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- PDB-7f7b: Crystal structure of Non-specific class-C acid phosphatase from S... -

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Basic information

Entry
Database: PDB / ID: 7f7b
TitleCrystal structure of Non-specific class-C acid phosphatase from Sphingobium sp. RSMS bound to BIS-TRIS at pH 5.5
ComponentsAcid phosphatase
KeywordsHYDROLASE / Non specific Phosphatase / Class c / HAD superfamily.
Function / homology5-nucleotidase lipoprotein e(P4) / Acid phosphatase, class B-like / HAD superfamily, subfamily IIIB (Acid phosphatase) / HAD superfamily / HAD-like superfamily / cell outer membrane / PHOSPHATE ION / Acid phosphatase
Function and homology information
Biological speciesSphingobium sp. 20006FA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.34 Å
AuthorsGaur, N.K. / Kumar, A. / Sunder, S. / Mukhopadhyaya, R. / Makde, R.D.
CitationJournal: To Be Published
Title: Non-Specific Class-c acidphosphatase from Sphingobium sp. RSMS
Authors: Gaur, N.K. / Kumar, A. / Sunder, S. / Mukhopadhyaya, R. / Makde, R.D.
History
DepositionJun 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5354
Polymers31,2071
Non-polymers3293
Water2,054114
1
A: Acid phosphatase
hetero molecules

A: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0718
Polymers62,4142
Non-polymers6576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation46_445z-1/4,-y-1/4,x+1/41
Buried area7740 Å2
ΔGint-74 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.380, 168.380, 168.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Space group name HallI4bd2c3

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Components

#1: Protein Acid phosphatase


Mass: 31206.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. 20006FA (bacteria) / Gene: A8O16_10785 / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 DE3 / References: UniProt: A0A197BYF0
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.19 Å3/Da / Density % sol: 66.96 % / Description: Hexagonal Crystals
Crystal growTemperature: 294 K / Method: microbatch
Details: 1M Ammonium sulphate, 0.1 M Bis-tris pH 5.5, 1% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.34→48.61 Å / Num. obs: 17523 / % possible obs: 99.6 % / Redundancy: 28.4 % / Biso Wilson estimate: 28.72 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.9
Reflection shellResolution: 2.34→2.42 Å / Rmerge(I) obs: 1.083 / Num. unique obs: 1620 / CC1/2: 0.833

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.34→42.1 Å / SU ML: 0.207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8649
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 836 4.78 %
Rwork0.1825 16667 -
obs0.184 17503 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.69 Å2
Refinement stepCycle: LAST / Resolution: 2.34→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 20 114 1973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821904
X-RAY DIFFRACTIONf_angle_d0.94132595
X-RAY DIFFRACTIONf_chiral_restr0.0532281
X-RAY DIFFRACTIONf_plane_restr0.0098344
X-RAY DIFFRACTIONf_dihedral_angle_d10.0185295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.480.2521410.20692651X-RAY DIFFRACTION97.38
2.48-2.670.27691420.20672733X-RAY DIFFRACTION100
2.68-2.940.29661230.21692763X-RAY DIFFRACTION100
2.94-3.370.22171270.20892795X-RAY DIFFRACTION100
3.37-4.240.18441640.16452772X-RAY DIFFRACTION100
4.25-42.10.17611390.15372953X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: 4.26229713283 Å / Origin y: -20.8422341845 Å / Origin z: 28.8956531614 Å
111213212223313233
T0.282758383084 Å2-0.057131897286 Å20.0208173072771 Å2-0.140778116233 Å20.0306843938899 Å2--0.247715135003 Å2
L1.14060816629 °20.105927827999 °2-0.482543813151 °2-0.703887339254 °20.117261619109 °2--1.5895752715 °2
S-0.067153860513 Å °0.189245428536 Å °0.00109688916279 Å °-0.198736930133 Å °0.0563120938297 Å °-0.00304682749351 Å °-0.0190098230949 Å °-0.0718199576948 Å °0.0151212593991 Å °
Refinement TLS groupSelection details: all

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