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- PDB-3tg0: E. coli alkaline phosphatase with bound inorganic phosphate -

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Basic information

Entry
Database: PDB / ID: 3tg0
TitleE. coli alkaline phosphatase with bound inorganic phosphate
ComponentsAlkaline phosphatase
KeywordsHYDROLASE
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBobyr, E. / Lassila, J.K. / Wiersma-Koch, H.I. / Fenn, T.D. / Lee, J.J. / Nikolic-Hughes, I. / Hodgson, K.O. / Rees, D.C. / Hedman, B. / Herschlag, D.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography.
Authors: Bobyr, E. / Lassila, J.K. / Wiersma-Koch, H.I. / Fenn, T.D. / Lee, J.J. / Nikolic-Hughes, I. / Hodgson, K.O. / Rees, D.C. / Hedman, B. / Herschlag, D.
History
DepositionAug 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)189,37820
Polymers188,3784
Non-polymers1,00016
Water33,8321878
1
A: Alkaline phosphatase
B: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,68910
Polymers94,1892
Non-polymers5008
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-184 kcal/mol
Surface area27760 Å2
MethodPISA
2
C: Alkaline phosphatase
D: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,68910
Polymers94,1892
Non-polymers5008
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-183 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.963, 98.457, 152.146
Angle α, β, γ (deg.)90.00, 94.61, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 10 - 447 / Label seq-ID: 10 - 447

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Alkaline phosphatase / APase


Mass: 47094.398 Da / Num. of mol.: 4 / Fragment: unp residues 23-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: phoA, b0383, JW0374 / Plasmid: pEK-48 / Production host: Escherichia coli (E. coli) / Strain (production host): SM547 / References: UniProt: P00634, alkaline phosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 1878 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 4000, 0.2 M HEPES, 1 mM ZnCl2, 0.01 mM MgCl2, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 501190 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Net I/σ(I): 15.9
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 3.1 / % possible all: 28.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ALK

1alk


Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.125 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16869 26546 5 %RANDOM
Rwork0.14846 ---
all0.14948 528070 --
obs0.14948 501190 87.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.209 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.5 Å2
2--0.05 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12952 0 32 1878 14862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02213560
X-RAY DIFFRACTIONr_bond_other_d0.0010.028849
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9618490
X-RAY DIFFRACTIONr_angle_other_deg0.97321856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22251857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.54425.632570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47152219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1771560
X-RAY DIFFRACTIONr_chiral_restr0.0880.22107
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022477
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1321.58923
X-RAY DIFFRACTIONr_mcbond_other0.6871.53698
X-RAY DIFFRACTIONr_mcangle_it1.762214251
X-RAY DIFFRACTIONr_scbond_it2.63734637
X-RAY DIFFRACTIONr_scangle_it3.9224.54211
X-RAY DIFFRACTIONr_rigid_bond_restr1.135322409
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2484MEDIUM POSITIONAL0.190.5
2B2484MEDIUM POSITIONAL0.160.5
3C2484MEDIUM POSITIONAL0.190.5
4D2484MEDIUM POSITIONAL0.170.5
1A2610LOOSE POSITIONAL0.295
2B2610LOOSE POSITIONAL0.315
3C2610LOOSE POSITIONAL0.325
4D2610LOOSE POSITIONAL0.325
1A2484MEDIUM THERMAL1.212
2B2484MEDIUM THERMAL1.52
3C2484MEDIUM THERMAL2.342
4D2484MEDIUM THERMAL1.462
1A2610LOOSE THERMAL1.0410
2B2610LOOSE THERMAL1.2310
3C2610LOOSE THERMAL1.8610
4D2610LOOSE THERMAL1.1910
LS refinement shellResolution: 1.199→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 562 -
Rwork0.383 10302 -
obs--24.43 %

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