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- PDB-1shn: Crystal structure of shrimp alkaline phosphatase with phosphate bound -

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Basic information

Entry
Database: PDB / ID: 1shn
TitleCrystal structure of shrimp alkaline phosphatase with phosphate bound
Componentsalkaline phosphatase
KeywordsHYDROLASE / alkaline phosphatase / phosphomonoester / phosphate / cold-active / shrimp / metal triad / zinc triad / beta sheet
Function / homology
Function and homology information


alkaline phosphatase / alkaline phosphatase activity / side of membrane / metal 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 speciesPandalus borealis (northern shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
Authorsde Backer, M.M.E. / McSweeney, S. / Lindley, P.F. / Hough, E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Ligand-binding and metal-exchange crystallographic studies on shrimp alkaline phosphatase.
Authors: de Backer, M.M. / McSweeney, S. / Lindley, P.F. / Hough, E.
History
DepositionFeb 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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)108,02714
Polymers106,8102
Non-polymers1,21712
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-263 kcal/mol
Surface area31190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.676, 170.677, 83.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 1 / Auth seq-ID: 1 - 476 / Label seq-ID: 1 - 476

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein alkaline phosphatase


Mass: 53404.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pandalus borealis (northern shrimp) / References: UniProt: Q9BHT8, alkaline phosphatase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 193 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.9 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 42% (w/v) saturated ammonium sulfate, 100mM tris-maleic acid pH 5.6, 1 mM MgCl2, 0.1mM ZnCl2, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2002
RadiationMonochromator: Laue 5x6mm2, Bragg 6x10mm2, uses [111] reflection, water cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 66456

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→39.64 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.316 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 3289 5 %RANDOM
Rwork0.18596 ---
all0.186 66456 --
obs0.18758 61853 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7462 0 54 183 7699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0217673
X-RAY DIFFRACTIONr_bond_other_d0.0070.026630
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.94210422
X-RAY DIFFRACTIONr_angle_other_deg1.153315412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8593950
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37151287
X-RAY DIFFRACTIONr_chiral_restr0.1140.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028702
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021576
X-RAY DIFFRACTIONr_nbd_refined0.2440.31885
X-RAY DIFFRACTIONr_nbd_other0.2190.37114
X-RAY DIFFRACTIONr_nbtor_other0.3750.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.5513
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0410.53
X-RAY DIFFRACTIONr_metal_ion_refined0.2130.515
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.339
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.53
X-RAY DIFFRACTIONr_mcbond_it0.9271.54710
X-RAY DIFFRACTIONr_mcangle_it1.64827562
X-RAY DIFFRACTIONr_scbond_it2.77232963
X-RAY DIFFRACTIONr_scangle_it4.3434.52860
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 7036 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.110.05
tight thermal0.220.5
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 158
Rwork0.21 3260

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