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- PDB-7f7a: Crystal structure of Non-specific class-C acid phosphatase from S... -

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Basic information

Entry
Database: PDB / ID: 7f7a
TitleCrystal structure of Non-specific class-C acid phosphatase from Sphingobium sp. RSMS bound to Adenine at pH 9
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 / ADENINE / Acid phosphatase
Function and homology information
Biological speciesSphingobium sp. 20006FA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.7 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 20, 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)31,3663
Polymers31,2071
Non-polymers1592
Water84747
1
A: Acid phosphatase
hetero molecules

A: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7336
Polymers62,4142
Non-polymers3194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation46_445z-1/4,-y-1/4,x+1/41
Buried area7150 Å2
ΔGint-60 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.581, 168.581, 168.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-414-

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
Details: ADE is the Ligand found in crystal structure / 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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.2 Å3/Da / Density % sol: 66.87 % / Description: Hexagonal Crystals
Crystal growTemperature: 294 K / Method: microbatch / pH: 9 / Details: 0.1 M Bicine pH 9.0, 20% PEG 6000

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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: Aug 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→45.06 Å / Num. obs: 11574 / % possible obs: 100 % / Redundancy: 36.4 % / CC1/2: 0.998 / Net I/σ(I): 16.5
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 1506 / CC1/2: 0.792

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.7→45.06 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 571 4.94 %
Rwork0.1923 --
obs0.1951 11552 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 11 47 1893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021890
X-RAY DIFFRACTIONf_angle_d0.4522578
X-RAY DIFFRACTIONf_dihedral_angle_d11.5221099
X-RAY DIFFRACTIONf_chiral_restr0.039281
X-RAY DIFFRACTIONf_plane_restr0.004343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.97180.33111530.27772680X-RAY DIFFRACTION100
2.9718-3.40170.32741360.22532686X-RAY DIFFRACTION100
3.4017-4.28510.22711360.17722744X-RAY DIFFRACTION100
4.2851-42.154040.21781460.16932871X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.2485 Å / Origin y: -21.0937 Å / Origin z: 28.9572 Å
111213212223313233
T0.386 Å2-0.0373 Å20.0318 Å2-0.2528 Å20.0513 Å2--0.3987 Å2
L1.5143 °20.1169 °2-0.8904 °2-1.0752 °20.2171 °2--2.7818 °2
S-0.021 Å °0.2404 Å °0.0288 Å °-0.1925 Å °-0.0214 Å °-0.034 Å °-0.0533 Å °-0.0689 Å °0.0522 Å °
Refinement TLS groupSelection details: all

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