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- PDB-7kwd: Crystal structure of Thermus thermophilus alkaline phosphatase -

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Basic information

Entry
Database: PDB / ID: 7kwd
TitleCrystal structure of Thermus thermophilus alkaline phosphatase
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / homodimeric enzyme / dephosphorylate compounds
Function / homology
Function and homology information


phosphatase activity / metal ion binding
Similarity search - Function
Alkaline phosphatase, crown domain / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Alkaline phosphatase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGallo, G. / Coelho, C. / Borges, B. / Negri, N. / Maiello, F. / Hardy, L. / Wurtele, M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)11/50963 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)448833/2014-0 Brazil
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Dynamic cross correlation analysis of Thermus thermophilus alkaline phosphatase and determinants of thermostability.
Authors: Borges, B. / Gallo, G. / Coelho, C. / Negri, N. / Maiello, F. / Hardy, L. / Wurtele, M.
History
DepositionNov 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 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: Alkaline phosphatase
B: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,32310
Polymers109,7122
Non-polymers6108
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-153 kcal/mol
Surface area31410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.175, 163.175, 163.175
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

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Components

#1: Protein Alkaline phosphatase


Mass: 54856.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHB067 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53W95
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium pH 7.5, 0.8 M Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54187 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.1→45.26 Å / Num. obs: 182535 / % possible obs: 97.8 % / Redundancy: 8.1 % / CC1/2: 0.99 / Net I/σ(I): 11.98
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 6.4 % / Num. unique obs: 28026 / CC1/2: 0.58 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3e2d

3e2d


Resolution: 2.1→45.26 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 4195 5 %
Rwork0.163 79696 -
obs0.1649 83891 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.93 Å2 / Biso mean: 35.5066 Å2 / Biso min: 14.31 Å2
Refinement stepCycle: final / Resolution: 2.1→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7304 0 34 493 7831
Biso mean--52.86 34.27 -
Num. residues----946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.120.28631300.24952482261293
2.12-2.150.25851350.2332561269696
2.15-2.170.26451350.23652571270698
2.18-2.20.26541390.222326392778100
2.2-2.230.25311380.213126132751100
2.23-2.260.24781410.203626832824100
2.26-2.290.24791390.193726402779100
2.29-2.330.2411400.187226652805100
2.33-2.370.23321400.184426502790100
2.37-2.40.24341390.177726462785100
2.4-2.450.21451380.181226252763100
2.45-2.490.23921390.180826402779100
2.49-2.540.23071400.172126542794100
2.54-2.590.22261410.173126892830100
2.59-2.650.23431390.173626442783100
2.65-2.710.24881390.182726392778100
2.71-2.770.23191420.180726882830100
2.78-2.850.2371400.18926562796100
2.85-2.930.22291380.18626242762100
2.93-3.030.2121410.173426842825100
3.03-3.140.21181400.176426642804100
3.14-3.260.21041410.170626792820100
3.26-3.410.20211410.168726802821100
3.41-3.590.19451400.154826652805100
3.59-3.820.17451420.136126812823100
3.82-4.110.17191410.123726822823100
4.11-4.520.141410.114326932834100
4.52-5.180.12651430.116527062849100
5.18-6.520.18441440.144927352879100
6.52-45.260.18181490.161228182967100

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