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- PDB-5wru: Crystal structure of type I inorganic pyrophosphatase from P falc... -

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Basic information

Entry
Database: PDB / ID: 5wru
TitleCrystal structure of type I inorganic pyrophosphatase from P falciparum
ComponentsProbable inorganic pyrophosphatase
KeywordsHYDROLASE / PPi / PPase / novel interfaces
Function / homology
Function and homology information


Cytosolic tRNA aminoacylation / Mitochondrial tRNA aminoacylation / Pyrophosphate hydrolysis / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase
Similarity search - Domain/homology
PHOSPHATE ION / Probable inorganic pyrophosphatase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.193 Å
AuthorsJamwal, A. / Yogavel, M. / Sharma, A.
CitationJournal: Sci Rep / Year: 2017
Title: Structural and Biochemical Characterization of Apicomplexan Inorganic Pyrophosphatases
Authors: Jamwal, A. / Yogavel, M. / Abdin, M.Z. / Jain, S.K. / Sharma, A.
History
DepositionDec 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
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
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable inorganic pyrophosphatase
B: Probable inorganic pyrophosphatase
C: Probable inorganic pyrophosphatase
D: Probable inorganic pyrophosphatase
E: Probable inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,0617
Polymers227,8715
Non-polymers1902
Water00
1
A: Probable inorganic pyrophosphatase
B: Probable inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2433
Polymers91,1492
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-30 kcal/mol
Surface area26390 Å2
MethodPISA
2
C: Probable inorganic pyrophosphatase
D: Probable inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2433
Polymers91,1492
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-27 kcal/mol
Surface area25880 Å2
MethodPISA
3
E: Probable inorganic pyrophosphatase

E: Probable inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)91,1492
Polymers91,1492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5740 Å2
ΔGint-31 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)253.345, 85.220, 108.445
Angle α, β, γ (deg.)90.000, 114.950, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 37 and (name N or name...
21(chain B and ((resid 37 and (name N or name...
31(chain C and (resid 37 through 70 or (resid 71...
41(chain D and (resid 37 through 47 or (resid 48...
51(chain E and (resid 37 through 47 or (resid 48...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEPHEPHE(chain A and ((resid 37 and (name N or name...AA3737
12PHEPHEPROPRO(chain A and ((resid 37 and (name N or name...AA37 - 38037 - 380
13PHEPHEPROPRO(chain A and ((resid 37 and (name N or name...AA37 - 38037 - 380
14PHEPHEPROPRO(chain A and ((resid 37 and (name N or name...AA37 - 38037 - 380
15PHEPHEPROPRO(chain A and ((resid 37 and (name N or name...AA37 - 38037 - 380
21PHEPHEPHEPHE(chain B and ((resid 37 and (name N or name...BB3737
22TYRTYRPROPRO(chain B and ((resid 37 and (name N or name...BB36 - 38036 - 380
23TYRTYRPROPRO(chain B and ((resid 37 and (name N or name...BB36 - 38036 - 380
24TYRTYRPROPRO(chain B and ((resid 37 and (name N or name...BB36 - 38036 - 380
25TYRTYRPROPRO(chain B and ((resid 37 and (name N or name...BB36 - 38036 - 380
31PHEPHESERSER(chain C and (resid 37 through 70 or (resid 71...CC37 - 7037 - 70
32ASNASNASNASN(chain C and (resid 37 through 70 or (resid 71...CC7171
33PHEPHETHRTHR(chain C and (resid 37 through 70 or (resid 71...CC37 - 37937 - 379
34PHEPHETHRTHR(chain C and (resid 37 through 70 or (resid 71...CC37 - 37937 - 379
35PHEPHETHRTHR(chain C and (resid 37 through 70 or (resid 71...CC37 - 37937 - 379
36PHEPHETHRTHR(chain C and (resid 37 through 70 or (resid 71...CC37 - 37937 - 379
41PHEPHEASNASN(chain D and (resid 37 through 47 or (resid 48...DD37 - 4737 - 47
42LEULEULEULEU(chain D and (resid 37 through 47 or (resid 48...DD4848
43TYRTYRPROPRO(chain D and (resid 37 through 47 or (resid 48...DD36 - 38036 - 380
44TYRTYRPROPRO(chain D and (resid 37 through 47 or (resid 48...DD36 - 38036 - 380
45TYRTYRPROPRO(chain D and (resid 37 through 47 or (resid 48...DD36 - 38036 - 380
46TYRTYRPROPRO(chain D and (resid 37 through 47 or (resid 48...DD36 - 38036 - 380
51PHEPHEASNASN(chain E and (resid 37 through 47 or (resid 48...EE37 - 4737 - 47
52LEULEULEULEU(chain E and (resid 37 through 47 or (resid 48...EE4848
53TYRTYRTHRTHR(chain E and (resid 37 through 47 or (resid 48...EE36 - 37936 - 379
54TYRTYRTHRTHR(chain E and (resid 37 through 47 or (resid 48...EE36 - 37936 - 379
55TYRTYRTHRTHR(chain E and (resid 37 through 47 or (resid 48...EE36 - 37936 - 379
56TYRTYRTHRTHR(chain E and (resid 37 through 47 or (resid 48...EE36 - 37936 - 379

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Components

#1: Protein
Probable inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase / PPase


Mass: 45574.250 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: MAL3P6.3, PFC0710w / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O77392, inorganic diphosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 8% Tacsimate pH 8.0 and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97854 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 33201 / % possible obs: 99.7 % / Redundancy: 5.8 % / Net I/σ(I): 38

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
PHENIX(1.11.1_2575: ???)refinement
RefinementMethod to determine structure: SAD / Resolution: 3.193→44.915 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2769 1921 5.79 %RANDOM
Rwork0.234 ---
obs0.2366 33201 94.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.85 Å2 / Biso mean: 52.4254 Å2 / Biso min: 25.08 Å2
Refinement stepCycle: final / Resolution: 3.193→44.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13029 0 10 0 13039
Biso mean--62.3 --
Num. residues----1543
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7175X-RAY DIFFRACTION13.593TORSIONAL
12B7175X-RAY DIFFRACTION13.593TORSIONAL
13C7175X-RAY DIFFRACTION13.593TORSIONAL
14D7175X-RAY DIFFRACTION13.593TORSIONAL
15E7175X-RAY DIFFRACTION13.593TORSIONAL
Refinement TLS params.Method: refined / Origin x: -36.1398 Å / Origin y: -20.5101 Å / Origin z: 12.1829 Å
111213212223313233
T0.206 Å20.0153 Å20.0048 Å2-0.1625 Å20.0396 Å2--0.2285 Å2
L0.3478 °2-0.0396 °20.0524 °2-0.111 °20.0201 °2--0.1891 °2
S-0.002 Å °0.0763 Å °-0.039 Å °-0.0157 Å °-0.0274 Å °0.0969 Å °0.007 Å °0.0093 Å °0.0431 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA37 - 380
2X-RAY DIFFRACTION1allB36 - 380
3X-RAY DIFFRACTION1allC37 - 379
4X-RAY DIFFRACTION1allD36 - 380
5X-RAY DIFFRACTION1allE36 - 379

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