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- PDB-7d2f: Lp major histidine acid phosphatase mutant D281A/5'-AMP -

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Basic information

Entry
Database: PDB / ID: 7d2f
TitleLp major histidine acid phosphatase mutant D281A/5'-AMP
ComponentsMajor acid phosphatase
KeywordsHYDROLASE / Complex / 5'-AMP
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / nucleotide binding
Similarity search - Function
: / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Major acid phosphatase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGuo, Y. / Teng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700650 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural insights into a new substrate binding mode of a histidine acid phosphatase from Legionella pneumophila.
Authors: Guo, Y. / Zhou, D. / Zhang, H. / Zhang, N.N. / Qi, X. / Chen, X. / Chen, Q. / Li, J. / Ge, H. / Teng, Y.B.
History
DepositionSep 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _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: Major acid phosphatase
B: Major acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2844
Polymers73,5892
Non-polymers6942
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-43 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.610, 118.410, 118.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Major acid phosphatase / histidine acid phosphatase


Mass: 36794.629 Da / Num. of mol.: 2 / Mutation: D281A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Gene: lpg1119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZWG6, acid phosphatase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 15-25% w/v Polyethylene glycol 3350, 0.2M Sodium formate, 0.025% (w/v) low gelling temperature agarose

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Data collection

DiffractionMean temperature: 77.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→83.87 Å / Num. obs: 23466 / % possible obs: 94.2 % / Redundancy: 6.9 % / CC1/2: 0.989 / Net I/σ(I): 9.7
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 2448 / CC1/2: 0.752

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IT0

3it0


Resolution: 2.6→83.87 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.865 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.145 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1083 4.6 %RANDOM
Rwork0.2202 ---
obs0.2218 22330 94.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85 Å2 / Biso mean: 25.17 Å2 / Biso min: 12.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2---0.74 Å20 Å2
3---0.69 Å2
Refinement stepCycle: final / Resolution: 2.6→83.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5166 0 46 19 5231
Biso mean--33 21.06 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135346
X-RAY DIFFRACTIONr_bond_other_d0.0350.0174976
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.6447283
X-RAY DIFFRACTIONr_angle_other_deg2.2971.57211498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.995652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01523.961255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26815890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7331518
X-RAY DIFFRACTIONr_chiral_restr0.0610.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026044
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021178
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 73 -
Rwork0.319 1722 -
all-1795 -
obs--99.28 %

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