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- PDB-9l1i: Crystal structure of PpRib7 in complex with NADPH (P212121 form) -

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Basic information

Entry
Database: PDB / ID: 9l1i
TitleCrystal structure of PpRib7 in complex with NADPH (P212121 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: 2.08 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)56,9034
Polymers55,4162
Non-polymers1,4872
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-26 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.217, 79.439, 139.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 27708.232 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.: 156 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 6.5 45% v/v Polypropylene glycol P 400

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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: RAYONIX MX-225 / Detector: CCD / Date: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→30 Å / Num. obs: 32360 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.2
Reflection shellResolution: 2.08→2.15 Å / Rmerge(I) obs: 0.74 / Num. unique obs: 3194

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→24.75 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 1512 4.85 %
Rwork0.1986 --
obs0.2011 31205 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 96 156 3998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083924
X-RAY DIFFRACTIONf_angle_d0.965356
X-RAY DIFFRACTIONf_dihedral_angle_d17.2591556
X-RAY DIFFRACTIONf_chiral_restr0.063644
X-RAY DIFFRACTIONf_plane_restr0.008660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.150.28181000.21682037X-RAY DIFFRACTION73
2.15-2.220.27231370.21492468X-RAY DIFFRACTION91
2.22-2.310.27011450.2032678X-RAY DIFFRACTION98
2.31-2.420.2631300.21562756X-RAY DIFFRACTION99
2.42-2.540.30181330.21882770X-RAY DIFFRACTION100
2.54-2.70.29221240.22572780X-RAY DIFFRACTION100
2.7-2.910.27791570.20712774X-RAY DIFFRACTION100
2.91-3.20.26181500.2222791X-RAY DIFFRACTION100
3.2-3.670.29611530.20642812X-RAY DIFFRACTION100
3.67-4.610.21651420.16952842X-RAY DIFFRACTION100
4.61-24.750.1921410.1762985X-RAY DIFFRACTION100

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