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- PDB-7f7c: Crystal structure of Non-specific class-C acid phosphatase from S... -

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Basic information

Entry
Database: PDB / ID: 7f7c
TitleCrystal structure of Non-specific class-C acid phosphatase from Sphingobium sp. RSMS bound to Adenosine 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 / ADENOSINE / PHOSPHATE ION / Acid phosphatase
Function and homology information
Biological speciesSphingobium sp. 20006FA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 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 1.1Nov 13, 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)31,5934
Polymers31,2071
Non-polymers3873
Water2,288127
1
A: Acid phosphatase
hetero molecules

A: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1878
Polymers62,4142
Non-polymers7736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation46_445z-1/4,-y-1/4,x+1/41
Buried area7950 Å2
ΔGint-81 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.998, 167.998, 167.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Space group name HallI4bd2c3
Components on special symmetry positions
IDModelComponents
11A-570-

HOH

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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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.17 Å3/Da / Density % sol: 66.66 % / 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: 2.2→48.5 Å / Num. obs: 20831 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 30.79 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 1758 / CC1/2: 0.686

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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: 2.2→48.5 Å / SU ML: 0.2296 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.767
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2253 1051 5.05 %
Rwork0.1837 19757 -
obs0.1858 20808 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 25 127 1985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01031906
X-RAY DIFFRACTIONf_angle_d1.01652605
X-RAY DIFFRACTIONf_chiral_restr0.062285
X-RAY DIFFRACTIONf_plane_restr0.0081345
X-RAY DIFFRACTIONf_dihedral_angle_d6.4752275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.28751380.25022411X-RAY DIFFRACTION100
2.3-2.420.24261310.22212427X-RAY DIFFRACTION99.96
2.42-2.570.26731220.1932433X-RAY DIFFRACTION100
2.57-2.770.28561290.18982430X-RAY DIFFRACTION100
2.77-3.050.24171190.19112463X-RAY DIFFRACTION100
3.05-3.490.23881430.1782455X-RAY DIFFRACTION100
3.49-4.40.16631190.14832512X-RAY DIFFRACTION99.96
4.4-48.50.21111500.18732626X-RAY DIFFRACTION99.82
Refinement TLS params.Method: refined / Origin x: 4.35166904967 Å / Origin y: -20.8422872627 Å / Origin z: 29.0058386633 Å
111213212223313233
T0.384792167991 Å2-0.0615011570093 Å20.0186193494389 Å2-0.149130311869 Å20.0151010460803 Å2--0.27807220711 Å2
L1.05206442893 °20.308289420497 °2-0.333968451569 °2-1.01519016158 °2-0.0494498732554 °2--1.22240503552 °2
S-0.0896834489912 Å °0.18001919353 Å °-0.0162710570909 Å °-0.303948348278 Å °0.0787279445999 Å °0.0482438983539 Å °-0.0579167345041 Å °-0.0141577741691 Å °0.00220654221043 Å °
Refinement TLS groupSelection details: all

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