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- PDB-4clh: Crystal structure of pteridine reductase 1 (PTR1) from Trypanosom... -

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Basic information

Entry
Database: PDB / ID: 4clh
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor
ComponentsPTERIDINE REDUCTASE 1
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-W8G / Pteridine reductase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBarrack, K.L. / Hunter, W.N.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structure-Based Design and Synthesis of Antiparasitic Pyrrolopyrimidines Targeting Pteridine Reductase 1.
Authors: Khalaf, A.I. / Huggan, J.K. / Suckling, C.J. / Gibson, C.L. / Stewart, K. / Giordani, F. / Barrett, M.P. / Wong, P.E. / Barrack, K.L. / Hunter, W.N.
History
DepositionJan 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 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 1
B: PTERIDINE REDUCTASE 1
C: PTERIDINE REDUCTASE 1
D: PTERIDINE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,65318
Polymers122,6794
Non-polymers4,97414
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19890 Å2
ΔGint-132.9 kcal/mol
Surface area32860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.680, 89.670, 82.820
Angle α, β, γ (deg.)90.00, 115.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7727, -0.03316, -0.6339), (-0.03405, -0.995, 0.09357), (-0.6338, 0.09389, 0.7677)-2.184, 3.971, -1.038
2given(0.7692, 0.01694, 0.6388), (0.02095, -0.9998, 0.001291), (0.6387, 0.01239, -0.7694)-13.75, 6.147, 37.93
3given(-0.9999, 0.01081, -0.003902), (0.01115, 0.9946, -0.1035), (0.002762, -0.1036, -0.9946)-15.86, 2.105, 37.51

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Components

#1: Protein
PTERIDINE REDUCTASE 1 / PTR1


Mass: 30669.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase
#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-W8G / 4-thiomorpholino-7H-pyrrolo[2,3-d]pyrimidin-2-amine


Mass: 235.309 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N5S
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 718 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CONTAINS ADDITIONAL 20 AMINO ACID HISTIDINE TAG AT N-TERMINUS.

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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: 2.04 Å3/Da / Density % sol: 39.56 % / Description: NONE
Crystal growDetails: RESERVOIR CONTAINED 1.7-2.7 M SODIUM ACETATE, 20-50 MM SODIUM CITRATE PH 4.5-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV IMAGING PLATE / Date: Mar 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→41.72 Å / Num. obs: 67566 / % possible obs: 80.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 / % possible all: 28.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C7V

2c7v


Resolution: 1.85→41.72 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.183 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES WITH INSUFFICIENT ELECTRON DENSITY WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19342 3426 5.1 %RANDOM
Rwork0.14415 ---
obs0.14665 64114 80.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.667 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20 Å2-0.96 Å2
2--3.82 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7477 0 328 718 8523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198139
X-RAY DIFFRACTIONr_bond_other_d0.0010.027851
X-RAY DIFFRACTIONr_angle_refined_deg1.6892.01611111
X-RAY DIFFRACTIONr_angle_other_deg0.8243.00417860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15351035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16924.212311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.199151299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4921552
X-RAY DIFFRACTIONr_chiral_restr0.0870.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021793
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_it1.6021.9854067
X-RAY DIFFRACTIONr_mcbond_other1.6021.9854064
X-RAY DIFFRACTIONr_mcangle_it2.5682.9575071
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.042.2514072
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 57 -
Rwork0.318 1285 -
obs--21.89 %

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