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- PDB-3mjd: 1.9 Angstrom Crystal Structure of Orotate Phosphoribosyltransfera... -

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Basic information

Entry
Database: PDB / ID: 3mjd
Title1.9 Angstrom Crystal Structure of Orotate Phosphoribosyltransferase (pyrE) Francisella tularensis.
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / Orotate / Phosphoribosyltransferase / idp02311 / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


pyrimidine ribonucleoside biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / 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 speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.9 Angstrom Crystal Structure of Orotate Phosphoribosyltransferase (pyrE) Francisella tularensis.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
C: Orotate phosphoribosyltransferase
D: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6446
Polymers104,4594
Non-polymers1842
Water12,466692
1
A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)52,2302
Polymers52,2302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-22 kcal/mol
Surface area20130 Å2
MethodPISA
2
C: Orotate phosphoribosyltransferase
D: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4144
Polymers52,2302
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-20 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.553, 97.903, 110.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsChains A and B, C and D form two biological dimers.

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Components

#1: Protein
Orotate phosphoribosyltransferase


Mass: 26114.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Strain: SCHU S4 / Gene: FTT0437c, FTT_0437c, pyrE / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: Q5NHL5, orotate phosphoribosyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein solution: 7.5 mg/mL, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: Classics II G1, 0.2M Sodium chloride, 0.1M TRIS (pH 8.5), 25% PEG 3350., VAPOR DIFFUSION, ...Details: Protein solution: 7.5 mg/mL, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: Classics II G1, 0.2M Sodium chloride, 0.1M TRIS (pH 8.5), 25% PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 24, 2010 / Details: Beryllium lenses
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 71519 / Num. obs: 71519 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3530 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ORO

1oro


Resolution: 1.9→29.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.323 / SU ML: 0.099 / Isotropic thermal model: Refined Individually / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23477 3607 5.1 %RANDOM
Rwork0.18559 ---
all0.18802 67705 --
obs0.18802 67705 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.671 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å2-0 Å2-0 Å2
2---0.81 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6577 0 12 692 7281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226989
X-RAY DIFFRACTIONr_bond_other_d0.0010.024735
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9679451
X-RAY DIFFRACTIONr_angle_other_deg0.803311624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8395872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1725.238315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.114151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1031518
X-RAY DIFFRACTIONr_chiral_restr0.0810.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027811
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021443
X-RAY DIFFRACTIONr_mcbond_it1.0371.54280
X-RAY DIFFRACTIONr_mcbond_other0.2551.51731
X-RAY DIFFRACTIONr_mcangle_it1.87926922
X-RAY DIFFRACTIONr_scbond_it2.84232709
X-RAY DIFFRACTIONr_scangle_it4.6774.52529
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 263 -
Rwork0.22 4946 -
obs-4946 99.88 %

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