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- PDB-7z32: Escherichia coli periplasmic phytase AppA D304A mutant, phosphohi... -

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Basic information

Entry
Database: PDB / ID: 7z32
TitleEscherichia coli periplasmic phytase AppA D304A mutant, phosphohistidine intermediate
ComponentsAcidphosphatase
KeywordsHYDROLASE / histidine acid phosphatase / phytase
Function / homology
Function and homology information


4-phytase / 4-phytase activity / acid phosphatase / acid phosphatase activity
Similarity search - Function
Histidine acid phosphatases active site signature. / : / 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
NICKEL (II) ION / Acidphosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAcquistapace, I.M. / Brearley, C.A. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M022978/1 United Kingdom
CitationJournal: Int J Mol Sci / Year: 2022
Title: Insights to the Structural Basis for the Stereospecificity of the Escherichia coli Phytase, AppA.
Authors: Acquistapace, I.M. / Thompson, E.J. / Kuhn, I. / Bedford, M.R. / Brearley, C.A. / Hemmings, A.M.
History
DepositionMar 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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: Acidphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9812
Polymers44,9231
Non-polymers591
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.750, 47.960, 65.970
Angle α, β, γ (deg.)90.000, 101.080, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Acidphosphatase / AppA family phytase/histidine-type acid phosphatase / AppA_2 protein / Bifunctional acid ...AppA family phytase/histidine-type acid phosphatase / AppA_2 protein / Bifunctional acid phosphatase/4-phytase / Hypothetical protein / Periplasmic AppA protein / Periplasmic AppA protein [includes: phosphoanhydrid phosphohydrolase and 4-phytase] / Phosphoanhydride phosphohydrolase (pH 2.5 acid phosphatase) (AP) / 4- phytase / Phosphoanhydride phosphorylase / Phytase AppA


Mass: 44922.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: appA, appA_1, appA_2, A8C65_14190, ABE90_015325, ACN81_22175, ACU57_13335, AM464_22895, AML23_15750, AT845_000200, B7C15_002169, BANRA_01347, BANRA_01497, BANRA_01938, BANRA_04663, BHS87_05220, ...Gene: appA, appA_1, appA_2, A8C65_14190, ABE90_015325, ACN81_22175, ACU57_13335, AM464_22895, AML23_15750, AT845_000200, B7C15_002169, BANRA_01347, BANRA_01497, BANRA_01938, BANRA_04663, BHS87_05220, BJI68_21075, BJJ90_16615, BO068_002094, BON73_13465, BON93_08495, BON98_05845, BTQ06_12390, BUE81_23535, BvCms2454_01079, BvCmsHHP019_04940, BvCmsHHP056_02151, BvCmsKKP061_02619, BvCmsKSNP073_03019, BvCmsKSP011_04200, BvCmsKSP067_04712, C2U48_04610, C3F40_07155, C5F72_16390, C5N07_03615, C5Y87_10555, C6N50_004791, C7B02_01415, C9160_17160, CA593_23620, CG831_002343, D0X26_04185, D3O91_18420, D3Y67_02885, D5H22_11490, D9D77_12200, D9J11_05545, DAH34_01475, DAH37_00935, DEN89_03775, DEN95_10355, DIV22_11465, DM968_16120, DRW19_20065, DTL43_09820, DXT71_05565, DXT73_09385, E2119_16940, E2135_21350, E4K51_09405, E4K54_00245, EAI46_03420, EC1094V2_2850, EC95NR1_05304, EGC08_19360, EI041_12345, EIZ93_00240, ERS139208_02859, ETECE36_03929, ETECE925_02991, F2N31_24545, F9400_05360, F9407_14150, F9V24_04715, F9X20_013415, F9X20_13515, FDM60_03565, FOI11_008030, FOI11_12015, FQE77_13130, FQF29_10640, FV293_21365, G4A38_18295, G5632_05905, G7635_003041, GBE29_03585, GF646_03565, GKF89_10795, GKG12_05120, GP662_14105, GQE64_05300, GQE87_11110, GQM04_09625, GQM06_15635, GRQ19_09290, GRW05_05690, GRW57_05130, GRW80_07395, GRW81_11950, H4P50_16180, H4P51_16030, HJN04_004452, HJO75_001864, HMS79_12845, HMV95_15325, HNC36_01680, HNC52_01435, HPE39_08845, HVV53_00565, HVY77_16815, HVZ33_15560, HX136_16165, HZ71_004423, I6H02_23730, NCTC11022_00303, NCTC11181_00321, NCTC13216_03584, NCTC8008_02712, NCTC8960_00665, NCTC9048_03264, NCTC9706_00521, NCTC9962_02002, SAMEA3472044_00046, SAMEA3472064_00229, SAMEA3472080_00519, SAMEA3484427_04507, SAMEA3484429_04453, SAMEA3751407_00914, SAMEA3752386_03823, SAMEA3752557_01451, SAMEA3753300_02779, WP2S18E08_29460, WQ89_13085, WR15_11565
Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle Express T7 / References: UniProt: G0ZGJ8, 4-phytase, acid phosphatase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES pH 6.5, 18 % w/v PEG 8000, 200 mM calcium acetate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→38.54 Å / Num. obs: 32709 / % possible obs: 97.12 % / Redundancy: 3.2 % / Biso Wilson estimate: 16.31 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.088 / Net I/σ(I): 10.04
Reflection shellResolution: 1.85→1.916 Å / Mean I/σ(I) obs: 2.12 / Num. unique obs: 3234 / CC1/2: 0.59 / Rpim(I) all: 0.407

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DKL

1dkl


Resolution: 1.85→38.54 Å / SU ML: 0.2122 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5347
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 1676 5.12 %
Rwork0.163 31031 -
obs0.1662 32707 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.82 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 1 399 3555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743223
X-RAY DIFFRACTIONf_angle_d0.86514400
X-RAY DIFFRACTIONf_chiral_restr0.049506
X-RAY DIFFRACTIONf_plane_restr0.0064579
X-RAY DIFFRACTIONf_dihedral_angle_d7.5302440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.30081480.242546X-RAY DIFFRACTION97.01
1.9-1.970.31231370.2162542X-RAY DIFFRACTION97.24
1.97-2.040.27421190.19882594X-RAY DIFFRACTION96.75
2.04-2.120.27831570.19052523X-RAY DIFFRACTION96.51
2.12-2.210.27521640.17792544X-RAY DIFFRACTION96.34
2.21-2.330.25651380.16552538X-RAY DIFFRACTION96.4
2.33-2.480.23331490.15612558X-RAY DIFFRACTION96.47
2.48-2.670.23951170.14932587X-RAY DIFFRACTION96.16
2.67-2.940.19191180.1472606X-RAY DIFFRACTION97.81
2.94-3.360.18651230.14192653X-RAY DIFFRACTION98.37
3.36-4.230.18361460.13592641X-RAY DIFFRACTION98.34
4.24-38.540.19721600.16522699X-RAY DIFFRACTION98.15

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