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- PDB-7z1j: Escherichia coli periplasmic phytase AppA, complex with phosphate -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z1j | ||||||
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Title | Escherichia coli periplasmic phytase AppA, complex with phosphate | ||||||
![]() | Acidphosphatase | ||||||
![]() | HYDROLASE / histidine acid phosphatase / phytase | ||||||
Function / homology | ![]() 4-phytase / 4-phytase activity / sugar-phosphatase activity / acid phosphatase / acid phosphatase activity / lysosome organization / dephosphorylation / outer membrane-bounded periplasmic space / lysosome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Acquistapace, I.M. / Brearley, C.A. / Hemmings, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.1 KB | Display | ![]() |
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PDB format | ![]() | 142.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z2sC ![]() 7z2tC ![]() 7z2wC ![]() 7z2yC ![]() 7z32C ![]() 7z3vC ![]() 1dklS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44887.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() 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: ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.45 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 100 mM MES pH 6.5, 18 % w/v PEG 8000, 200 mM calcium acetate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→49.85 Å / Num. obs: 33227 / % possible obs: 99.96 % / Redundancy: 7 % / Biso Wilson estimate: 15.48 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.0917 / Net I/σ(I): 7.84 |
Reflection shell | Resolution: 1.85→1.916 Å / Num. unique obs: 3295 / CC1/2: 0.573 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DKL Resolution: 1.85→49.85 Å / SU ML: 0.2313 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8024 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→49.85 Å
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Refine LS restraints |
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LS refinement shell |
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