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- PDB-4lr2: Crystal Structure of Human ENPP4 (apo) -

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Basic information

Entry
Database: PDB / ID: 4lr2
TitleCrystal Structure of Human ENPP4 (apo)
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 / metal ion binding / membrane / plasma membrane
Similarity search - Function
Gyrase A; domain 2 - #180 / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Bis(5'-adenosyl)-triphosphatase ENPP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)47,2977
Polymers46,1101
Non-polymers1,1876
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)181.506, 51.293, 53.065
Angle α, β, γ (deg.)90.000, 102.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-712-

HOH

21A-885-

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 25-402
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


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, 502 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.64 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 71681 / % possible obs: 93.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.084 / Χ2: 1.023 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.5350.54828460.934160.2
1.53-1.575.30.44335610.952174.3
1.57-1.615.50.38344491.05193
1.61-1.6560.32245781.056196.2
1.65-1.76.80.27345771.047196.6
1.7-1.757.10.2346011.035196.9
1.75-1.827.10.20546041.026197.2
1.82-1.897.10.18147021.037197.3
1.89-1.987.10.15746281.033197.7
1.98-2.087.10.13646491.015197.8
2.08-2.217.20.12147101.008198.2
2.21-2.387.30.11447131.044198.4
2.38-2.627.40.09947390.997198.6
2.62-37.50.08547630.968199
3-3.787.40.06747981.04199.3
3.78-507.20.05647631.057196.2

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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 ID 2GSU WITHOUT LIGAND

2gsu


Resolution: 1.5→22.73 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8631 / SU ML: 0.16 / σ(F): 1.37 / Phase error: 21.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 3601 5.02 %
Rwork0.1543 --
obs0.1566 71672 93.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.86 Å2 / Biso mean: 25.7043 Å2 / Biso min: 8.61 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 71 499 3638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093235
X-RAY DIFFRACTIONf_angle_d1.1984410
X-RAY DIFFRACTIONf_chiral_restr0.086480
X-RAY DIFFRACTIONf_plane_restr0.006563
X-RAY DIFFRACTIONf_dihedral_angle_d15.2591181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51840.2533770.20571479155653
1.5184-1.53920.28111130.19551832194566
1.5392-1.56110.2761260.18152020214673
1.5611-1.58440.28951200.1782414253487
1.5844-1.60920.2441210.18022733285496
1.6092-1.63560.271430.17072643278696
1.6356-1.66380.20881320.16732693282596
1.6638-1.6940.26981530.15922671282496
1.694-1.72660.22291440.15392719286397
1.7266-1.76180.20861290.15672729285897
1.7618-1.80010.23751460.1692697284397
1.8001-1.8420.25971270.16422745287297
1.842-1.8880.24051510.17092742289397
1.888-1.9390.21331550.17012671282698
1.939-1.9960.23561630.17182746290998
1.996-2.06040.24041390.15682746288598
2.0604-2.1340.20181460.15722731287798
2.134-2.21940.18821380.14922774291298
2.2194-2.32030.19431210.1552777289898
2.3203-2.44250.20981380.15742774291299
2.4425-2.59530.23951450.15682772291799
2.5953-2.79540.19551580.15972775293399
2.7954-3.07610.20271650.16032788295399
3.0761-3.51980.17591550.14362802295799
3.5198-4.42920.16041380.12612825296399
4.4292-22.730.15981580.15592773293195

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