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- PDB-2xox: Crystal structure of pteridine reductase (PTR1) from Leishmania d... -

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Basic information

Entry
Database: PDB / ID: 2xox
TitleCrystal structure of pteridine reductase (PTR1) from Leishmania donovani
ComponentsPTERIDINE REDUCTASE
KeywordsOXIDOREDUCTASE / ANTIFOLATES / SHORT-CHAIN REDUCTASE
Function / homology
Function and homology information


pteridine reductase / oxidoreductase activity
Similarity search - Function
Pteridine reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLEISHMANIA DONOVANI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBarrack, K.L. / Tulloch, L.B. / Burke, L.A. / Fyfe, P.K. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of Recombinant Leishmania Donovani Pteridine Reductase Reveals a Disordered Active Site.
Authors: Barrack, K.L. / Tulloch, L.B. / Burke, L.A. / Fyfe, P.K. / Hunter, W.N.
History
DepositionAug 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: PTERIDINE REDUCTASE
B: PTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7534
Polymers60,5612
Non-polymers1922
Water43224
1
A: PTERIDINE REDUCTASE
B: PTERIDINE REDUCTASE
hetero molecules

A: PTERIDINE REDUCTASE
B: PTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5068
Polymers121,1224
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9030 Å2
ΔGint-145.4 kcal/mol
Surface area36580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.509, 126.443, 87.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PTERIDINE REDUCTASE


Mass: 30280.471 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-288 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA DONOVANI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6QDB5, pteridine reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 61 TO PRO ENGINEERED RESIDUE IN CHAIN B, THR 61 TO PRO
Sequence detailsT61P AND 13 RESIDUES AT C TERMINUS TRUNCATED

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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: 2.44 Å3/Da / Density % sol: 49.7 % / Description: NONE
Crystal growDetails: RESERVOIR CONTAINED 0.1M MES PH 6.5, 10% (V/V) DIOXANE, 1.6M AMMONIUM SULFATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.973
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.5→32 Å / Num. obs: 21006 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E7W

1e7w


Resolution: 2.5→29.9 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / SU B: 10.219 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28448 1077 5.1 %RANDOM
Rwork0.22735 ---
obs0.23027 19844 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.465 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å2-0 Å2
2---6.18 Å20 Å2
3---7.91 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 10 24 3214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223259
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9614430
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4325424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85622.96125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.97515505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7551525
X-RAY DIFFRACTIONr_chiral_restr0.1250.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212415
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1261.52143
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0823412
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68331116
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2674.51018
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 73 -
Rwork0.281 1453 -
obs--99.8 %

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