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- PDB-2c7v: Structure of Trypanosoma brucei pteridine reductase (PTR1) in ter... -

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Basic information

Entry
Database: PDB / ID: 2c7v
TitleStructure of Trypanosoma brucei pteridine reductase (PTR1) in ternary complex with cofactor and the antifolate methotrexate
ComponentsPTERIDINE REDUCTASE
KeywordsOXIDOREDUCTASE / PTERIDINE REDUCTASE / TRYPANOSOMATIDS / DRUG RESISTANCE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / METHOTREXATE RESISTANCE
Function / homology
Function and homology information


pteridine reductase activity / nucleotide binding
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
ACETATE ION / METHOTREXATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NICKEL (II) ION / Pteridine reductase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDawson, A. / Gibellini, F. / Sienkiewicz, N. / Fyfe, P.K. / McLuskey, K. / Fairlamb, A.H. / Hunter, W.N.
CitationJournal: Mol.Microbiol. / Year: 2006
Title: Structure and Reactivity of Trypanosoma Brucei Pteridine Reductase: Inhibition by the Archetypal Antifolate Methotrexate
Authors: Dawson, A. / Gibellini, F. / Sienkiewicz, N. / Tulloch, L.B. / Fyfe, P.K. / Mcluskey, K. / Fairlamb, A.H. / Hunter, W.N.
History
DepositionNov 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 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_conn
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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: PTERIDINE REDUCTASE
D: PTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,98016
Polymers114,9544
Non-polymers5,02712
Water14,394799
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.655, 90.244, 82.841
Angle α, β, γ (deg.)90.00, 115.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7768, -0.03223, -0.6289), (-0.04331, -0.9936, 0.1044), (-0.6282, 0.1084, 0.7704)-2.299, 3.748, -1.05
2given(-0.9996, 0.02639, -0.007474), (0.02703, 0.9942, -0.1039), (0.00469, -0.104, -0.9946)-15.65, 2.198, 37.03
3given(0.7736, 0.001934, 0.6337), (0.009831, -0.9999, -0.00895), (0.6336, 0.01315, -0.7735)-13.41, 6.358, 37.49

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PTERIDINE REDUCTASE


Mass: 28738.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET-TBPTR1H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase

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Non-polymers , 5 types, 811 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.22 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: PROTEIN BUFFER WAS 20 MM TRIS HCL, PH 7.0 WITH 1MM NADP, 1 MM METHOTREXATE AND 20 MM DITHIOTHREITOL, PROTEIN CONCENTRATION WAS 6 MG/ML. HANGING DROP RESERVOIR SOLUTION WAS 0.1 M SODIUM ...Details: PROTEIN BUFFER WAS 20 MM TRIS HCL, PH 7.0 WITH 1MM NADP, 1 MM METHOTREXATE AND 20 MM DITHIOTHREITOL, PROTEIN CONCENTRATION WAS 6 MG/ML. HANGING DROP RESERVOIR SOLUTION WAS 0.1 M SODIUM CACODYLATE PH 6.5 AND 1.4 M SODIUM ACETATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 30, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→74.5 Å / Num. obs: 50048 / % possible obs: 99.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.5 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 1E92

1e92


Resolution: 2.2→74.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.551 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2534 5.1 %RANDOM
Rwork0.153 ---
obs0.157 47369 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å2-0.58 Å2
2--2.67 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.2→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7648 0 334 799 8781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228302
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.99911359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76351064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42424.421328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.943151315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8191553
X-RAY DIFFRACTIONr_chiral_restr0.5380.21326
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026175
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.24453
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.25701
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2822
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5841.55338
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02628363
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46633350
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3494.52973
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 175
Rwork0.182 3269

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