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- PDB-9l1h: Crystal structure of PpRib7 -

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Basic information

Entry
Database: PDB / ID: 9l1h
TitleCrystal structure of PpRib7
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 / 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: 2.1 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

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)55,4162
Polymers55,4162
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-16 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.877, 93.732, 113.901
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium acetate tetrahydrate 0.1 M Sodium cacodylate trihydrate pH 6.5 20% w/v Polyethylene glycol 8,000

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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: 2.1→30 Å / Num. obs: 28595 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 20.2
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.76 / Num. unique obs: 28793

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→27.69 Å / SU ML: 0.2396 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2532 1452 5.08 %
Rwork0.1972 27143 -
obs0.2 28595 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.81 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 0 212 3958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893820
X-RAY DIFFRACTIONf_angle_d1.00195196
X-RAY DIFFRACTIONf_chiral_restr0.0627628
X-RAY DIFFRACTIONf_plane_restr0.0091654
X-RAY DIFFRACTIONf_dihedral_angle_d16.83751422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.28261360.2132550X-RAY DIFFRACTION94.91
2.18-2.260.35191380.24542659X-RAY DIFFRACTION98.8
2.26-2.370.29421530.22532687X-RAY DIFFRACTION99.93
2.37-2.490.30171230.22162714X-RAY DIFFRACTION100
2.49-2.650.29051410.21252709X-RAY DIFFRACTION100
2.65-2.850.23761620.20562683X-RAY DIFFRACTION99.96
2.85-3.140.29861610.20872707X-RAY DIFFRACTION100
3.14-3.590.26681470.19492740X-RAY DIFFRACTION100
3.59-4.520.18971480.16842786X-RAY DIFFRACTION100
4.52-27.690.22031430.18122908X-RAY DIFFRACTION99.9

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