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- PDB-8gtz: Crystal structure of exopolyphosphatase (PPX) mutant E137A from Z... -

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Basic information

Entry
Database: PDB / ID: 8gtz
TitleCrystal structure of exopolyphosphatase (PPX) mutant E137A from Zymomonas mobilis in complex with magnesium ions
ComponentsPpx/GppA phosphatase
KeywordsMETAL BINDING PROTEIN / Polyphosphate / PPX/GppA
Function / homology
Function and homology information


pyrophosphatase activity / metal ion binding
Similarity search - Function
: / Exopolyphosphatase, C-terminal / : / Ppx/GppA phosphatase / Ppx/GppA phosphatase family / Exopolyphosphatase. Domain 2 / Hypothetical protein af1432 / Hypothetical protein af1432 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...: / Exopolyphosphatase, C-terminal / : / Ppx/GppA phosphatase / Ppx/GppA phosphatase family / Exopolyphosphatase. Domain 2 / Hypothetical protein af1432 / Hypothetical protein af1432 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ppx/GppA phosphatase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsLu, Z. / Wang, J. / Zhang, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of exopolyphosphatase (PPX) from Zymomonas mobilis in complex with magnesium ions
Authors: Aili, Z. / Lu, Z.
History
DepositionSep 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ppx/GppA phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6197
Polymers53,4181
Non-polymers2026
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-24 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.740, 47.901, 94.892
Angle α, β, γ (deg.)90.000, 126.530, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-892-

HOH

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Components

#1: Protein Ppx/GppA phosphatase


Mass: 53417.562 Da / Num. of mol.: 1 / Mutation: E137A, I169V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
Strain: ATCC 31821 / ZM4 / Gene: ZMO0713 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NPM3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 50 mM Tris pH 8.0, 500 mM NaCl, 5% glycerol 0.2 M magnesium chloride hexahydrate, 0.1 M Tris pH 6.5, 25%(w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 63367 / % possible obs: 99.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Χ2: 0.967 / Net I/σ(I): 9.9 / Num. measured all: 206483
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.56-1.592.90.30830940.8720.2120.3750.83998.2
1.59-1.623.30.28931330.890.1850.3450.85799.3
1.62-1.653.30.24831800.9210.1590.2950.85499.7
1.65-1.683.30.23131260.9390.1480.2750.87499.9
1.68-1.723.30.20431920.9450.1320.2440.88599.9
1.72-1.763.20.17631140.9540.1160.2110.88399.7
1.76-1.83.10.15431370.9620.1040.1870.89199.1
1.8-1.853.20.13231590.9730.0870.1590.90899.4
1.85-1.93.40.12731690.9810.080.150.99699.8
1.9-1.973.40.11531620.9770.0740.1371.32100
1.97-2.043.30.0831250.990.0520.0960.93799.2
2.04-2.123.10.06631680.9920.0440.080.92999.4
2.12-2.213.10.06131680.9930.0410.0741.01199.7
2.21-2.333.40.06531450.9920.0410.0771.49298.9
2.33-2.483.40.04731760.9950.030.0560.943100
2.48-2.673.30.04132040.9960.0260.0490.952100
2.67-2.943.20.03531700.9970.0230.0420.958100
2.94-3.363.50.03132120.9980.0190.0360.95799.9
3.36-4.233.20.02632280.9980.0170.0310.98599.9
4.23-503.30.02533050.9980.0160.030.79899.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GTY

8gty


Resolution: 1.56→42.55 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 3212 5.08 %
Rwork0.1701 60008 -
obs0.1718 63220 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.6 Å2 / Biso mean: 18.2207 Å2 / Biso min: 3.82 Å2
Refinement stepCycle: final / Resolution: 1.56→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 6 637 4243
Biso mean--22.7 27.72 -
Num. residues----462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.580.23911360.2132363249991
1.58-1.60.26511550.20592593274899
1.61-1.630.25881410.19612568270999
1.63-1.660.21861420.195226182760100
1.66-1.690.26541210.188426222743100
1.69-1.720.22021400.18825882728100
1.72-1.760.2061350.177526092744100
1.76-1.80.21091270.18012590271799
1.8-1.840.20191490.17292612276199
1.84-1.880.22081360.176725852721100
1.88-1.930.23731300.191226612791100
1.93-1.990.23461310.172726022733100
1.99-2.060.1941350.16972610274599
2.06-2.130.21231430.171625892732100
2.13-2.210.17881440.172126212765100
2.21-2.310.20141660.17052564273099
2.31-2.440.23331250.177526432768100
2.44-2.590.221470.169726202767100
2.59-2.790.20711270.174726742801100
2.79-3.070.19191230.175426472770100
3.07-3.510.19731390.159526572796100
3.51-4.430.16221600.137226552815100
4.43-42.550.19331600.162227172877100

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