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- PDB-1mxf: Crystal Structure of Inhibitor Complex of Putative Pteridine Redu... -

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Basic information

Entry
Database: PDB / ID: 1mxf
TitleCrystal Structure of Inhibitor Complex of Putative Pteridine Reductase 2 (PTR2) from Trypanosoma cruzi
ComponentsPTERIDINE REDUCTASE 2
KeywordsOXIDOREDUCTASE / SDR TOPOLOGY / PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


oxidoreductase 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
METHOTREXATE / Chem-NDP / Putative pteridine reductase 2
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSchormann, N. / Pal, B. / Senkovich, O. / Carson, M. / Howard, A. / Smith, C. / Delucas, L. / Chattopadhyay, D.
Citation
Journal: J.Struct.Biol. / Year: 2005
Title: Crystal structure of Trypanosoma cruzi pteridine reductase 2 in complex with a substrate and an inhibitor.
Authors: Schormann, N. / Pal, B. / Senkovich, O. / Carson, M. / Howard, A. / Smith, C. / Delucas, L. / Chattopadhyay, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Expression, purification, crystallization and preliminary crystallographic analysis of recombinant pteridine reductase of Trypanosoma cruzi
Authors: Schormann, N. / Pal, B. / Chattopadhyay, D.
History
DepositionOct 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence the sequence of this molecule is not yet deposited in any sequence database

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTERIDINE REDUCTASE 2
B: PTERIDINE REDUCTASE 2
C: PTERIDINE REDUCTASE 2
D: PTERIDINE REDUCTASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,08712
Polymers117,2884
Non-polymers4,7998
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24130 Å2
ΔGint-135 kcal/mol
Surface area31460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.790, 74.790, 180.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
PTERIDINE REDUCTASE 2


Mass: 29321.957 Da / Num. of mol.: 4 / Fragment: pteridine reductase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: Sylvio, X10 / Gene: ptr2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834pLysS / References: UniProt: Q8I814
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / pH: 6.3
Details: Sodium acetate, cacodylate buffer, pH 6.30, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 8 / Method: vapor diffusion, hanging drop
Details: Schormann, N., (2001) Acta Crystallogr.,Sect.D, 57, 1671.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1reservoirpH8.0
21 mMmethotrexate1reservoir
31 mMNADPH1reservoir
420 mM1reservoirNaCl
55 mMbeta-mercaptoethanol1reservoir
615 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9537, 0.9791, 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 20, 2000 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97911
30.97921
ReflectionResolution: 1.76→36 Å / Num. obs: 89619 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 11.8
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Num. obs: 48846 / % possible obs: 97.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.44 Å / % possible obs: 91.9 % / Redundancy: 1.9 % / Num. unique obs: 7734 / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
X-GENdata reduction
SOLVEphasing
CNS1refinement
HKL-2000data reduction
X-GENdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→19.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 187450.3 / Data cutoff high rms absF: 187450.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2526 5.3 %RANDOM
Rwork0.197 ---
obs0.197 47319 94.2 %-
all-48788 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.982 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å24.53 Å20 Å2
2--3.28 Å20 Å2
3----6.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7348 0 324 346 8018
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 394 5.6 %
Rwork0.252 6658 -
obs--83.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ndp.parndp.top
X-RAY DIFFRACTION2mtx.parmtx.top
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.027
X-RAY DIFFRACTIONc_angle_deg2.76
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Rfactor Rfree: 0.308 / Rfactor Rwork: 0.274

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