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- PDB-3dyc: Structure of E322Y Alkaline Phosphatase in Complex with Inorganic... -

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Basic information

Entry
Database: PDB / ID: 3dyc
TitleStructure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / alpha/beta/alpha / Magnesium / Metal-binding / Periplasm / Phosphoprotein / Zinc
Function / homology
Function and homology information


oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / dephosphorylation / protein dephosphorylation / outer membrane-bounded periplasmic space / periplasmic space / magnesium ion binding / zinc ion binding
Similarity search - Function
Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Alkaline phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.303 Å
AuthorsZalatan, J.G. / Fenn, T.D. / Herschlag, D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active-Site Metal Ion.
Authors: Zalatan, J.G. / Fenn, T.D. / Herschlag, D.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkaline phosphatase
B: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,83910
Polymers94,2572
Non-polymers5828
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-251 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.609, 161.609, 139.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Alkaline phosphatase / APase


Mass: 47128.457 Da / Num. of mol.: 2 / Fragment: alkaline phosphatase / Mutation: E322Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 MG1655 / Gene: phoA / Plasmid: pMAL_p2X / Production host: Escherichia coli (E. coli) / Strain (production host): SM547 (DE3) / References: UniProt: P00634, alkaline phosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M ammonium fluoride, 20% PEG 3350, and 0.5 mM zinc chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.2825 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2007 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2825 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 86186 / Num. obs: 86186 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.174

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
BOS(data collection software)data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.303→49.452 Å / Occupancy max: 1 / Occupancy min: 0.88 / FOM work R set: 0.793 / SU ML: 0.37 / σ(F): 1.13 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 4331 5.1 %
Rwork0.181 80638 -
obs0.184 84969 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.277 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 121.59 Å2 / Biso mean: 40.852 Å2 / Biso min: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.688 Å2-0 Å2-0 Å2
2--6.688 Å20 Å2
3----13.375 Å2
Refinement stepCycle: LAST / Resolution: 2.303→49.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6568 0 16 440 7024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066690
X-RAY DIFFRACTIONf_angle_d19080
X-RAY DIFFRACTIONf_chiral_restr0.071036
X-RAY DIFFRACTIONf_plane_restr0.0041208
X-RAY DIFFRACTIONf_dihedral_angle_d18.9032398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.303-2.3290.347790.2921675175458
2.329-2.3570.3681060.2811884199067
2.357-2.3850.2951000.2652128222874
2.385-2.4150.381330.2772355248883
2.415-2.4470.3261270.2572596272390
2.447-2.4810.3221210.2532779290096
2.481-2.5160.3371690.2492786295599
2.516-2.5540.3121390.2362838297799
2.554-2.5940.3211640.21328342998100
2.594-2.6360.2861360.2142824296099
2.636-2.6820.2781720.2052796296899
2.682-2.730.2991660.2162818298499
2.73-2.7830.321490.21928162965100
2.783-2.840.2991570.2172824298199
2.84-2.9010.2931480.22809295799
2.901-2.9690.3121470.2032804295198
2.969-3.0430.3291740.1972784295898
3.043-3.1250.2681670.1962772293998
3.125-3.2170.2241650.1762786295198
3.217-3.3210.2311240.1722809293398
3.321-3.440.1921360.1562772290897
3.44-3.5780.2011600.152738289897
3.578-3.740.2341400.1522788292897
3.74-3.9380.2081610.1432766292798
3.938-4.1840.2091390.1442783292297
4.184-4.5070.1681630.1282759292297
4.507-4.960.1821380.1192799293797
4.96-5.6770.1781770.1342793297099
5.677-7.1490.2081440.15928432987100
7.149-49.4630.171300.162880301099
Refinement TLS params.

S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3950.3613-0.0460.62460.14690.31620.1367-0.10990.01570.0644-0.14790.00870.0915-0.06610.2125-0.051-0.01170.1892-0.00130.180754.2322-31.2482-10.2225
20.30280.0364-0.01760.54170.13610.39330.1139-0.05040.0363-0.1497-0.09320.0216-0.10030.00360.25880.02530.04840.138-0.02070.197862.6917-0.2302-24.2904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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