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

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Basic information

Entry
Database: PDB / ID: 7doq
TitleLp major histidine acid phosphatase mutant D281A/5'-AMP
ComponentsAcid phosphatase
KeywordsHYDROLASE / Complex / 5'-AMP
Function / homologyHistidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / PHOSPHATE ION / Acid phosphatase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionDec 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: 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
B: Acid phosphatase
C: Acid phosphatase
D: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,48711
Polymers150,8224
Non-polymers6657
Water4,666259
1
A: Acid phosphatase
B: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7916
Polymers75,4112
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-56 kcal/mol
Surface area28640 Å2
MethodPISA
2
C: Acid phosphatase
D: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6965
Polymers75,4112
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-53 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.498, 56.479, 146.349
Angle α, β, γ (deg.)90.000, 110.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acid phosphatase / histidine acid phosphatase / Histidine-type phosphatase


Mass: 37705.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_05010, DI026_02700 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F805
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 20% 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: 298.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2016
RadiationMonochromator: 0.978 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→35.62 Å / Num. obs: 66012 / % possible obs: 96.37 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.255 Å / Rmerge(I) obs: 0.479 / Num. unique obs: 4815

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IT0

3it0


Resolution: 2.2→35.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 3517 5.1 %RANDOM
Rwork0.1916 ---
obs0.1935 66012 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 258.21 Å2 / Biso mean: 40.252 Å2 / Biso min: 18.51 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å2-1.72 Å2
2--0.1 Å20 Å2
3----0.72 Å2
Refinement stepCycle: final / Resolution: 2.2→35.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10501 0 35 259 10795
Biso mean--111.95 40.58 -
Num. residues----1328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310847
X-RAY DIFFRACTIONr_bond_other_d0.0350.01710112
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.64314772
X-RAY DIFFRACTIONr_angle_other_deg2.2421.57323383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73551340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29124.068526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.936151832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2391536
X-RAY DIFFRACTIONr_chiral_restr0.0680.21429
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212290
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022390
LS refinement shellResolution: 2.2→2.255 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.296 261 -
Rwork0.262 4815 -
obs--96.05 %

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