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- PDB-8b5u: Crystal structure of Quinonoid dihydropteridine reductase from Le... -

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Basic information

Entry
Database: PDB / ID: 8b5u
TitleCrystal structure of Quinonoid dihydropteridine reductase from Leishmania donovani
ComponentsQuinonoid dihydropteridine reductase
KeywordsOXIDOREDUCTASE / QDPR / LEISHMANIA
Function / homology
Function and homology information


6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / NADPH binding / cytoplasm
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Quinonoid dihydropteridine reductase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRobinson, D.A. / Fairlamb, A.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Quinonoid dihydropteridine reductase from Leishmania donovani
Authors: Robinson, D.A. / Fairlamb, A.H.
History
DepositionSep 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Quinonoid dihydropteridine reductase


Theoretical massNumber of molelcules
Total (without water)25,8521
Polymers25,8521
Non-polymers00
Water2,828157
1
A: Quinonoid dihydropteridine reductase

A: Quinonoid dihydropteridine reductase


Theoretical massNumber of molelcules
Total (without water)51,7042
Polymers51,7042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3260 Å2
ΔGint-32 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.762, 66.762, 242.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

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Components

#1: Protein Quinonoid dihydropteridine reductase / Quinonoid_dihydropteridine_reductase/GeneDB:LmjF. 34.4330/GeneDB:LmjF.34.4360/GeneDB:LmjF.34. ...Quinonoid_dihydropteridine_reductase/GeneDB:LmjF. 34.4330/GeneDB:LmjF.34.4360/GeneDB:LmjF.34.4390/GeneDB:LmjF.34.4420/GeneDB:LmjF.34.4450/GeneDB:LmjF.34.4480/GeneDB:Lmj F.34.4510 / Short chain dehydrogenase family protein


Mass: 25852.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote)
Gene: CGC21_27355, LdCL_340051200, LdCL_340051500, LDHU3_34.6510
Production host: Escherichia coli (E. coli)
References: UniProt: A0A3S5H7Y1, 6,7-dihydropteridine reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 13-18% PEG 8000, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→48.58 Å / Num. obs: 29308 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.017 / Rrim(I) all: 0.071 / Net I/σ(I): 21.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) all% possible allRmerge(I) obsRrim(I) all
1.8-1.8419.517600.7930.477100
9-48.5813.93430.9930.01599.40.0520.055

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DIR

1dir


Resolution: 1.8→47.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.485 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1527 5 %RANDOM
Rwork0.1983 ---
obs0.1994 29308 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.28 Å2 / Biso mean: 41.637 Å2 / Biso min: 24.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å2-0.74 Å2-0 Å2
2---1.48 Å20 Å2
3---4.81 Å2
Refinement stepCycle: final / Resolution: 1.8→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 0 157 1792
Biso mean---54.6 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151593
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.622267
X-RAY DIFFRACTIONr_angle_other_deg1.51.573655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4935225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08322.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93515253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.085158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02362
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 117 -
Rwork0.362 2083 -
all-2200 -
obs--100 %

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