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- PDB-1zef: structure of alkaline phosphatase from human placenta in complex ... -

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Basic information

Entry
Database: PDB / ID: 1zef
Titlestructure of alkaline phosphatase from human placenta in complex with its uncompetitive inhibitor L-Phe
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / ALKALINE PHOSPHATASE / UNCOMPETITIVE INHIBITOR / INTERMEDIATE STATE / L-PHE
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
PHENYLALANINE / Alkaline phosphatase, placental type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsLlinas, P. / Stura, E.A. / Menez, A. / Kiss, Z. / Stigbrand, T. / Millan, J.L. / Le Du, M.H.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural Studies of Human Placental Alkaline Phosphatase in Complex with Functional Ligands.
Authors: Llinas, P. / Stura, E.A. / Menez, A. / Kiss, Z. / Stigbrand, T. / Millan, J.L. / Le Du, M.H.
History
DepositionApr 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8569
Polymers52,8881
Non-polymers9688
Water12,647702
1
A: Alkaline phosphatase
hetero molecules

A: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,71218
Polymers105,7762
Non-polymers1,93616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9760 Å2
ΔGint-119 kcal/mol
Surface area31180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.791, 114.944, 106.341
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, 3 molecules A

#1: Protein 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) / Tissue: 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.: 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 , 5 types, 708 molecules

#3: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.74 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.89→99 Å / Num. all: 43600 / Num. obs: 43024 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.066
Reflection shellResolution: 1.89→1.93 Å / Mean I/σ(I) obs: 4.6 / Rsym value: 0.183 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.181 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17322 2115 5 %RANDOM
Rwork0.12625 ---
all0.12861 41986 --
obs0.12861 39871 100 %-
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: 18.647 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--0.83 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3669 0 56 702 4427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213806
X-RAY DIFFRACTIONr_bond_other_d0.0030.023391
X-RAY DIFFRACTIONr_angle_refined_deg1.721.9575161
X-RAY DIFFRACTIONr_angle_other_deg1.07537865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615480
X-RAY DIFFRACTIONr_chiral_restr0.1750.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024292
X-RAY DIFFRACTIONr_gen_planes_other0.0240.02781
X-RAY DIFFRACTIONr_nbd_refined0.2470.21052
X-RAY DIFFRACTIONr_nbd_other0.2640.24719
X-RAY DIFFRACTIONr_nbtor_other0.0910.22383
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2593
X-RAY DIFFRACTIONr_metal_ion_refined0.1640.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.2205
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.279
X-RAY DIFFRACTIONr_mcbond_it0.9131.52397
X-RAY DIFFRACTIONr_mcangle_it1.67923824
X-RAY DIFFRACTIONr_scbond_it2.86231409
X-RAY DIFFRACTIONr_scangle_it4.6264.51337
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.195 138
Rwork0.139 2897

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