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- PDB-1ew2: CRYSTAL STRUCTURE OF A HUMAN PHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1ew2
TitleCRYSTAL STRUCTURE OF A HUMAN PHOSPHATASE
ComponentsPHOSPHATASE
KeywordsHYDROLASE / phosphatase / non covalent complex
Function / homology
Function and homology information


Intra-Golgi traffic / alkaline phosphatase / alkaline phosphatase activity / side of membrane / dephosphorylation / magnesium ion binding / cell surface / zinc ion binding / plasma membrane
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, placental type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.82 Å
AuthorsLe Du, M.H. / Stigbrand, T. / Taussig, M.J. / Menez, A. / Stura, E.A.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of alkaline phosphatase from human placenta 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.
History
DepositionApr 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: 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 / 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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1517
Polymers55,6561
Non-polymers4966
Water10,845602
1
A: PHOSPHATASE
hetero molecules

A: PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,30214
Polymers111,3112
Non-polymers99112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9970 Å2
ΔGint-268 kcal/mol
Surface area31580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.800, 114.500, 106.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein PHOSPHATASE /


Mass: 55655.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PLACENTA / References: UniProt: P05187, 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.: 1
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, 607 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: PEG, pH 6.0, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-16 mg/mlprotein1drop
210 mMTris-HCl1drop
32 mM1dropMgCl2
40.02 %1dropNaN3
512 %PEG40001reservoir
62 mMzinc acetate1reservoir
7200 mMimidazole malate1reservoir

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→22 Å / Num. all: 49278 / Num. obs: 49278 / % possible obs: 79.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.34 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.5
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 1.32 % / Rmerge(I) obs: 0.686 / Num. unique all: 2523 / % possible all: 66.2
Reflection
*PLUS
Highest resolution: 1.82 Å / Num. obs: 41585 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
Highest resolution: 1.82 Å / Lowest resolution: 1.87 Å / % possible obs: 67.6 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 1.82→22 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ARP/wARP version 5.0
RfactorNum. reflectionSelection details
Rfree0.242 2050 RANDOM
Rwork0.185 --
all0.185 41585 -
obs0.185 41585 -
Refinement stepCycle: LAST / Resolution: 1.82→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 23 602 4277

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