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- PDB-7f18: Crystal Structure of a mutant of acid phosphatase from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 7f18
TitleCrystal Structure of a mutant of acid phosphatase from Pseudomonas aeruginosa (Q57H/W58P/D135R)
ComponentsAcid phosphatase
KeywordsHYDROLASE / phosphorylation hydrolysis
Function / homologyAcid phosphatase, class A, bacterial / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / Acid phosphatase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsXu, X. / Hou, X.D. / Song, W. / Yin, D.J. / Rao, Y.J. / Liu, L.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)21878126 China
CitationJournal: Acs Catalysis / Year: 2021
Title: Local Electric Field Modulated Reactivity of Pseudomonas aeruginosa Acid Phosphatase for Enhancing Phosphorylation of l-Ascorbic Acid
Authors: Xu, X. / Yan, S. / Hou, X. / Song, W. / Wang, L. / Wu, T. / Qi, M. / Wu, J. / Rao, Y. / Wang, B. / Liu, L.
History
DepositionJun 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acid phosphatase
B: Acid phosphatase
C: Acid phosphatase


Theoretical massNumber of molelcules
Total (without water)70,6793
Polymers70,6793
Non-polymers00
Water00
1
A: Acid phosphatase


Theoretical massNumber of molelcules
Total (without water)23,5601
Polymers23,5601
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acid phosphatase


Theoretical massNumber of molelcules
Total (without water)23,5601
Polymers23,5601
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acid phosphatase


Theoretical massNumber of molelcules
Total (without water)23,5601
Polymers23,5601
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.822, 119.587, 190.059
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acid phosphatase


Mass: 23559.756 Da / Num. of mol.: 3 / Mutation: Q57H/W58P/D135R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: phoC, C0044_01345, CAZ10_16160, DT376_10070, DZ962_30070, IPC116_25940, IPC1295_25655, IPC1323_25265, IPC1481_23795, IPC1505_26850, IPC1509_05755, IPC36_01875, IPC582_09790, IPC620_15205, ...Gene: phoC, C0044_01345, CAZ10_16160, DT376_10070, DZ962_30070, IPC116_25940, IPC1295_25655, IPC1323_25265, IPC1481_23795, IPC1505_26850, IPC1509_05755, IPC36_01875, IPC582_09790, IPC620_15205, IPC669_21580, NCTC13621_04764, RW109_RW109_00792
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6FFE3, acid phosphatase

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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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M BIS-TRIS pH 6.5, 50% v/v Polypropylene glycol P 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 3.189→23.63 Å / Num. obs: 13485 / % possible obs: 99.07 % / Redundancy: 4.92 % / Rsym value: 0.126 / Net I/av σ(I): 30.468 / Net I/σ(I): 9.9
Reflection shellResolution: 3.26→3.52 Å / Num. unique obs: 855 / Rsym value: 0.394

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTV8.38Adata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F17

7f17


Resolution: 3.3→23.63 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.892 / SU B: 28.836 / SU ML: 0.437 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.6 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 590 4.8 %RANDOM
Rwork0.191 ---
obs0.1948 11592 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.91 Å2 / Biso mean: 76.538 Å2 / Biso min: 44.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å2-0 Å2
2--4.82 Å20 Å2
3----5.86 Å2
Refinement stepCycle: final / Resolution: 3.3→23.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4869 0 0 0 4869
Num. residues----635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135037
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174692
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.6586879
X-RAY DIFFRACTIONr_angle_other_deg1.1581.56810872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97720.22273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.05115732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1361548
X-RAY DIFFRACTIONr_chiral_restr0.0780.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021077
LS refinement shellResolution: 3.3→3.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 44 -
Rwork0.286 814 -
all-858 -
obs--98.51 %

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