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- PDB-8b5t: Crystal structure of Quinonoid dihydropteridine reductase from Le... -

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Basic information

Entry
Database: PDB / ID: 8b5t
TitleCrystal structure of Quinonoid dihydropteridine reductase from Leishmania major
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, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Dihydropteridine reductase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 major
Authors: Robinson, D.A. / Fairlamb, A.H.
History
DepositionSep 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Quinonoid dihydropteridine reductase
B: Quinonoid dihydropteridine reductase
C: Quinonoid dihydropteridine reductase


Theoretical massNumber of molelcules
Total (without water)71,1233
Polymers71,1233
Non-polymers00
Water6,521362
1
A: Quinonoid dihydropteridine reductase

A: Quinonoid dihydropteridine reductase


Theoretical massNumber of molelcules
Total (without water)47,4162
Polymers47,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area3230 Å2
ΔGint-32 kcal/mol
Surface area18290 Å2
MethodPISA
2
B: Quinonoid dihydropteridine reductase
C: Quinonoid dihydropteridine reductase


Theoretical massNumber of molelcules
Total (without water)47,4162
Polymers47,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-31 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.986, 78.986, 187.649
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-358-

HOH

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Components

#1: Protein Quinonoid dihydropteridine reductase


Mass: 23707.775 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote)
Gene: QDPR-7, QDPR, QDPR-2, QDPR-3, QDPR-4, QDPR-5, QDPR-6, LMJF_34_4360, LMJF_34_4390, LMJF_34_4420, LMJF_34_4450, LMJF_34_4480, LMJF_34_4510
Production host: Escherichia coli (E. coli)
References: UniProt: Q4Q290, 6,7-dihydropteridine reductase, EC: 1.6.99.7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 15% PEG4000, 0.2M MgCl2, 0.1M Na ACETATE pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92045 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92045 Å / Relative weight: 1
ReflectionResolution: 2.1→39.5 Å / Num. obs: 39899 / % possible obs: 99.2 % / Redundancy: 8.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.072 / Net I/σ(I): 19
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3192 / CC1/2: 0.8 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1dir


Resolution: 2.1→39.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.131 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1981 5 %RANDOM
Rwork0.1822 ---
obs0.1848 37914 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.29 Å2 / Biso mean: 36.974 Å2 / Biso min: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å2-0 Å2
2--0.14 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 2.1→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4845 0 0 362 5207
Biso mean---41.61 -
Num. residues----681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134922
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154688
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.6196718
X-RAY DIFFRACTIONr_angle_other_deg1.3871.56910751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27322.872188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40815735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2331523
X-RAY DIFFRACTIONr_chiral_restr0.0670.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025708
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021054
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 131 -
Rwork0.243 2754 -
all-2885 -
obs--97.73 %

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