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- PDB-5c66: E. Coli Alkaline Phosphatase in complex with tungstate -

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Basic information

Entry
Database: PDB / ID: 5c66
TitleE. Coli Alkaline Phosphatase in complex with tungstate
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
TUNGSTATE(VI)ION / Alkaline phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsPeck, A. / Herschlag, D.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase.
Authors: Peck, A. / Sunden, F. / Andrews, L.D. / Pande, V.S. / Herschlag, D.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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
Revision 1.3Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,47810
Polymers96,5892
Non-polymers8888
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.260, 161.260, 139.432
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.871609, -0.490201, 0.000215), (-0.4902, 0.871609, 0.001213), (-0.000782, 0.000952, -0.999999)-0.63987, -0.14596, -34.81894

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Components

#1: Protein Alkaline phosphatase / APase


Mass: 48294.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: phoA, b0383, JW0374 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(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-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium MOPS, sodium chloride, zinc chloride, magnesium chloride, PEG3350, ammonium fluoride, sodium tungstate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.03→52.74 Å / Num. all: 64098 / Num. obs: 64098 / % possible obs: 93.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 14.1
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.9 / % possible all: 93.4

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Processing

Software
NameVersionClassification
iMOSFLM7.1.1data reduction
Aimless0.3.6data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TG0

3tg0


Resolution: 2.03→52.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.712 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23987 3281 5.1 %RANDOM
Rwork0.19469 ---
obs0.19702 60751 92.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.057 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20.96 Å20 Å2
2--1.92 Å20 Å2
3----6.24 Å2
Refinement stepCycle: 1 / Resolution: 2.03→52.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 16 156 6654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196727
X-RAY DIFFRACTIONr_bond_other_d0.0010.026340
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.969085
X-RAY DIFFRACTIONr_angle_other_deg0.881314616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.56625.571280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.565151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7241530
X-RAY DIFFRACTIONr_chiral_restr0.110.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217842
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021432
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_it2.9273.8263566
X-RAY DIFFRACTIONr_mcbond_other2.9263.8253565
X-RAY DIFFRACTIONr_mcangle_it3.8115.7254468
X-RAY DIFFRACTIONr_mcangle_other3.8115.7264469
X-RAY DIFFRACTIONr_scbond_it3.8344.1483161
X-RAY DIFFRACTIONr_scbond_other3.7574.1483159
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.136.0844615
X-RAY DIFFRACTIONr_long_range_B_refined6.29230.5677714
X-RAY DIFFRACTIONr_long_range_B_other6.29730.5697683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2570medium positional0.090.5
3778loose positional0.325
2570medium thermal1.692
3778loose thermal2.3310
LS refinement shellResolution: 2.031→2.084 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 235 -
Rwork0.31 4417 -
obs--93 %

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