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- PDB-1k7h: CRYSTAL STRUCTURE OF SHRIMP ALKALINE PHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1k7h
TitleCRYSTAL STRUCTURE OF SHRIMP ALKALINE PHOSPHATASE
ComponentsALKALINE PHOSPHATASE
KeywordsHYDROLASE / TRANSFERASE / PHOSPHOMONOESTER / EXTENDED BETA SHEET / ZINC TRIAD / METAL TRIAD
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
MALEIC ACID / Alkaline phosphatase
Similarity search - Component
Biological speciesPandalus borealis (northern shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsDe Backer, M.E. / Mc Sweeney, S. / Rasmussen, H.B. / Riise, B.W. / Lindley, P. / Hough, E.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: The 1.9 A Crystal Structure of Heat-Labile Shrimp Alkaline Phosphatase
Authors: De Backer, M.E. / Mc Sweeney, S. / Rasmussen, H.B. / Riise, B.W. / Lindley, P. / Hough, E.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Crystal Structure of Alkaline Phosphatase from Huma at 1.8 A Resolution. Implication for a Substrate Specificity
Authors: Le Du, M.H. / Stigbrand, T. / Taussig, M.J. / Menez, A. / Stura, E.A.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two-Metal Ion Catalysis
Authors: Kim, E.E. / Wyckoff, H.W.
History
DepositionOct 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_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)107,82419
Polymers106,0652
Non-polymers1,75917
Water9,872548
1
B: ALKALINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8549
Polymers53,0321
Non-polymers8228
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ALKALINE PHOSPHATASE
hetero molecules

B: ALKALINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,82419
Polymers106,0652
Non-polymers1,75917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y+1/2,-z+3/41
Buried area10880 Å2
ΔGint-198 kcal/mol
Surface area31520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.169, 171.169, 84.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein ALKALINE PHOSPHATASE /


Mass: 53032.336 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, 563 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MAE / MALEIC ACID / Maleic acid


Mass: 116.072 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 47 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
20.1 mMZn2+1drop
31.0 mMMg2+1drop
442.5 %(w/v)ammonium sulfate1reservoir
510 %(v/v)glycerol1reservoir
6100 mMTris-maleate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9310,1.2820,1.2825,0.933
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 1, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND(111) DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9311
21.2821
31.28251
40.9331
ReflectionResolution: 1.85→99 Å / Num. obs: 95547 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.176 / Net I/σ(I): 11.8
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.597 / % possible all: 99.2
Reflection
*PLUS
Num. obs: 103370 / Redundancy: 2.6 % / Num. measured all: 1131014
Reflection shell
*PLUS
% possible obs: 99.2 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLOMONphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 1.92→119.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.79 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4581 4.9 %RANDOM
Rwork0.198 ---
obs0.2 88009 96.9 %-
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: 25.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2---1.52 Å20 Å2
3---3.04 Å2
Refinement stepCycle: LAST / Resolution: 1.92→119.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7464 0 88 548 8100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0217701
X-RAY DIFFRACTIONr_bond_other_d0.0080.026636
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.94510456
X-RAY DIFFRACTIONr_angle_other_deg1.451315424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6253950
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.109151295
X-RAY DIFFRACTIONr_chiral_restr0.1120.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028726
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021576
X-RAY DIFFRACTIONr_nbd_refined0.2380.31827
X-RAY DIFFRACTIONr_nbd_other0.2190.37052
X-RAY DIFFRACTIONr_nbtor_other0.1160.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.5609
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1110.58
X-RAY DIFFRACTIONr_metal_ion_refined0.130.519
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.344
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.3152
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.532
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0880.51
X-RAY DIFFRACTIONr_mcbond_it0.8851.54710
X-RAY DIFFRACTIONr_mcangle_it1.52827562
X-RAY DIFFRACTIONr_scbond_it2.62632991
X-RAY DIFFRACTIONr_scangle_it4.0944.52894
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free8.74326
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 327
Rwork0.272 6631
Refinement
*PLUS
% reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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