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- PDB-7cle: Non-Specific Class-c acidphosphatase from Sphingobium sp. RSMS -

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Basic information

Entry
Database: PDB / ID: 7cle
TitleNon-Specific Class-c acidphosphatase from Sphingobium sp. RSMS
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 / Acid phosphatase
Function and homology information
Biological speciesSphingobium sp. 20006FA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.342 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
DepositionJul 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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)31,2312
Polymers31,2071
Non-polymers241
Water2,342130
1
A: Acid phosphatase
hetero molecules

A: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4624
Polymers62,4142
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation46_445z-1/4,-y-1/4,x+1/41
Buried area6490 Å2
ΔGint-63 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.622, 170.622, 170.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

21A-522-

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.32 Å3/Da / Density % sol: 62.91 % / Description: Hexagonal Crystals
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.5
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 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.34→45.6 Å / Num. obs: 18061 / % possible obs: 99.4 % / Redundancy: 28.9 % / Biso Wilson estimate: 25.643 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.7
Reflection shellResolution: 2.34→2.42 Å / Num. unique obs: 1632 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.342→42.656 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 885 4.91 %
Rwork0.1915 17148 -
obs0.1931 18033 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.49 Å2 / Biso mean: 35.047 Å2 / Biso min: 18.06 Å2
Refinement stepCycle: final / Resolution: 2.342→42.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 1 130 1963
Biso mean--18.97 39.79 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031875
X-RAY DIFFRACTIONf_angle_d0.6172556
X-RAY DIFFRACTIONf_chiral_restr0.044280
X-RAY DIFFRACTIONf_plane_restr0.004341
X-RAY DIFFRACTIONf_dihedral_angle_d9.5631098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3423-2.48910.26051330.2235272297
2.4891-2.68120.26941450.21212839100
2.6812-2.9510.29831560.23362821100
2.951-3.37790.25661440.21912850100
3.3779-4.25520.22411520.17512876100
4.2552-42.6560.16261550.16183040100
Refinement TLS params.Method: refined / Origin x: 4.1833 Å / Origin y: -21.1355 Å / Origin z: 29.3795 Å
111213212223313233
T0.3086 Å2-0.0215 Å2-0.0036 Å2-0.1637 Å20.028 Å2--0.2761 Å2
L1.2555 °20.0996 °2-0.8316 °2-0.8784 °2-0.027 °2--1.7703 °2
S-0.0274 Å °0.1981 Å °0.0322 Å °-0.2131 Å °-0.0057 Å °0.0099 Å °-0.0228 Å °-0.0891 Å °0.0381 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA19 - 272
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 130

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