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- PDB-4brh: Legionella pneumophila NTPDase1 crystal form II (closed) in compl... -

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Basic information

Entry
Database: PDB / ID: 4brh
TitleLegionella pneumophila NTPDase1 crystal form II (closed) in complex with MG AND THIAMINE PHOSPHOVANADATE
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
DECAVANADATE / THIAMINE-PHOSPHOVANADATE / Ectonucleoside triphosphate diphosphohydrolase I
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.69 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. / Schafer, P. / Lauble, P. / Strater, 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 2.0Jan 30, 2019Group: Atomic model / Data collection / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.1Oct 16, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,20513
Polymers83,7612
Non-polymers3,44311
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-30.6 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.435, 85.759, 72.306
Angle α, β, γ (deg.)90.00, 106.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.413, 0.068, -0.908), (0.062, -0.997, -0.046), (-0.908, -0.037, -0.416)
Vector: 58.738, 3.177, 91.683)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I / NTPDASE1


Mass: 41880.594 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-393
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 , 7 types, 445 molecules

#2: Chemical ChemComp-TMV / THIAMINE-PHOSPHOVANADATE


Mass: 463.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21N4O8PSV
#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-DVT / DECAVANADATE


Mass: 957.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O28V10
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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 THIAMINE-PHOSPHOVANADATE (TMV): TRANSITION ...2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES): PH BUFFER MES THIAMINE-PHOSPHOVANADATE (TMV): TRANSITION STATE MIMIC FOR TPP

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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: 5.6 / Details: 100MM NAMES PH 5.6, 11% PEG3350, 20MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→29 Å / Num. obs: 80289 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 34.3

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Processing

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

Resolution: 1.69→29.04 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.084 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19187 1175 1.5 %RANDOM
Rwork0.15943 ---
obs0.15991 79084 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.783 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.8 Å2
2---0.94 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.69→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5744 0 164 434 6342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.026466
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9552.0119088
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.62626.14329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.208151035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9091512
X-RAY DIFFRACTIONr_chiral_restr0.1410.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215009
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.694→1.738 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.188 81 -
Rwork0.175 5550 -
obs--94.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.58080.22250.13510.3072-0.16271.2605-0.01830.01630.0258-0.0486-0.0206-0.02390.05090.11220.03890.0647-0.003-0.00420.05670.02910.019468.137611.3672-0.705
21.01330.6599-0.97130.4969-0.81331.6964-0.12110.21850.0655-0.07180.10340.01220.0634-0.23670.01770.0807-0.0066-0.0260.12350.02780.022850.92797.9298-1.1929
30.2852-0.12560.1360.386-0.20770.38090.01580.0376-0.0059-0.009-0.01340.01920.0052-0.0187-0.00240.04020.0017-0.01410.0584-0.00250.025350.5545-3.359815.5355
40.6729-0.10810.18710.31540.1460.8194-0.01810.08390.0083-0.0012-0.0126-0.0248-0.04080.0830.03070.03010.0063-0.0130.05920.01620.020988.1247-4.17429.2934
51.4821-0.85710.01050.5704-0.03270.5721-0.0546-0.18710.09240.03410.0654-0.06480.09960.0882-0.01080.0750.0241-0.02530.0874-0.00790.024681.377-1.798945.5783
60.3141-0.09380.12910.6381-0.25390.2545-0.0104-0.04390.01590.06490.0050.0394-0.0192-0.00530.00540.05930.0048-0.0060.0504-0.00720.013165.38778.788239.3832
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 155
2X-RAY DIFFRACTION2A156 - 179
3X-RAY DIFFRACTION2A377 - 394
4X-RAY DIFFRACTION3A180 - 376
5X-RAY DIFFRACTION4B34 - 155
6X-RAY DIFFRACTION5B156 - 179
7X-RAY DIFFRACTION5B377 - 394
8X-RAY DIFFRACTION6B180 - 376

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