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- PDB-1zed: Alkaline phosphatase from human placenta in complex with p-nitrop... -

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Basic information

Entry
Database: PDB / ID: 1zed
TitleAlkaline phosphatase from human placenta in complex with p-nitrophenyl-phosphonate
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / ALKALINE PHOSPHATASE / PHOSPHOSERINE / SUBSTRATE ANALOG
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
Chem-PNP / PHOSPHITE ION / Alkaline phosphatase, placental type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.57 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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_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: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,95910
Polymers52,8081
Non-polymers1,1519
Water13,709761
1
A: Alkaline phosphatase
hetero molecules

A: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,91820
Polymers105,6162
Non-polymers2,30218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area11330 Å2
ΔGint-205 kcal/mol
Surface area32070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.346, 114.573, 106.568
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: 52808.129 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 , 6 types, 768 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#7: Chemical ChemComp-PNP / METHYL-PHOSPHONIC ACID MONO-(4-NITRO-PHENYL) ESTER / 4-NITROPHENYL HYDROGEN METHYLPHOSPHONATE


Mass: 217.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8NO5P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 761 / 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: 1.57→99 Å / Num. all: 76000 / Num. obs: 74477 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.045
Reflection shellResolution: 1.57→1.61 Å / Rsym value: 0.411 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.57→24.92 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.225 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18753 3641 5 %RANDOM
Rwork0.14911 ---
obs0.15103 68749 97.23 %-
all-74477 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.79 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.57→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 64 761 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213790
X-RAY DIFFRACTIONr_bond_other_d0.0020.023384
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9495143
X-RAY DIFFRACTIONr_angle_other_deg0.87337853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8685480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73823.605172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75515599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5931529
X-RAY DIFFRACTIONr_chiral_restr0.1050.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02771
X-RAY DIFFRACTIONr_nbd_refined0.230.21021
X-RAY DIFFRACTIONr_nbd_other0.1950.23996
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21960
X-RAY DIFFRACTIONr_nbtor_other0.0850.22275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2651
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.2177
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.265
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9551.52441
X-RAY DIFFRACTIONr_mcbond_other0.271.5982
X-RAY DIFFRACTIONr_mcangle_it1.34323815
X-RAY DIFFRACTIONr_scbond_it1.97431504
X-RAY DIFFRACTIONr_scangle_it2.984.51328
X-RAY DIFFRACTIONr_rigid_bond_restr1.36737800
X-RAY DIFFRACTIONr_sphericity_free3.1573765
X-RAY DIFFRACTIONr_sphericity_bonded1.28737090
LS refinement shellResolution: 1.57→1.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 196 -
Rwork0.243 3953 -
obs--84.28 %

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