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- PDB-4ha7: Structural insights into the reduction mechanism of Saccharomyces... -

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Basic information

Entry
Database: PDB / ID: 4ha7
TitleStructural insights into the reduction mechanism of Saccharomyces cerevisia Riboflavin Biosynthesis Reductase Rib7
Components2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
KeywordsOXIDOREDUCTASE / reductase / NADPH binding
Function / homology
Function and homology information


2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / NADP binding
Similarity search - Function
Riboflavin-specific deaminase, C-terminal / : / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsLv, Z. / Sun, J. / Liu, Y.
CitationJournal: Plos One / Year: 2013
Title: Structural and functional insights into Saccharomyces cerevisiae riboflavin biosynthesis reductase RIB7.
Authors: Lv, Z. / Sun, J. / Liu, Y.
History
DepositionSep 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)55,1152
Polymers55,1152
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-19 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.500, 68.623, 148.954
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 / DAROPP reductase / DARP reductase / 2 / 5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one ...DAROPP reductase / DARP reductase / 2 / 5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one reductase / 2 / 5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate synthase / DARIPP synthase


Mass: 27557.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RIB7, YBR153W, YBR1203 / Production host: Escherichia coli (E. coli)
References: UniProt: P33312, 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M Calcium chloride dihydrate, 0.1M BIS-TRIS, 30% v/v Polyethylene glycol monomethyl ether 550 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→36.75 Å / Num. all: 27980 / Num. obs: 27560 / % possible obs: 98.5 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.14 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→36.749 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2661 1375 4.99 %
Rwork0.1997 --
obs0.203 27560 97.61 %
all-27560 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.15 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4455 Å2-0 Å20 Å2
2---6.5063 Å2-0 Å2
3---7.9517 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3373 0 0 141 3514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083442
X-RAY DIFFRACTIONf_angle_d1.2354673
X-RAY DIFFRACTIONf_dihedral_angle_d16.4961281
X-RAY DIFFRACTIONf_chiral_restr0.094546
X-RAY DIFFRACTIONf_plane_restr0.005590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0953-2.17010.29621240.23142527X-RAY DIFFRACTION96
2.1701-2.2570.27861390.22072580X-RAY DIFFRACTION99
2.257-2.35970.35071380.22632621X-RAY DIFFRACTION99
2.3597-2.48410.28411320.23072607X-RAY DIFFRACTION99
2.4841-2.63970.30651570.21022633X-RAY DIFFRACTION99
2.6397-2.84340.29641350.22492681X-RAY DIFFRACTION100
2.8434-3.12940.27951380.21632630X-RAY DIFFRACTION99
3.1294-3.58190.25161420.19222686X-RAY DIFFRACTION100
3.5819-4.51160.23921210.17812645X-RAY DIFFRACTION96
4.5116-36.7550.25191490.19152575X-RAY DIFFRACTION90
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)
11.751-1.51070.67642.6205-0.82660.8846-0.04870.0597-0.01920.03830.08040.1522-0.0032-0.1225-0.03640.2265-0.03370.01560.36740.05310.27376.19064.06817.9894
21.4224-0.9690.97383.801-2.60662.46880.17490.0142-0.3055-0.0607-0.02840.09540.66190.0253-0.03130.5165-0.0082-0.05280.2156-0.03280.311318.9503-26.327928.3969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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