 'B' and (resid 85 through 133 )B85 - 133
7X-RAY DIFFRACTION7chain 'B' and (resid 134 through 148 )B134 - 148
8X-RAY DIFFRACTION8chain 'B' and (resid 149 through 174 )B149 - 174
9X-RAY DIFFRACTION9chain 'B' and (resid 175 through 191 )B175 - 191
10X-RAY DIFFRACTION10chain 'B' and (resid 192 through 215 )B192 - 215
11X-RAY DIFFRACTION11chain 'B' and (resid 216 through 234 )B216 - 234
12X-RAY DIFFRACTION12chain 'B' and (resid 235 through 253 )B235 - 253
13X-RAY DIFFRACTION13chain 'B' and (resid 254 through 288 )B254 - 288
14X-RAY DIFFRACTION14chain 'C' and (resid 6 through 135 )C6 - 135
15X-RAY DIFFRACTION15chain 'C' and (resid 136 through 173 )C136 - 173
16X-RAY DIFFRACTION16chain 'C' and (resid 174 through 215 )C174 - 215
17X-RAY DIFFRACTION17chain 'C' and (resid 216 through 244 )C216 - 244
18X-RAY DIFFRACTION18chain 'C' and (resid 245 through 288 )C245 - 288
19X-RAY DIFFRACTION19chain 'D' and (resid 5 through 54 )D5 - 54
20X-RAY DIFFRACTION20chain 'D' and (resid 55 through 84 )D55 - 84
21X-RAY DIFFRACTION21chain 'D' and (resid 85 through 191 )D85 - 191
22X-RAY DIFFRACTION22chain 'D' and (resid 192 through 215 )D192 - 215
23X-RAY DIFFRACTION23chain 'D' and (resid 216 through 244 )D216 - 244
24X-RAY DIFFRACTION24chain 'D' and (resid 245 through 288 )D245 - 288

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