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

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Basic information

Entry
Database: PDB / ID: 4clr
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor
Components(PTERIDINE REDUCTASE 1) x 2
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
Chem-FDB / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 15, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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)126,34112
Polymers122,7114
Non-polymers3,6308
Water16,754930
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19820 Å2
ΔGint-128.5 kcal/mol
Surface area32450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.346, 90.775, 84.378
Angle α, β, γ (deg.)90.00, 115.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7838, 0.03053, 0.6203), (0.03301, -0.9953, 0.0907), (0.6202, 0.09157, 0.7791)4.498, -1.955, -1.446
2given(0.7851, -0.03504, -0.6183), (-0.03676, -0.9993, 0.009963), (-0.6182, 0.01491, -0.7859)13.55, 0.2582, 39.11
3given(-1, 0.005359, 0.001317), (0.005188, 0.9943, -0.1067), (-0.001881, -0.1067, -0.9943)18.03, 1.99, 37.45

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Components

#1: Protein PTERIDINE REDUCTASE 1


Mass: 30685.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase
#2: Protein PTERIDINE REDUCTASE 1


Mass: 30669.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase
#3: 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
#4: Chemical
ChemComp-FDB / 2-amino-5-methyl-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one


Mass: 164.165 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 930 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsS-OXY CYSTEINE (CSX): CYSTEINE MODIFIED TO S-OXY CYSTEINE IN CHAINS A AND D
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: 2.1 Å3/Da / Density % sol: 41.39 % / 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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→29.2 Å / Num. obs: 100986 / % possible obs: 99 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.4 / % possible all: 94.8

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Processing

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

2c7v


Resolution: 1.75→29.2 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.905 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.091 / 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
Rfree0.16917 5111 5.1 %RANDOM
Rwork0.13724 ---
obs0.13888 95850 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.774 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å2-0.1 Å2
2--2.45 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7445 0 240 930 8615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197894
X-RAY DIFFRACTIONr_bond_other_d0.0010.027629
X-RAY DIFFRACTIONr_angle_refined_deg1.6092.00210785
X-RAY DIFFRACTIONr_angle_other_deg0.8013.00217477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78851017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99424.314306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.919151259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4361549
X-RAY DIFFRACTIONr_chiral_restr0.0860.21280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021758
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_it1.3561.5684014
X-RAY DIFFRACTIONr_mcbond_other1.3551.5684013
X-RAY DIFFRACTIONr_mcangle_it2.1872.3355004
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8881.8233880
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 349 -
Rwork0.225 6444 -
obs--90.5 %

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