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- PDB-4lqy: Crystal Structure of Human ENPP4 with AMP -

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Basic information

Entry
Database: PDB / ID: 4lqy
TitleCrystal Structure of Human ENPP4 with AMP
ComponentsBis(5'-adenosyl)-triphosphatase ENPP4
KeywordsHYDROLASE / NPP4 / ENPP4 / phosphodiesterase
Function / homology
Function and homology information


purine ribonucleoside catabolic process / bis(5'-adenosyl)-triphosphatase / bis(5'-adenosyl)-triphosphatase activity / ficolin-1-rich granule membrane / positive regulation of blood coagulation / blood coagulation / Neutrophil degranulation / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Gyrase A; domain 2 - #180 / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Bis(5'-adenosyl)-triphosphatase ENPP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsAlbright, R.A. / Braddock, D.T.
Citation
Journal: J.Biol.Chem. / Year: 2014
Title: Molecular basis of purinergic signal metabolism by ectonucleotide pyrophosphatase/phosphodiesterases 4 and 1 and implications in stroke.
Authors: Albright, R.A. / Ornstein, D.L. / Cao, W. / Chang, W.C. / Robert, D. / Tehan, M. / Hoyer, D. / Liu, L. / Stabach, P. / Yang, G. / De La Cruz, E.M. / Braddock, D.T.
#1: Journal: Blood / Year: 2012
Title: NPP4 is a procoagulant enzyme on the surface of vascular endothelium
Authors: Albright, R.A. / Chang, W.C. / Robert, D. / Ornstein, D.L. / Cao, W. / Liu, L. / Redick, M.E. / Young, J.I. / De La Cruz, E.M. / Braddock, D.T.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_label_asym_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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bis(5'-adenosyl)-triphosphatase ENPP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4557
Polymers46,1101
Non-polymers1,3456
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)181.533, 51.143, 52.741
Angle α, β, γ (deg.)90.000, 102.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-873-

HOH

21A-981-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bis(5'-adenosyl)-triphosphatase ENPP4 / AP3A hydrolase / AP3Aase / Ectonucleotide pyrophosphatase/phosphodiesterase family member 4 / E-NPP 4 / NPP-4


Mass: 46109.957 Da / Num. of mol.: 1 / Fragment: UNP residues 16-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENPP4, KIAA0879, NPP4 / Plasmid: pFASTBAC1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HIGH5
References: UniProt: Q9Y6X5, bis(5'-adenosyl)-triphosphatase

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / 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 , 3 types, 467 molecules

#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 6.5
Details: 200 mM ammonium citrate dibasic, 17.5% to 19.5% (w/v) PEG 3350, pH 6.5, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 74645 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Χ2: 1.872 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.543.40.66249911.309194.2
1.54-1.583.90.53453101.247198.6
1.58-1.633.90.42352891.229198.9
1.63-1.683.90.33952801.308198.8
1.68-1.743.90.24853191.4199.1
1.74-1.813.90.19853441.453199.1
1.81-1.893.90.15453711.696199.5
1.89-1.993.90.1253331.884199.6
1.99-2.113.90.09353652.151199.6
2.11-2.2840.07753772.239199.9
2.28-2.5140.06654112.1931100
2.51-2.874.10.06354032.7161100
2.87-3.6140.04754532.486199.9
3.61-5040.0453992.609197.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GSU

2gsu


Resolution: 1.54→37.852 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8934 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1844 3515 5.06 %
Rwork0.1402 --
obs0.1424 69525 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.61 Å2 / Biso mean: 26.3885 Å2 / Biso min: 8.67 Å2
Refinement stepCycle: LAST / Resolution: 1.54→37.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 81 464 3613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093248
X-RAY DIFFRACTIONf_angle_d1.274431
X-RAY DIFFRACTIONf_chiral_restr0.088484
X-RAY DIFFRACTIONf_plane_restr0.007561
X-RAY DIFFRACTIONf_dihedral_angle_d15.4731174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.54-1.5610.28841290.1812557268696
1.561-1.58330.26131580.1712569272799
1.5833-1.60690.24161390.16392635277499
1.6069-1.6320.24981530.16042592274599
1.632-1.65880.23571260.15462614274099
1.6588-1.68740.23011590.14192590274999
1.6874-1.71810.20051380.14032642278099
1.7181-1.75110.20811430.13732659280299
1.7511-1.78680.23471210.13982600272199
1.7868-1.82570.17841150.13352690280599
1.8257-1.86820.1911340.1272602273699
1.8682-1.91490.17481150.127126772792100
1.9149-1.96670.16341420.127426702812100
1.9667-2.02450.1811420.128826272769100
2.0245-2.08990.18951460.129426482794100
2.0899-2.16460.17141450.12826302775100
2.1646-2.25120.19651400.128526642804100
2.2512-2.35370.16291410.131626552796100
2.3537-2.47770.17341410.138126602801100
2.4777-2.63290.19491460.140626872833100
2.6329-2.83610.17691480.141226642812100
2.8361-3.12140.17161540.143626682822100
3.1214-3.57280.15351400.131526752815100
3.5728-4.50020.16851360.1332717285399
4.5002-37.8520.1971640.16942618278295

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