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- PDB-4fzi: Crystal structure of prostaglandin F synthase from Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 4fzi
TitleCrystal structure of prostaglandin F synthase from Trypanosoma cruzi
ComponentsProstaglandin F synthase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / prostaglandin D2 / trypanosomiasis / eukaryotic pathogen / parasite / NADP+ / NADPH / rutin / bimatoprost
Function / homology
Function and homology information


prostaglandin H2 endoperoxidase reductase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / prostaglandin biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / 9,11-endoperoxide prostaglandin H2 reductase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structures of prostaglandin F synthase from the protozoa Leishmania major and Trypanosoma cruzi with NADP.
Authors: Moen, S.O. / Fairman, J.W. / Barnes, S.R. / Sullivan, A. / Nakazawa-Hewitt, S. / Van Voorhis, W.C. / Staker, B.L. / Lorimer, D.D. / Myler, P.J. / Edwards, T.E.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Sep 13, 2023Group: 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Prostaglandin F synthase
B: Prostaglandin F synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5745
Polymers67,1842
Non-polymers3903
Water1,51384
1
A: Prostaglandin F synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7392
Polymers33,5921
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Prostaglandin F synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8353
Polymers33,5921
Non-polymers2432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.560, 66.620, 87.310
Angle α, β, γ (deg.)90.000, 94.290, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _

Dom-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA5 - 28113 - 289
2BB - D5 - 30113

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Components

#1: Protein Prostaglandin F synthase


Mass: 33592.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053511287.49 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4DJ07, prostaglandin-F synthase
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: TrcrA.00019.a.B1 PW35698 at 18 mg/mL against Morpheus screen condition H1: 0.1 M MES/imidazole, pH 6.5, 10% PEG20000, 20% PEG550 MME, 0.02 M glutamic acid, glycine, serine, alanine, and ...Details: TrcrA.00019.a.B1 PW35698 at 18 mg/mL against Morpheus screen condition H1: 0.1 M MES/imidazole, pH 6.5, 10% PEG20000, 20% PEG550 MME, 0.02 M glutamic acid, glycine, serine, alanine, and lysine, crystal tracking ID 234961h1, kyb3-12, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2012
RadiationMonochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 19400 / Num. obs: 19336 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 39.766 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.6-2.670.5293.3570151416199.5
2.67-2.740.4384.1566671376199.6
2.74-2.820.3524.9865461339199.9
2.82-2.910.2826.0664021314199.7
2.91-30.2496.8262351275199.8
3-3.110.1988.4959471215199.8
3.11-3.220.1649.859111213199.6
3.22-3.360.13112.8254641122199.9
3.36-3.510.10215.4252681088199.5
3.51-3.680.07520.2150801066199.7
3.68-3.880.06323.534789995199.7
3.88-4.110.05527.154499948199.7
4.11-4.390.04333.024243893199.7
4.39-4.750.03835.883854830199.6
4.75-5.20.0434.253497767199.5
5.2-5.810.04630.643285689199.9
5.81-6.710.04630.663057625199.7
6.71-8.220.03240.022488519199.6
8.22-11.630.0259.031926410199.8
11.63-500.0261.61034236197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å47.77 Å
Translation2.6 Å47.77 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
ADSCdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F40

4f40


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 19.71 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.124 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 988 5.1 %RANDOM
Rwork0.1858 ---
obs0.1879 19335 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.01 Å2 / Biso mean: 35.8206 Å2 / Biso min: 10.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20.58 Å2
2--1.3 Å20 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 25 84 4361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194402
X-RAY DIFFRACTIONr_bond_other_d0.0040.022891
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9275999
X-RAY DIFFRACTIONr_angle_other_deg1.14137010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44123.768207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91215673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8731528
X-RAY DIFFRACTIONr_chiral_restr0.0850.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214985
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02947
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRms dev position (Å)Weight position
11A9416X-RAY DIFFRACTION0.070.05
12B9416X-RAY DIFFRACTION0.070.05
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 67 -
Rwork0.267 1298 -
all-1365 -
obs--99.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3651-0.2359-0.0430.81680.2660.42060.01340.02760.03570.0642-0.01130.03570.0911-0.0655-0.0020.1364-0.03610.00170.0895-0.01120.09416.294715.87958.7526
20.67550.3141-0.40530.7341.25034.05510.04030.01920.05270.0669-0.0454-0.01990.2135-0.21530.00510.07520.00910.03440.1394-0.01470.070618.627514.3181-31.5631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 281
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B5 - 280
4X-RAY DIFFRACTION2B301

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