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- PDB-1p33: Pteridine reductase from Leishmania tarentolae complex with NADPH... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1p33
TitlePteridine reductase from Leishmania tarentolae complex with NADPH and MTX
ComponentsPteridine reductase 1
KeywordsOXIDOREDUCTASE / Pteridine reductase / complex / NADPH / MTX
Function / homology
Function and homology information


pteridine reductase / pteridine reductase activity / tetrahydrobiopterin biosynthetic process / response to methotrexate
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
METHOTREXATE / Chem-NDP / Pteridine reductase 1
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsZhao, H. / Bray, T. / Ouellette, M. / Zhao, M. / Ferre, R.A. / Matthews, D. / Whiteley, J.M. / Varughese, K.I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of pteridine reductase (PTR1) from Leishmania tarentolae.
Authors: Zhao, H. / Bray, T. / Ouellette, M. / Zhao, M. / Ferre, R.A. / Matthews, D. / Whiteley, J.M. / Varughese, K.I.
History
DepositionApr 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1
B: Pteridine reductase 1
C: Pteridine reductase 1
D: Pteridine reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,89012
Polymers123,0914
Non-polymers4,7998
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25010 Å2
ΔGint-122 kcal/mol
Surface area37360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.301, 96.103, 195.545
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
Pteridine reductase 1 / H region methotrexate resistance protein


Mass: 30772.764 Da / Num. of mol.: 4 / Fragment: PTERIDINE REDUCTASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania tarentolae (eukaryote) / Gene: PTR1 OR LTDH / Plasmid: pMALc-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42556, EC: 1.1.1.253
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.48 Å3/Da / Density % sol: 64.69 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% 1,4-butandiol, 12.5mM CTMC, 100mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal grow
*PLUS
Temperature: 287 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMTris-HCl1droppH7.0
34 mMNADPH1drop
44 mMmethotrexate1drop
510 mMMOPS1droppH7.0
628 %1,4-butanediol1reservoir
712.5 mMCTMC1reservoir
8100 mMHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 28, 1999
RadiationMonochromator: double crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.86→300 Å / Num. all: 215242 / Num. obs: 211913 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 60.497 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.9
Reflection shellResolution: 2.86→2.91 Å / Redundancy: 5 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1858 / % possible all: 90
Reflection
*PLUS
Num. obs: 40939 / % possible obs: 96.1 % / Num. measured all: 215242
Reflection shell
*PLUS
Rmerge(I) obs: 0.395

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E7W

1e7w


Resolution: 2.86→19.98 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4096 -Random
Rwork0.213 ---
all-43020 --
obs-40720 94.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-23.974 Å20 Å20 Å2
2---9.606 Å20 Å2
3----14.368 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.86→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8067 0 324 173 8564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d1.63
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.341 567 -
Rwork0.293 --
obs-5049 79.4 %
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection Rfree: 4095 / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.93
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.63

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