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- PDB-1mxh: Crystal Structure of Substrate Complex of Putative Pteridine Redu... -

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Basic information

Entry
Database: PDB / ID: 1mxh
TitleCrystal Structure of Substrate Complex of Putative Pteridine Reductase 2 (PTR2) from Trypanosoma cruzi
ComponentsPTERIDINE REDUCTASE 2
KeywordsOXIDOREDUCTASE / SDR TOPOLOGY / PROTEIN-SUBSTRATE 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
DIHYDROFOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative pteridine reductase 2
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.4Feb 14, 2024Group: 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
Remark 600Heterogen Ligand coordinates were taken from PDB entry 1RF7. The coordinate file was missing a ...Heterogen Ligand coordinates were taken from PDB entry 1RF7. The coordinate file was missing a carboxylate group in the glutamate portion. No correction was made since the glutamate portion of ligand DHF shows no clear density in this structure.

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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)121,47212
Polymers116,7254
Non-polymers4,7478
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23810 Å2
ΔGint-133 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.610, 74.610, 181.260
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: 29181.277 Da / Num. of mol.: 4
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): BL21(DE3)pLysS / References: UniProt: Q8I814
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-DHF / DIHYDROFOLIC ACID / Dihydrofolic acid


Mass: 443.413 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H21N7O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.3 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / pH: 6.5
Details: Sodium acetate, cacodylate buffer, pH 6.50, 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
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 20, 2000 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.77→36 Å / Num. obs: 87817 / % possible obs: 79.8 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 12.4
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Num. obs: 47858 / % possible obs: 95.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.44 Å / % possible obs: 91.2 % / Redundancy: 1.8 % / Num. unique obs: 7590 / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
X-GENdata reduction
AMoREphasing
CNS1refinement
HKL-2000data reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INHIBITOR COMPLEX SOLVED BY MAD METHOD (PDBID 1MXF)

1mxf


Resolution: 2.2→19.45 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 220622 / Data cutoff high rms absF: 220622 / 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
Rfree0.251 2799 5 %RANDOM
Rwork0.205 ---
obs0.205 55590 97.2 %-
all-55984 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.225 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å22.45 Å20 Å2
2---0.36 Å20 Å2
3---0.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7380 0 308 457 8145
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.32
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 447 5.1 %
Rwork0.247 8326 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1NAD.PARNAD.TOP
X-RAY DIFFRACTION2DHF.PARDHF.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.44 Å / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.246

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