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- PDB-8gdl: Acid phosphatase pseudoenzyme from flea -

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Basic information

Entry
Database: PDB / ID: 8gdl
TitleAcid phosphatase pseudoenzyme from flea
ComponentsSecreted salivary acid phosphatase
KeywordsLIPID BINDING PROTEIN / fatty acid / leukotriene / serotonin / cysteinyl leukotriene / histamine
Function / homologyPALMITOLEIC ACID / SEROTONIN
Function and homology information
Biological speciesXenopsylla cheopis (oriental rat flea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLu, S. / Andersen, J.F. / Ribeiro, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Commun Biol / Year: 2023
Title: Acid phosphatase-like proteins, a biogenic amine and leukotriene-binding salivary protein family from the flea Xenopsylla cheopis.
Authors: Lu, S. / Andersen, J.F. / Bosio, C.F. / Hinnebusch, B.J. / Ribeiro, J.M.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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: Secreted salivary acid phosphatase
B: Secreted salivary acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,98310
Polymers80,7382
Non-polymers1,2458
Water5,405300
1
A: Secreted salivary acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0886
Polymers40,3691
Non-polymers7195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Secreted salivary acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8954
Polymers40,3691
Non-polymers5273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.968, 71.898, 113.513
Angle α, β, γ (deg.)90.00, 91.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Secreted salivary acid phosphatase


Mass: 40368.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopsylla cheopis (oriental rat flea) / Plasmid: VR-1020 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Chemical ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O / Comment: neurotransmitter*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C16H30O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 3 M ammonium sulfate, 0.1 M MES pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 75041 / % possible obs: 96.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.15 / Χ2: 1.307 / Net I/σ(I): 4.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.75-1.784.10.74535400.4761
1.78-1.814.50.69636390.5191.4
1.81-1.854.50.60936980.54194.1
1.85-1.894.70.55637730.596195.5
1.89-1.934.80.50437670.639196.6
1.93-1.974.90.4437970.717197.1
1.97-2.024.90.40937480.784197.4
2.02-2.074.90.36137970.919197.2
2.07-2.144.90.3337191.007196.1
2.14-2.24.60.28336571.198193.6
2.2-2.285.40.26737981.253198.2
2.28-2.385.60.24338431.382198.7
2.38-2.485.50.21937601.4198.6
2.48-2.615.50.20338221.487198.6
2.61-2.785.40.17538171.642198.3
2.78-2.995.30.14637881.867197.8
2.99-3.2950.11736802.241195.7
3.29-3.775.30.08538142.506198.1
3.77-4.7550.06537672.322195.5
4.75-505.10.05538171.806195.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→44.54 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 3674 4.9 %
Rwork0.2154 --
obs0.2172 75002 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5475 0 82 300 5857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075661
X-RAY DIFFRACTIONf_angle_d0.8997647
X-RAY DIFFRACTIONf_dihedral_angle_d8.177777
X-RAY DIFFRACTIONf_chiral_restr0.053846
X-RAY DIFFRACTIONf_plane_restr0.007970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.3362960.3251728X-RAY DIFFRACTION61
1.78-1.80.37221340.29822648X-RAY DIFFRACTION95
1.8-1.830.36451290.27962717X-RAY DIFFRACTION97
1.83-1.850.29421260.25622786X-RAY DIFFRACTION98
1.85-1.880.2531230.25152776X-RAY DIFFRACTION99
1.88-1.910.26691130.23542854X-RAY DIFFRACTION99
1.91-1.950.32391420.2342787X-RAY DIFFRACTION99
1.95-1.980.25441490.23432784X-RAY DIFFRACTION99
1.98-2.020.31641320.22822806X-RAY DIFFRACTION99
2.02-2.060.2881550.22522821X-RAY DIFFRACTION99
2.06-2.110.27981380.2192786X-RAY DIFFRACTION98
2.11-2.150.28221530.2212711X-RAY DIFFRACTION98
2.16-2.210.27241600.22672710X-RAY DIFFRACTION96
2.21-2.270.26661290.20862812X-RAY DIFFRACTION99
2.27-2.340.23921360.21282801X-RAY DIFFRACTION100
2.34-2.410.27681460.21522849X-RAY DIFFRACTION99
2.41-2.50.26811460.21922786X-RAY DIFFRACTION100
2.5-2.60.28631820.2262785X-RAY DIFFRACTION100
2.6-2.710.28351620.22082820X-RAY DIFFRACTION100
2.72-2.860.25411250.23182850X-RAY DIFFRACTION100
2.86-3.040.27251310.22432799X-RAY DIFFRACTION99
3.04-3.270.24221530.22212707X-RAY DIFFRACTION95
3.27-3.60.26541540.20342816X-RAY DIFFRACTION99
3.6-4.120.20561320.1852813X-RAY DIFFRACTION98
4.12-5.190.17681720.17132746X-RAY DIFFRACTION97
5.19-44.540.19151560.20232830X-RAY DIFFRACTION97
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)
11.20320.3645-0.41451.0654-0.34870.87080.0389-0.04150.07550.04480.0109-0.0311-0.07890.0262-0.04310.10080.0113-0.00990.1118-0.00990.09670.2857-0.727512.3592
20.8946-0.1647-0.1271.1338-0.17020.6696-0.00260.04060.0298-0.03770.0072-0.04430.03240.0244-0.00540.1236-0.0057-0.02770.1194-0.00850.088322.4684-7.557244.4368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 405)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 403)

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