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- PDB-6mt2: Crystal structure of Inorganic Pyrophosphatase from Medicago trun... -

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Basic information

Entry
Database: PDB / ID: 6mt2
TitleCrystal structure of Inorganic Pyrophosphatase from Medicago truncatula (I23 crystal form)
ComponentsSoluble inorganic pyrophosphatase
KeywordsHYDROLASE / pyrophosphate / PPA / autoproteolysis
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / nucleoplasm / cytosol
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 speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsRuszkowski, M. / Grzechowiak, M. / Dauter, Z.
CitationJournal: Biochem.J. / Year: 2019
Title: Crystal structures of plant inorganic pyrophosphatase, an enzyme with a moonlighting autoproteolytic activity.
Authors: Grzechowiak, M. / Ruszkowski, M. / Sliwiak, J. / Szpotkowski, K. / Sikorski, M. / Jaskolski, M.
History
DepositionOct 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble inorganic pyrophosphatase
B: Soluble inorganic pyrophosphatase
C: Soluble inorganic pyrophosphatase
D: Soluble inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)98,6254
Polymers98,6254
Non-polymers00
Water1,38777
1
A: Soluble inorganic pyrophosphatase
B: Soluble inorganic pyrophosphatase

A: Soluble inorganic pyrophosphatase
B: Soluble inorganic pyrophosphatase

A: Soluble inorganic pyrophosphatase
B: Soluble inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)147,9376
Polymers147,9376
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area17680 Å2
ΔGint-91 kcal/mol
Surface area39750 Å2
MethodPISA
2
C: Soluble inorganic pyrophosphatase
D: Soluble inorganic pyrophosphatase

C: Soluble inorganic pyrophosphatase
D: Soluble inorganic pyrophosphatase

C: Soluble inorganic pyrophosphatase
D: Soluble inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)147,9376
Polymers147,9376
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area12920 Å2
ΔGint-78 kcal/mol
Surface area42450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.202, 235.202, 235.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

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Components

#1: Protein
Soluble inorganic pyrophosphatase


Mass: 24656.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 25500596, MTR_8g024050
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A072TMB0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 5.5 Å3/Da / Density % sol: 81.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 4% Tacsimate pH 6.0, 12% PEG 3350 crystal after 3 months 20% Ethylene glycol as cryoprotectant MtPPA1 at 16.3 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 11, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 48141 / % possible obs: 99.7 % / Redundancy: 16 % / CC1/2: 1 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.14 / Net I/σ(I): 23.4
Reflection shellResolution: 2.89→3.07 Å / Redundancy: 15 % / Rmerge(I) obs: 1.7 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7620 / CC1/2: 0.65 / Rrim(I) all: 1.8 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lug

4lug


Resolution: 2.89→48.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 20.492 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.2 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19529 1060 2.2 %RANDOM
Rwork0.17227 ---
obs0.17278 47082 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 83.382 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.89→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5737 0 0 77 5814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195883
X-RAY DIFFRACTIONr_bond_other_d0.0020.025609
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9747968
X-RAY DIFFRACTIONr_angle_other_deg0.944313003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74824.786280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.796151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8871525
X-RAY DIFFRACTIONr_chiral_restr0.0820.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216498
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021259
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6226.5442830
X-RAY DIFFRACTIONr_mcbond_other2.6216.5442829
X-RAY DIFFRACTIONr_mcangle_it4.4759.7973527
X-RAY DIFFRACTIONr_mcangle_other4.4759.7983528
X-RAY DIFFRACTIONr_scbond_it2.9417.0113053
X-RAY DIFFRACTIONr_scbond_other2.9417.0123054
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.98910.3384442
X-RAY DIFFRACTIONr_long_range_B_refined7.37151.2436212
X-RAY DIFFRACTIONr_long_range_B_other7.3751.2356207
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.892→2.967 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 75 -
Rwork0.459 3329 -
obs--96 %
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)
10.55040.24180.01991.54270.67560.31720.0440.02490.00130.1755-0.0374-0.03120.0937-0.0311-0.00660.1504-0.0336-0.08150.0921-0.02490.10834.0816.03841.398
21.0420.54380.43980.32930.39180.8840.09260.0524-0.02190.06040.0864-0.0891-0.01120.1898-0.17890.1511-0.0323-0.11530.1857-0.11690.223663.70738.18344.875
30.66930.14430.24171.92120.58060.74860.00880.00880.027-0.18010.0531-0.20410.03710.0625-0.06190.15360.0233-0.01790.0633-0.00560.104936.601-9.89720.209
40.5754-0.38410.43981.3118-0.23721.5995-0.2998-0.19080.06850.14340.1842-0.0769-0.1469-0.13640.11560.25250.1245-0.12530.18420.02680.171641.559-28.02655.241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 208
2X-RAY DIFFRACTION2B30 - 210
3X-RAY DIFFRACTION3C33 - 209
4X-RAY DIFFRACTION4D33 - 210

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