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- PDB-8yc1: Acid phosphate hydrolase from Shigella flexneri (apo) -

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Basic information

Entry
Database: PDB / ID: 8yc1
TitleAcid phosphate hydrolase from Shigella flexneri (apo)
ComponentsAcid phosphatase
KeywordsHYDROLASE / apo
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space
Similarity search - Function
: / Acid phosphatase, class A, bacterial, conserved site / Class A bacterial acid phosphatases signature. / Acid phosphatase, class A, bacterial / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDu, W.Y. / Pan, X.M. / Dong, L.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073746 China
CitationJournal: To be published
Title: Acid phosphate hydrolase from Shigella flexneri (apo)
Authors: Du, W.Y. / Pan, X.M. / Dong, L.B.
History
DepositionFeb 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acid phosphatase
B: Acid phosphatase
C: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4274
Polymers85,3353
Non-polymers921
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.840, 98.840, 144.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Acid phosphatase


Mass: 28444.904 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: phoN / Production host: Escherichia coli (E. coli) / References: UniProt: O50542, acid phosphatase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M sodium acetate trihydrate, 0.2M magnesium formate dihydrate, 18% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.7→41.03 Å / Num. obs: 22925 / % possible obs: 99.91 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.03683 / Net I/σ(I): 13.1
Reflection shellResolution: 2.7→2.797 Å / Redundancy: 2 % / Num. unique obs: 2255 / CC1/2: 0.868

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Processing

Software
NameVersionClassification
PHENIX(1.18.1_3865: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→41.03 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1999 8.72 %
Rwork0.1953 --
obs0.1993 22920 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 6 0 5191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015296
X-RAY DIFFRACTIONf_angle_d1.4257188
X-RAY DIFFRACTIONf_dihedral_angle_d18.9731953
X-RAY DIFFRACTIONf_chiral_restr0.107798
X-RAY DIFFRACTIONf_plane_restr0.009949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.31591410.25471479X-RAY DIFFRACTION100
2.77-2.840.31261390.23981471X-RAY DIFFRACTION100
2.84-2.930.35111410.24371450X-RAY DIFFRACTION100
2.93-3.020.30761430.2341489X-RAY DIFFRACTION100
3.02-3.130.30961370.24021457X-RAY DIFFRACTION100
3.13-3.250.30291390.22711486X-RAY DIFFRACTION100
3.25-3.40.30031400.22241488X-RAY DIFFRACTION100
3.4-3.580.27681450.19631475X-RAY DIFFRACTION100
3.58-3.80.23961440.20081504X-RAY DIFFRACTION100
3.81-4.10.23651440.18311480X-RAY DIFFRACTION100
4.1-4.510.20881380.16921515X-RAY DIFFRACTION100
4.51-5.160.181460.16751499X-RAY DIFFRACTION100
5.16-6.50.22731470.20521527X-RAY DIFFRACTION100
6.5-41.030.19071550.16221601X-RAY DIFFRACTION100

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