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- PDB-2aee: Crystal structure of Orotate phosphoribosyltransferase from Strep... -

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Basic information

Entry
Database: PDB / ID: 2aee
TitleCrystal structure of Orotate phosphoribosyltransferase from Streptococcus pyogenes
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / Structural Genomics / Orotate phosphoribosyltransferase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / 'de novo' UMP biosynthetic process / magnesium ion binding
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsChang, C. / Li, H. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Orotate phosphoribosyltransferase from Streptococcus pyogenes
Authors: Chang, C. / Li, H. / Collart, F. / Joachimiak, A.
History
DepositionJul 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3308
Polymers45,8232
Non-polymers5086
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-64 kcal/mol
Surface area17300 Å2
MethodPISA
2
A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
hetero molecules

A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,66116
Polymers91,6454
Non-polymers1,01612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10930 Å2
ΔGint-145 kcal/mol
Surface area31600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.131, 118.131, 72.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Orotate phosphoribosyltransferase / OPRT / OPRTase


Mass: 22911.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: pyrE / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-derivative
References: UniProt: Q9A076, orotate phosphoribosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.8 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tris-Cl, Ammonium sulfate, Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97922 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 15, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 37927 / Num. obs: 37510 / % possible obs: 98.9 % / Observed criterion σ(I): -5 / Redundancy: 31 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 32.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.62 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.204 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22942 1860 5 %RANDOM
Rwork0.18932 ---
all0.19131 37278 --
obs0.19131 37278 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 28 179 3342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223228
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.984382
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.935411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69125.207121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56215566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.5161510
X-RAY DIFFRACTIONr_chiral_restr0.1180.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022332
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21473
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22221
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8961.52120
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37923296
X-RAY DIFFRACTIONr_scbond_it2.62131284
X-RAY DIFFRACTIONr_scangle_it4.0714.51083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 111 -
Rwork0.24 2211 -
obs--84.07 %
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)
12.31340.1621-0.26521.98890.23135.45410.01230.0852-0.0802-0.15440.0939-0.07540.31980.2934-0.1063-0.0140.03330.00810.0058-0.0192-0.224320.64337.38911.155
20.38750.06070.06361.3108-0.0612.54720.0802-0.0494-0.08740.06350.00410.01820.05970.0472-0.08430.00510.0246-0.01780.0354-0.0033-0.157515.00735.01133.82
32.5508-0.09491.01292.1298-0.87516.5595-0.0109-0.0445-0.04790.0531-0.0769-0.1961-0.11510.45060.0878-0.0015-0.0203-0.0172-0.0378-0.0037-0.212827.08347.80863.432
40.82770.3771-0.06111.11420.28793.97750.0540.08920.0436-0.15880.0571-0.1572-0.57390.4748-0.11120.1068-0.07840.04970.0176-0.0209-0.183726.34753.55441.344
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 371 - 39
2X-RAY DIFFRACTION1AA174 - 208176 - 210
3X-RAY DIFFRACTION2AA38 - 17340 - 175
4X-RAY DIFFRACTION3BB1 - 373 - 39
5X-RAY DIFFRACTION3BB174 - 209176 - 211
6X-RAY DIFFRACTION4BB38 - 17340 - 175

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