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- PDB-4qmb: The structure of inorganic pyrophosphatase from Schistosoma japonicum -

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Basic information

Entry
Database: PDB / ID: 4qmb
TitleThe structure of inorganic pyrophosphatase from Schistosoma japonicum
ComponentsSJCHGC07024 protein
KeywordsHYDROLASE / METAL BINDING PROTEIN / pyrophosphatase
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
inorganic diphosphatase
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsWu, Q.F.
CitationJournal: To be Published
Title: The structure and function of inorganic pyrophosphatase from Schistosoma japonicum
Authors: Wu, Q.F.
History
DepositionJun 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SJCHGC07024 protein
B: SJCHGC07024 protein


Theoretical massNumber of molelcules
Total (without water)65,4262
Polymers65,4262
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-15 kcal/mol
Surface area25240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.750, 75.750, 122.962
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein SJCHGC07024 protein / Inorganic pyrophosphatase


Mass: 32713.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5DE13
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Tris-HCl pH 6.8, 2M NH4SO4, 0.04M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9707 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9707 Å / Relative weight: 1
ReflectionResolution: 2.603→37.88 Å / Num. all: 24093 / Num. obs: 24093 / % possible obs: 99.69 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0
Reflection shellResolution: 2.603→2.696 Å / % possible all: 99.33

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E9G

1e9g


Resolution: 2.603→37.875 Å / SU ML: 0.37 / σ(F): 1.98 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 1984 8.24 %
Rwork0.2024 --
obs0.2075 24077 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.603→37.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 0 88 4618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014629
X-RAY DIFFRACTIONf_angle_d1.4676280
X-RAY DIFFRACTIONf_dihedral_angle_d15.8361701
X-RAY DIFFRACTIONf_chiral_restr0.06658
X-RAY DIFFRACTIONf_plane_restr0.009810
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6031-2.66820.35091460.2261156199
2.6682-2.74030.351380.24071559100
2.7403-2.82090.36231500.24041610100
2.8209-2.91190.31641360.23031605100
2.9119-3.01590.33871470.22891566100
3.0159-3.13660.27061350.22481591100
3.1366-3.27930.30151440.21511589100
3.2793-3.45210.2661510.2041590100
3.4521-3.66820.26411310.19971556100
3.6682-3.95120.28691410.1855155899
3.9512-4.34830.18761330.1742159999
4.3483-4.97630.2281460.16121583100
4.9763-6.2650.26991410.20061588100
6.265-37.8790.23361450.2275153898
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)
11.57830.60690.41582.5831.12862.04550.05140.0804-0.1331-0.0703-0.18120.07770.1256-0.08520.10450.32890.06380.01670.3456-0.04610.350616.5504-14.3978-12.9527
21.6639-0.4909-0.39392.53261.10452.0590.0303-0.07640.1280.113-0.16970.093-0.0602-0.09180.09590.3326-0.0533-0.01710.3478-0.03340.335716.519114.427714.797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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