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- PDB-7f7d: Crystal structure of Non-specific class-C acid phosphatase from S... -

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Basic information

Entry
Database: PDB / ID: 7f7d
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 / homology
Function and homology information


cell outer membrane
Similarity search - Function
5-nucleotidase lipoprotein e(P4) / Acid phosphatase, class B-like / HAD superfamily, subfamily IIIB (Acid phosphatase) / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
ADENOSINE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Acid phosphatase
Similarity search - Component
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 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7005
Polymers31,2071
Non-polymers4934
Water3,387188
1
A: Acid phosphatase
hetero molecules

A: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,39910
Polymers62,4142
Non-polymers9858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation46_445z-1/4,-y-1/4,x+1/41
Buried area7980 Å2
ΔGint-78 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.937, 167.937, 167.937
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Space group name HallI4bd2c3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y,-z+1/2,x
#11: z,-x,-y+1/2
#12: -y+1/2,z,-x
#13: -z,-x+1/2,y
#14: -z+1/2,x,-y
#15: y,-z,-x+1/2
#16: x,-y,-z+1/2
#17: -x+1/2,y,-z
#18: -x,-y+1/2,z
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x+1/2,y+1/2,z+1/2
#26: x+3/4,-z+3/4,y+5/4
#27: x+3/4,z+5/4,-y+5/4
#28: z+3/4,y+5/4,-x+5/4
#29: -z+3/4,y+5/4,x+3/4
#30: -y+3/4,x+5/4,z+3/4
#31: y+3/4,-x+3/4,z+5/4
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1,x+1/2
#35: z+1/2,-x+1/2,-y+1
#36: -y+1,z+1/2,-x+1/2
#37: -z+1/2,-x+1,y+1/2
#38: -z+1,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1
#40: x+1/2,-y+1/2,-z+1
#41: -x+1,y+1/2,-z+1/2
#42: -x+1/2,-y+1,z+1/2
#43: y+3/4,x+5/4,-z+5/4
#44: -y+3/4,-x+3/4,-z+3/4
#45: z+3/4,-y+3/4,x+5/4
#46: -z+3/4,-y+3/4,-x+3/4
#47: -x+3/4,z+5/4,y+3/4
#48: -x+3/4,-z+3/4,-y+3/4
Components on special symmetry positions
IDModelComponents
11A-484-

HOH

21A-558-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 192 molecules

#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.16 Å3/Da / Density % sol: 66.63 % / 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 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→44.88 Å / Num. obs: 20809 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 23.27 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 1778 / CC1/2: 0.875

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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→41.98 Å / SU ML: 0.2156 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2015 1051 5.06 %
Rwork0.1649 19737 -
obs0.1667 20788 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 32 188 2062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861937
X-RAY DIFFRACTIONf_angle_d0.89272647
X-RAY DIFFRACTIONf_chiral_restr0.0541289
X-RAY DIFFRACTIONf_plane_restr0.0092351
X-RAY DIFFRACTIONf_dihedral_angle_d6.7055283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.24961380.17912427X-RAY DIFFRACTION100
2.3-2.420.23191300.18072410X-RAY DIFFRACTION100
2.42-2.570.24321220.17552423X-RAY DIFFRACTION100
2.57-2.770.22691290.17932432X-RAY DIFFRACTION100
2.77-3.050.20991190.17672463X-RAY DIFFRACTION100
3.05-3.490.21051430.16952457X-RAY DIFFRACTION100
3.49-4.40.1691200.13462513X-RAY DIFFRACTION100
4.4-41.980.17441500.16632612X-RAY DIFFRACTION99.71
Refinement TLS params.Method: refined / Origin x: 4.28133847574 Å / Origin y: -20.8988980116 Å / Origin z: 28.8324085356 Å
111213212223313233
T0.227832709543 Å2-0.0284787783109 Å20.0124958466973 Å2-0.10179466996 Å20.0168299338255 Å2--0.194501596061 Å2
L1.00774268881 °2-0.00751827662477 °2-0.527476599113 °2-0.464092498859 °20.10239803752 °2--1.42279623023 °2
S-0.0205346639149 Å °0.126079696899 Å °-0.0049766455754 Å °-0.158490501205 Å °0.0135219843757 Å °-0.00016262225588 Å °-0.064998615241 Å °-0.0385152650466 Å °0.0118654934698 Å °
Refinement TLS groupSelection details: all

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