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- PDB-1s1d: Structure and protein design of human apyrase -

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Basic information

Entry
Database: PDB / ID: 1s1d
TitleStructure and protein design of human apyrase
Componentsapyrase
KeywordsHYDROLASE / ADPase / five-blade beta propeller / calcium-binding protein / nucleotide-binding motif
Function / homology
Function and homology information


nucleoside diphosphate phosphatase / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / proteoglycan biosynthetic process / Golgi cisterna membrane / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / positive regulation of canonical NF-kappaB signal transduction ...nucleoside diphosphate phosphatase / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / proteoglycan biosynthetic process / Golgi cisterna membrane / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / positive regulation of canonical NF-kappaB signal transduction / calcium ion binding / Neutrophil degranulation / endoplasmic reticulum membrane / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Apyrase / Apyrase / Apyrase superfamily / Apyrase / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHOMETHYLPHOSPHONIC ACID GUANOSYL ESTER / Soluble calcium-activated nucleotidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDai, J. / Liu, J. / Deng, Y. / Smith, T.M. / Lu, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structure and protein design of a human platelet function inhibitor.
Authors: Dai, J. / Liu, J. / Deng, Y. / Smith, T.M. / Lu, M.
History
DepositionJan 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: apyrase
B: apyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,15316
Polymers74,0842
Non-polymers2,06914
Water11,710650
1
A: apyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0718
Polymers37,0421
Non-polymers1,0297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: apyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0828
Polymers37,0421
Non-polymers1,0407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.163, 52.450, 77.478
Angle α, β, γ (deg.)98.99, 106.99, 100.09
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a monomer

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein apyrase / Ca2+-dependent endoplasmic reticulum nucleoside diphosphatase / apyrase / soluble calcium-activated ...Ca2+-dependent endoplasmic reticulum nucleoside diphosphatase / apyrase / soluble calcium-activated nucleotidase SCAN-1


Mass: 37042.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHAPY / Plasmid details: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: Q8WVQ1, apyrase

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Non-polymers , 6 types, 664 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GP2 / PHOSPHOMETHYLPHOSPHONIC ACID GUANOSYL ESTER


Mass: 441.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N5O10P2
#5: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.24 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG MME 2000, sodium acetate, ammonium sulfate, strontium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-15 %PEG2000 MME1reservoir
2100 mM1reservoirpH5.0NaOAc
30.3-0.4 Mammonium sulfate1reservoir
415 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→46.6 Å / Num. all: 79084 / Num. obs: 79084 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7743 / % possible all: 93.8
Reflection
*PLUS
Highest resolution: 1.6 Å
Reflection shell
*PLUS
% possible obs: 93.8 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S18

1s18


Resolution: 1.6→46.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.685 / SU ML: 0.059 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.09 / ESU R Free: 0.089
RfactorNum. reflection% reflectionSelection details
Rfree0.19399 3982 5 %RANDOM
Rwork0.16427 ---
all0.16581 79084 --
obs0.16581 75102 95 %-
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: 18.372 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20.24 Å2-0.07 Å2
2---0.07 Å2-0.37 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4998 0 128 650 5776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215244
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9637132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635630
X-RAY DIFFRACTIONr_chiral_restr0.1070.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023984
X-RAY DIFFRACTIONr_nbd_refined0.2120.22362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2544
X-RAY DIFFRACTIONr_metal_ion_refined0.1570.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.236
X-RAY DIFFRACTIONr_mcbond_it0.9751.53161
X-RAY DIFFRACTIONr_mcangle_it1.74725080
X-RAY DIFFRACTIONr_scbond_it2.6632083
X-RAY DIFFRACTIONr_scangle_it4.2754.52052
LS refinement shellResolution: 1.6→1.634 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.302 243
Rwork0.253 5334
obs-5577
Refinement
*PLUS
Num. reflection obs: 79084 / % reflection Rfree: 5 % / Rfactor Rfree: 0.194 / Rfactor Rwork: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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