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- PDB-4ift: Crystal structure of double mutant thermostable NPPase from Geoba... -

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Basic information

Entry
Database: PDB / ID: 4ift
TitleCrystal structure of double mutant thermostable NPPase from Geobacillus stearothermophilus
ComponentsThermostable NPPase
KeywordsHYDROLASE / thermostable NPPase
Function / homology
Function and homology information


phosphatase activity / metal ion binding
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIA, hypothetical 1 / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsGuo, Z. / Huang, J. / Wang, F. / Qiu, R. / Wang, Y. / Ji, C.
CitationJournal: To be Published
Title: Crystal structure of thermostable NPPase from Geobacillus stearothermophilus
Authors: Guo, Z. / Huang, J. / Wang, F. / Qiu, R. / Wang, Y. / Ji, C.
History
DepositionDec 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
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: Thermostable NPPase
B: Thermostable NPPase


Theoretical massNumber of molelcules
Total (without water)59,3702
Polymers59,3702
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-17 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.822, 83.287, 176.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thermostable NPPase


Mass: 29684.793 Da / Num. of mol.: 2 / Mutation: A150V, F157L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8L1N9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.4 Å3/Da / Density % sol: 48.68 % / Mosaicity: 0.795 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES sodium, 2.0M Ammonium sulfate, 3% PEG400, 30% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 18, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.995→50 Å / Num. all: 39885 / Num. obs: 35856 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.037 / Χ2: 2.565 / Net I/σ(I): 31.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.995-2.032.60.06719072.458196.7
2.03-2.072.60.06419012.514197.3
2.07-2.112.60.05918582.449197.2
2.11-2.152.60.05819472.565196.4
2.15-2.22.60.05518892.569197.4
2.2-2.252.60.05318992.555197
2.25-2.312.60.04918962.519196.2
2.31-2.372.60.04718882.639197
2.37-2.442.60.04818822.669194.9
2.44-2.522.50.04718702.799195.4
2.52-2.612.50.04718632.881192.9
2.61-2.712.50.04518462.945193.8
2.71-2.842.40.04418332.947192.7
2.84-2.992.40.04117933.013188.7
2.99-3.172.30.04117443.053188.7
3.17-3.422.30.03617082.719185.2
3.42-3.762.10.02815722.162178
3.76-4.312.10.02815112.066173.4
4.31-5.432.40.02715601.888175.6
5.43-502.60.02514891.485167.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_1186refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PDW

3pdw


Resolution: 1.995→29.112 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8763 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 19.22 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1810 5.05 %RANDOM
Rwork0.1781 ---
all0.1806 39940 --
obs0.1806 35814 89.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.87 Å2 / Biso mean: 24.1679 Å2 / Biso min: 7.77 Å2
Refinement stepCycle: LAST / Resolution: 1.995→29.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 0 223 4129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084019
X-RAY DIFFRACTIONf_angle_d1.075453
X-RAY DIFFRACTIONf_chiral_restr0.07634
X-RAY DIFFRACTIONf_plane_restr0.005701
X-RAY DIFFRACTIONf_dihedral_angle_d14.2151489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9948-2.04870.20981330.17232692282593
2.0487-2.1090.24941570.16452739289698
2.109-2.1770.22751440.16752773291796
2.177-2.25480.23031490.16962807295697
2.2548-2.3450.23971570.16962750290797
2.345-2.45170.23011320.16872791292395
2.4517-2.58090.20471210.16792756287794
2.5809-2.74250.19951440.17482682282693
2.7425-2.9540.23571520.17482652280491
2.954-3.2510.24021390.19382560269987
3.251-3.72060.21131260.18592374250081
3.7206-4.68430.2221320.1662165229773
4.6843-29.11550.24831240.20582263238772

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