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- PDB-5cs2: Crystal structure of Plasmodium falciparum diadenosine triphospha... -

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Basic information

Entry
Database: PDB / ID: 5cs2
TitleCrystal structure of Plasmodium falciparum diadenosine triphosphate hydrolase in complex with Cyclomarin A
Components
  • Cyclomarin A
  • Histidine triad protein
KeywordsHYDROLASE / Cyclomarin A / diadenosine triphosphate hydrolase / anti-plasmodial activity / malaria / Plasmodium falciparum
Function / homology
Function and homology information


bis(5'-adenosyl)-triphosphatase / bis(5'-adenosyl)-triphosphatase activity / nucleotide binding / zinc ion binding
Similarity search - Function
FHIT family / Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily ...FHIT family / Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bis(5'-adenosyl)-triphosphatase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Streptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsOstermann, N. / Schmitt, E. / Gerhartz, B. / Hinniger, A. / Delmas, C.
CitationJournal: Chembiochem / Year: 2015
Title: Gift from Nature: Cyclomarin A Kills Mycobacteria and Malaria Parasites by Distinct Modes of Action.
Authors: Burstner, N. / Roggo, S. / Ostermann, N. / Blank, J. / Delmas, C. / Freuler, F. / Gerhartz, B. / Hinniger, A. / Hoepfner, D. / Liechty, B. / Mihalic, M. / Murphy, J. / Pistorius, D. / ...Authors: Burstner, N. / Roggo, S. / Ostermann, N. / Blank, J. / Delmas, C. / Freuler, F. / Gerhartz, B. / Hinniger, A. / Hoepfner, D. / Liechty, B. / Mihalic, M. / Murphy, J. / Pistorius, D. / Rottmann, M. / Thomas, J.R. / Schirle, M. / Schmitt, E.K.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 2.0May 15, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 3.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine triad protein
B: Cyclomarin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7453
Polymers24,7092
Non-polymers351
Water2,000111
1
A: Histidine triad protein
B: Cyclomarin A
hetero molecules

A: Histidine triad protein
B: Cyclomarin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4896
Polymers49,4184
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Unit cell
Length a, b, c (Å)45.953, 45.953, 138.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Histidine triad protein


Mass: 23647.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF14_0349 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1 resistant / References: UniProt: Q8IL97
#2: Protein/peptide Cyclomarin A


Mass: 1061.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces (bacteria)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.71 Å3/Da / Density % sol: 27.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 uL of protein-inhibitor solution (11 mg/ml PFAp3Aase, 50 mM TRIS pH 8, 150 mM NaCl, 5% glycerol and 1 mM TCEP, 1mM cyclomarin A) was mixed with 0.2 uL reservoir solution (100 mM HEPES pH ...Details: 0.2 uL of protein-inhibitor solution (11 mg/ml PFAp3Aase, 50 mM TRIS pH 8, 150 mM NaCl, 5% glycerol and 1 mM TCEP, 1mM cyclomarin A) was mixed with 0.2 uL reservoir solution (100 mM HEPES pH 7.5, 30% Iso-propanol, 200 mM Magnesium chloride hexahydrate) and equilibrated against 80 uL reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.65→17.5 Å / Num. obs: 20919 / % possible obs: 98.5 % / Redundancy: 8 % / Biso Wilson estimate: 26.19 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.3
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FHI

2fhi


Resolution: 1.65→17.5 Å / Cor.coef. Fo:Fc: 0.9496 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.096
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1044 5 %RANDOM
Rwork0.1953 ---
obs0.1967 20891 98.49 %-
Displacement parametersBiso mean: 31.74 Å2
Baniso -1Baniso -2Baniso -3
1--4.1758 Å20 Å20 Å2
2---4.1758 Å20 Å2
3---8.3517 Å2
Refine analyzeLuzzati coordinate error obs: 0.238 Å
Refinement stepCycle: 1 / Resolution: 1.65→17.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 1 111 1347
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011339HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.071810HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d478SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes182HARMONIC5
X-RAY DIFFRACTIONt_it1339HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion16.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion180SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1577SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.74 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2812 151 4.98 %
Rwork0.2377 2883 -
all0.2398 3034 -
obs--98.49 %

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