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- PDB-4brk: Legionella pneumophila NTPDase1 N302Y variant crystal form III (c... -

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Basic information

Entry
Database: PDB / ID: 4brk
TitleLegionella pneumophila NTPDase1 N302Y variant crystal form III (closed) in complex with MG UMPPNP
ComponentsECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
KeywordsHYDROLASE / APYRASE / ATPASE / ADPASE / CD39 / PURINERGIC SIGNALLING / DOMAIN ROTATION / TRANSITION STATE / NTPDASE
Function / homology
Function and homology information


nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / nucleotide binding / metal ion binding / membrane
Similarity search - Function
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
Chem-UNP / Ectonucleoside triphosphate diphosphohydrolase I
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å
AuthorsZebisch, M. / Schaefer, P. / Lauble, P. / Straeter, N.
CitationJournal: Structure / Year: 2013
Title: Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases
Authors: Zebisch, M. / Krauss, M. / Schaefer, P. / Lauble, P. / Straeter, N.
History
DepositionJun 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Structure summary
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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.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.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.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_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: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,55513
Polymers83,8592
Non-polymers1,69611
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-49.6 kcal/mol
Surface area27880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.600, 82.967, 109.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.985, 0.063, 0.158), (-0.04, -0.988, 0.15), (0.166, 0.141, 0.976)
Vector: -12.985, -2.355, 1.414)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I / NTPDASE1


Mass: 41929.664 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-393 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5ZUA2, apyrase

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Non-polymers , 6 types, 777 molecules

#2: Chemical ChemComp-UNP / 5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES): PH BUFFER MES PHOSPHOAMINOPHOSPHONIC ACID-URIDYLATE ...2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES): PH BUFFER MES PHOSPHOAMINOPHOSPHONIC ACID-URIDYLATE ESTER (UNP): UMPPNP UTP ANALOG

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 5.4
Details: 100MM NAMES PH 5.4, 10% PEG3350, 15% GLYCEROL, 10MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
ReflectionResolution: 1.5→28 Å / Num. obs: 117553 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.5→27.43 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.403 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17791 1183 1 %RANDOM
Rwork0.12877 ---
obs0.12929 116157 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.928 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5734 0 99 766 6599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0196226
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.9568568
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.26126.151317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.824151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7159
X-RAY DIFFRACTIONr_chiral_restr0.1270.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214861
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.79936226
X-RAY DIFFRACTIONr_sphericity_free32.7575182
X-RAY DIFFRACTIONr_sphericity_bonded15.64856620
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 82 -
Rwork0.189 8429 -
obs--98.86 %

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