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- PDB-2glq: X-ray structure of human alkaline phosphatase in complex with str... -

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Basic information

Entry
Database: PDB / ID: 2glq
TitleX-ray structure of human alkaline phosphatase in complex with strontium
ComponentsAlkaline phosphatase, placental type
KeywordsHYDROLASE / alkaline phosphatase / strontium / structure-function
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
STRONTIUM ION / Alkaline phosphatase, placental type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsLlinas, P. / Masella, M. / Stigbrand, T. / Menez, A. / Stura, E.A. / Le Du, M.H.
CitationJournal: Protein Sci. / Year: 2006
Title: Structural studies of human alkaline phosphatase in complex with strontium: Implication for its secondary effect in bones.
Authors: Llinas, P. / Masella, M. / Stigbrand, T. / Menez, A. / Stura, E.A. / Le Du, M.H.
History
DepositionApr 5, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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 / pdbx_struct_special_symmetry / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_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
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: Alkaline phosphatase, placental type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5737
Polymers52,8881
Non-polymers6856
Water10,755597
1
A: Alkaline phosphatase, placental type
hetero molecules

A: Alkaline phosphatase, placental type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,14714
Polymers105,7762
Non-polymers1,37012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area10130 Å2
ΔGint-241 kcal/mol
Surface area31780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.090, 115.299, 107.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2197-

HOH

21A-2321-

HOH

31A-2570-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Alkaline phosphatase, placental type / / Placental Alkaline Phosphatase / PLAP-1 / Regan isozyme


Mass: 52888.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / 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.: 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, 601 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.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystals were grown at 19 (2) using sitting drop vapor diffusion, with protein concentration of 10mg/ml, in the presence of 10mM p-nitrophenyl phosphate. Crystals were obtained from 12% PEG ...Details: Crystals were grown at 19 (2) using sitting drop vapor diffusion, with protein concentration of 10mg/ml, in the presence of 10mM p-nitrophenyl phosphate. Crystals were obtained from 12% PEG 3350, 100mM sodium cacodylate pH 6.5, 1mM zinc chloride, 2mM magnesium acetate, and 2mM strontium chloride over a period of five months, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 72276 / Num. obs: 72276 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.096 / Net I/σ(I): 19.25
Reflection shellResolution: 1.6→1.65 Å / Mean I/σ(I) obs: 2.88 / Rsym value: 0.431 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ADSCdata collection
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→9.99 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.808 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18813 3637 5.1 %RANDOM
Rwork0.14778 ---
all0.14991 71854 --
obs0.14991 68217 99 %-
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: 17.399 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 32 597 4289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213773
X-RAY DIFFRACTIONr_bond_other_d0.0030.023371
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.9585120
X-RAY DIFFRACTIONr_angle_other_deg1.0237821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9045478
X-RAY DIFFRACTIONr_chiral_restr0.1450.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024260
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02769
X-RAY DIFFRACTIONr_nbd_refined0.2630.2931
X-RAY DIFFRACTIONr_nbd_other0.2580.24187
X-RAY DIFFRACTIONr_nbtor_other0.0880.22167
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2441
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.2137
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.250
X-RAY DIFFRACTIONr_mcbond_it1.1841.52378
X-RAY DIFFRACTIONr_mcangle_it1.88423800
X-RAY DIFFRACTIONr_scbond_it2.86931395
X-RAY DIFFRACTIONr_scangle_it4.3734.51320
X-RAY DIFFRACTIONr_rigid_bond_restr1.59923773
X-RAY DIFFRACTIONr_sphericity_free3.3542601
X-RAY DIFFRACTIONr_sphericity_bonded2.11623689
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 239
Rwork0.296 4813

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