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- PDB-7tm9: Crystal structure of Bacterial alkaline phosphatase from Klebsiel... -

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Basic information

Entry
Database: PDB / ID: 7tm9
TitleCrystal structure of Bacterial alkaline phosphatase from Klebsiella pneumoniae
ComponentsBacterial alkaline phosphatase
KeywordsHYDROLASE / Bacterial alkaline phosphatase / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


phosphatase activity / metal ion binding
Similarity search - Function
Alkaline phosphatase, active site / Alkaline phosphatase active site. / 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
Bacterial alkaline phosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To be published
Title: Crystal structure of Bacterial alkaline phosphatase from Klebsiella pneumoniae
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C.
History
DepositionJan 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterial alkaline phosphatase
B: Bacterial alkaline phosphatase
C: Bacterial alkaline phosphatase
D: Bacterial alkaline phosphatase
E: Bacterial alkaline phosphatase
F: Bacterial alkaline phosphatase
G: Bacterial alkaline phosphatase
H: Bacterial alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,11532
Polymers390,8748
Non-polymers1,24124
Water67,0343721
1
A: Bacterial alkaline phosphatase
B: Bacterial alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0298
Polymers97,7192
Non-polymers3106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-142 kcal/mol
Surface area27010 Å2
MethodPISA
2
C: Bacterial alkaline phosphatase
D: Bacterial alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0298
Polymers97,7192
Non-polymers3106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-137 kcal/mol
Surface area27050 Å2
MethodPISA
3
E: Bacterial alkaline phosphatase
F: Bacterial alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0298
Polymers97,7192
Non-polymers3106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-141 kcal/mol
Surface area26920 Å2
MethodPISA
4
G: Bacterial alkaline phosphatase
H: Bacterial alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0298
Polymers97,7192
Non-polymers3106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-141 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.950, 240.600, 101.479
Angle α, β, γ (deg.)90.000, 105.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bacterial alkaline phosphatase


Mass: 48859.250 Da / Num. of mol.: 8 / Fragment: KlpnC.00059.a.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_10650 / Plasmid: KlpnC.00059.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3GK94
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3721 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.3 % / Mosaicity: 0.2 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus A9: 12% v/v PEG 500 MME: 6% (w/v) PEG 20000, 0.1 M Tris (base): BICINE, 0.03 M Magnesium chloride hexahydrate and 0.03 M Calcium chloride dihydrate), KlpnC.00059.a.B2.PS38688 at 27. ...Details: Morpheus A9: 12% v/v PEG 500 MME: 6% (w/v) PEG 20000, 0.1 M Tris (base): BICINE, 0.03 M Magnesium chloride hexahydrate and 0.03 M Calcium chloride dihydrate), KlpnC.00059.a.B2.PS38688 at 27.45 mg/mL, Tray: plate 12317 well A9 drop 1, Puck: PSL0501, Cryo: DIRECT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.95→49.66 Å / Num. obs: 449685 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.27 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.118 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.95-1.983.20.33337387117350.83398.7
10.68-49.663.70.057561915020.9157.399

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ED8

1ed8


Resolution: 1.95→46.09 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 22419 4.99 %
Rwork0.1722 427266 -
obs0.1741 449685 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.13 Å2 / Biso mean: 15.2813 Å2 / Biso min: 1.62 Å2
Refinement stepCycle: final / Resolution: 1.95→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25808 0 24 3721 29553
Biso mean--28.01 24.49 -
Num. residues----3528
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 (%)
1.95-1.970.28017510.23138821463393
1.97-20.28157580.2204142501500893
2-2.020.23957030.2102138721457592
2.02-2.050.26297950.2114141211491693
2.05-2.070.25947620.205141081487093
2.07-2.10.26017430.1997139191466293
2.1-2.130.25616750.2068142721494793
2.13-2.160.24237820.198141841496694
2.16-2.20.25027430.1925141201486393
2.2-2.230.24187700.1889141421491293
2.23-2.270.24747560.1887140161477293
2.27-2.310.22197110.1811143491506094
2.31-2.360.21826650.177135731423889
2.36-2.40.23436910.1795129391363086
2.4-2.460.22177700.1769143051507595
2.46-2.510.22787580.1789147411549997
2.51-2.580.22037420.1737147921553497
2.58-2.650.22837540.1817146761543097
2.65-2.720.21227700.1757146871545797
2.72-2.810.19698000.1721145661536696
2.81-2.910.20877810.1691146651544697
2.91-3.030.20747580.1641145711532996
3.03-3.170.20398100.1738145241533496
3.17-3.330.20147670.1682141661493394
3.33-3.540.18766690.157129311360085
3.54-3.820.18327570.1481148211557897
3.82-4.20.16617910.1374147971558897
4.2-4.810.1517450.1285147901553597
4.81-6.050.16947680.1557146461541497
6.06-46.090.19026740.1593138411451591

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