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- PDB-1shq: Crystal structure of shrimp alkaline phosphatase with magnesium in M3 -

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Basic information

Entry
Database: PDB / ID: 1shq
TitleCrystal structure of shrimp alkaline phosphatase with magnesium in M3
Componentsalkaline phosphatase
KeywordsHYDROLASE / alkaline phosphatase / phosphomonoester / cold-active / shrimp / metal triad / magnesium / metal exchange / beta sheet
Function / homology
Function and homology information


alkaline phosphatase / alkaline phosphatase activity / 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
Alkaline phosphatase
Similarity search - Component
Biological speciesPandalus borealis (northern shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_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_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_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_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

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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)107,94714
Polymers106,8102
Non-polymers1,13712
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-222 kcal/mol
Surface area31190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.007, 171.007, 84.098
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 label comp-ID: GLU / 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-Acetylglucosamine


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, 112 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.92 Å3/Da / Density % sol: 57.56 %
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, 100 mM MgCl2, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.2825 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 9, 2002
RadiationMonochromator: Si111 or Si311 crystals, LN2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2825 Å / Relative weight: 1

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.408 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23808 4171 5 %RANDOM
Rwork0.21529 ---
all0.2153 ---
obs0.21645 78786 98.46 %-
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: 29.869 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7462 0 54 102 7618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0217671
X-RAY DIFFRACTIONr_bond_other_d0.0070.026630
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.94110418
X-RAY DIFFRACTIONr_angle_other_deg1.223315412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8733950
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.104151287
X-RAY DIFFRACTIONr_chiral_restr0.1220.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028702
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021576
X-RAY DIFFRACTIONr_nbd_refined0.2420.31822
X-RAY DIFFRACTIONr_nbd_other0.2160.36962
X-RAY DIFFRACTIONr_nbtor_other0.6510.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.5452
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0310.52
X-RAY DIFFRACTIONr_metal_ion_refined0.2380.512
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.318
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.53
X-RAY DIFFRACTIONr_mcbond_it1.0931.54710
X-RAY DIFFRACTIONr_mcangle_it1.83527562
X-RAY DIFFRACTIONr_scbond_it2.85432961
X-RAY DIFFRACTIONr_scangle_it4.4314.52856
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 thermal0.230.5
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 318
Rwork0.259 5687

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