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- PDB-9l1f: Crystal structure of PpRib7 in complex NADPH (P1 form) -

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Basic information

Entry
Database: PDB / ID: 9l1f
TitleCrystal structure of PpRib7 in complex NADPH (P1 form)
Components2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
KeywordsBIOSYNTHETIC PROTEIN / Riboflavin / reductase / DAROPP
Function / homology2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / : / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / riboflavin biosynthetic process / Dihydrofolate reductase-like domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
Function and homology information
Biological speciesKomagataella pastoris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, S.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)NSTC 113 2311 B 992 001 Taiwan
CitationJournal: To Be Published
Title: Divergence of RibG/Rib7 reductases in riboflavin biosynthesis: A study of Pichia pastoris Rib7 reductase
Authors: Chen, S.C.
History
DepositionDec 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
B: 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7254
Polymers53,2382
Non-polymers1,4872
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-27 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.057, 50.609, 63.246
Angle α, β, γ (deg.)87.66, 86.43, 64.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase / 2 / 5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one reductase / 5-diamino-6-ribitylamino- ...2 / 5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one reductase / 5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate synthase


Mass: 26619.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella pastoris (fungus) / Gene: RIB7, PP7435_Chr3-1080 / Production host: Escherichia coli (E. coli)
References: UniProt: F2QX95, 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) polypropylene glycol 3350, and 0.1 M magnesium formate dehydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 61353 / % possible obs: 96.1 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 23.7
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.28 / Num. unique obs: 11385

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→26.17 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 3042 4.96 %
Rwork0.177 --
obs0.1786 61353 90.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 96 482 4324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073924
X-RAY DIFFRACTIONf_angle_d1.0535356
X-RAY DIFFRACTIONf_dihedral_angle_d10.409526
X-RAY DIFFRACTIONf_chiral_restr0.064644
X-RAY DIFFRACTIONf_plane_restr0.007660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.2702900.19911888X-RAY DIFFRACTION63
1.63-1.650.23421030.19692067X-RAY DIFFRACTION70
1.65-1.680.2321220.18142142X-RAY DIFFRACTION74
1.68-1.710.23361080.18122305X-RAY DIFFRACTION79
1.71-1.750.2421080.18492437X-RAY DIFFRACTION82
1.75-1.780.21341200.19162509X-RAY DIFFRACTION86
1.78-1.820.21721390.18882634X-RAY DIFFRACTION90
1.82-1.860.22931390.18692759X-RAY DIFFRACTION93
1.86-1.910.19781490.19562798X-RAY DIFFRACTION96
1.91-1.960.20361300.18372801X-RAY DIFFRACTION96
1.96-2.020.24371500.18112834X-RAY DIFFRACTION96
2.02-2.080.21251500.18122843X-RAY DIFFRACTION97
2.08-2.160.20611460.1782823X-RAY DIFFRACTION97
2.16-2.240.21991450.17372837X-RAY DIFFRACTION97
2.24-2.350.19351490.17932851X-RAY DIFFRACTION97
2.35-2.470.20311440.18342858X-RAY DIFFRACTION98
2.47-2.620.23851610.18482824X-RAY DIFFRACTION97
2.62-2.830.2341380.1912832X-RAY DIFFRACTION97
2.83-3.110.21351840.18582808X-RAY DIFFRACTION97
3.11-3.560.19021420.17332833X-RAY DIFFRACTION96
3.56-4.480.18841740.15162834X-RAY DIFFRACTION98
4.48-26.170.18461510.16032794X-RAY DIFFRACTION96

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