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- PDB-3zx3: Crystal Structure and Domain Rotation of NTPDase1 CD39 -

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Basic information

Entry
Database: PDB / ID: 3zx3
TitleCrystal Structure and Domain Rotation of NTPDase1 CD39
ComponentsECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
KeywordsHYDROLASE / DOMAIN ROTATION / PURINERGIC SIGNALING
Function / homology
Function and homology information


response to proline / CDP phosphatase activity / apyrase / ITPase activity / apyrase activity / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / IDP phosphatase activity / cellular response to aluminum ion ...response to proline / CDP phosphatase activity / apyrase / ITPase activity / apyrase activity / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / IDP phosphatase activity / cellular response to aluminum ion / CTPase activity / ADP phosphatase activity / GDP phosphatase activity / nucleoside diphosphate catabolic process / ADP catabolic process / nucleoside diphosphate phosphatase activity / negative regulation of dopamine secretion / cellular response to interferon-alpha / response to L-arginine / negative regulation of ATP biosynthetic process / response to auditory stimulus / response to caffeine / response to ATP / basement membrane / synaptic membrane / ribonucleoside triphosphate phosphatase activity / response to gamma radiation / caveola / platelet activation / platelet aggregation / synaptic vesicle / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to lipopolysaccharide / basolateral plasma membrane / G protein-coupled receptor signaling pathway / external side of plasma membrane / neuronal cell body / GTPase activity / cell surface / ATP hydrolysis activity / extracellular space / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
GDA1/CD39 family of nucleoside phosphatases signature. / Exopolyphosphatase. Domain 2 / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Ectonucleoside triphosphate diphosphohydrolase 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZebisch, M. / Schaefer, P. / Straeter, N.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystallographic Evidence for a Domain Motion in Rat Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) 1.
Authors: Zebisch, M. / Krauss, M. / Schafer, P. / Strater, N.
History
DepositionAug 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Oct 9, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 20, 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.ptnr2_auth_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 / _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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
C: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
D: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,80043
Polymers202,3084
Non-polymers1,49339
Water14,700816
1
A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,78218
Polymers101,1542
Non-polymers62916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-9.3 kcal/mol
Surface area39870 Å2
MethodPISA
2
C: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
D: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,01825
Polymers101,1542
Non-polymers86423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-10.3 kcal/mol
Surface area38920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.133, 81.136, 165.465
Angle α, β, γ (deg.)90.00, 117.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1 / NTPDASE 1 / ECTO-ATP DIPHOSPHOHYDROLASE 1 / ECTO-ATPDASE 1 / ECTO-ATPASE 1 / ECTO-APYRASE / ...NTPDASE 1 / ECTO-ATP DIPHOSPHOHYDROLASE 1 / ECTO-ATPDASE 1 / ECTO-ATPASE 1 / ECTO-APYRASE / LYMPHOID CELL ACTIVATION ANTIGEN / CD39


Mass: 50576.953 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 38-189,190-206
Source method: isolated from a genetically manipulated source
Details: A PUTATIVE MEMBRANE INTERACTION LOOP 190TQEQSWLNFISDSQKQA206 WAS REPLACED BY A SHORTER LINKER KTPGGS
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P97687, apyrase
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE LOOP T190 TO A206 WAS REPLACED WITH THE SEQUENCE KTPGGS OF GB EDL94186.1. THE RESIDUES 80, 220, ...THE LOOP T190 TO A206 WAS REPLACED WITH THE SEQUENCE KTPGGS OF GB EDL94186.1. THE RESIDUES 80, 220, AND 227 MATCH THE GENBANK SEQUENCE.

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 4.5 / Details: 3.6 M NACL, 100 MM NAAC PH 4.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→42.55 Å / Num. obs: 151721 / % possible obs: 72.4 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.4 / % possible all: 7.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CJ1

3cj1


Resolution: 1.7→146.62 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23308 1139 0.8 %RANDOM
Rwork0.17642 ---
obs0.17683 150524 72.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.504 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å2-0.34 Å2
2--0.93 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 1.7→146.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12528 0 60 816 13404
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.596 2 -
Rwork0.257 625 -
obs--4.08 %

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