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- PDB-3orf: Crystal Structure of Dihydropteridine Reductase from Dictyosteliu... -

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Basic information

Entry
Database: PDB / ID: 3orf
TitleCrystal Structure of Dihydropteridine Reductase from Dictyostelium discoideum
ComponentsDihydropteridine reductase6,7-dihydropteridine reductase
KeywordsOXIDOREDUCTASE / Alpha-Beta-Alpha Sandwich / Rossmann Fold / OXIDOREDUCTASE (acting on NADH) / NADH binding
Function / homology
Function and homology information


Phenylalanine metabolism / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / phagocytic vesicle / NADPH binding / NAD binding / response to oxidative stress ...Phenylalanine metabolism / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / phagocytic vesicle / NADPH binding / NAD binding / response to oxidative stress / identical protein 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dihydropteridine reductase
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsChen, C. / Zhuang, N.N. / Seo, K.H. / Park, Y.S. / Lee, K.H.
CitationJournal: Febs Lett. / Year: 2011
Title: Structural insights into the dual substrate specificities of mammalian and Dictyostelium dihydropteridine reductases toward two stereoisomers of quinonoid dihydrobiopterin
Authors: Chen, C. / Kim, H.L. / Zhuang, N. / Seo, K.H. / Park, K.H. / Han, C.-D. / Park, Y.S. / Lee, K.H.
History
DepositionSep 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Dihydropteridine reductase
B: Dihydropteridine reductase
C: Dihydropteridine reductase
D: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0508
Polymers107,3964
Non-polymers2,6544
Water2,612145
1
A: Dihydropteridine reductase
B: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0254
Polymers53,6982
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-22 kcal/mol
Surface area19000 Å2
MethodPISA
2
C: Dihydropteridine reductase
D: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0254
Polymers53,6982
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-20 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.808, 129.898, 78.763
Angle α, β, γ (deg.)90.00, 99.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 2 - 231 / Label seq-ID: 22 - 251

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Dihydropteridine reductase / 6,7-dihydropteridine reductase / Quinoid dihydropteridine reductase


Mass: 26849.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_G0272684, qdpr / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86A17, 6,7-dihydropteridine reductase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17% PEG 3350, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 2.16 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.16 Å / Relative weight: 1
ReflectionResolution: 2.16→37 Å / Num. all: 50235 / Num. obs: 46917 / % possible obs: 93.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.081
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.423 / Num. unique all: 50235 / Rsym value: 0.081 / % possible all: 96.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DHR

1dhr


Resolution: 2.16→36.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.783 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24014 2473 5 %RANDOM
Rwork0.18496 ---
obs0.18771 46917 93.57 %-
all-50235 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.939 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.16→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6908 0 176 145 7229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0227232
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.989816
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5295916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.67825.373268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.963151204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3411516
X-RAY DIFFRACTIONr_chiral_restr0.1390.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215288
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0741.54540
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85727268
X-RAY DIFFRACTIONr_scbond_it3.13632692
X-RAY DIFFRACTIONr_scangle_it4.8674.52548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1727 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.75
2Bloose positional0.495
3Cloose positional0.645
4Dloose positional0.525
1Aloose thermal3.8510
2Bloose thermal4.6910
3Cloose thermal4.4310
4Dloose thermal3.6410
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 171 -
Rwork0.281 3058 -
obs-46917 83.74 %
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)
10.5598-0.6233-0.31322.7306-0.14330.4096-0.07080.06790.14310.25690.0972-0.29130.03-0.09-0.02640.06740.0032-0.0770.07290.00260.133313.4284-9.44111.9007
20.4155-1.019-0.50372.51821.31941.41920.39080.07910.2079-0.8537-0.2048-0.5196-0.0895-0.1935-0.1860.46530.04190.20260.120.0760.123418.6517-16.9591-18.1776
30.79360.29180.46781.04390.2810.3146-0.07580.0038-0.0903-0.14670.08780.143-0.0632-0.0044-0.0120.0465-0.0360.02120.1252-0.02590.1254-0.1781-43.46189.4604
40.46370.20040.78211.00480.2532.05380.08180.0251-0.14910.24750.1573-0.20570.10330.1587-0.23920.08930.0405-0.01620.1202-0.0190.140318.4918-44.975634.9267
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 231
2X-RAY DIFFRACTION2B2 - 231
3X-RAY DIFFRACTION3C2 - 231
4X-RAY DIFFRACTION4D2 - 231

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