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- PDB-4brn: Legionella pneumophila NTPDase1 crystal form III (closed) in comp... -

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Basic information

Entry
Database: PDB / ID: 4brn
TitleLegionella pneumophila NTPDase1 crystal form III (closed) in complex with Mg AMP
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
ADENOSINE MONOPHOSPHATE / 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. / 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 1.3Oct 23, 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_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_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

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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)84,63510
Polymers83,7612
Non-polymers8748
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-75.1 kcal/mol
Surface area27970 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-62.5 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.333, 83.577, 104.110
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: (-0.986, -0.034, -0.165), (0.054, -0.991, -0.119), (-0.159, -0.126, 0.979)
Vector: 24.444, 0.86, 1.983)

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Components

#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
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 4.6
Details: 100MM NAMES PH 4.6 200MM NACL 12% PEG3350 5MM MGCL2 25MM AMP

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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: 1.7→30 Å / Num. obs: 78136 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4

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Processing

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

Resolution: 1.69→28.98 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.448 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23014 1132 1.5 %RANDOM
Rwork0.1861 ---
obs0.18676 76492 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.392 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2--0.77 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.69→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5703 0 52 310 6065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196000
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9488216
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1625742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.58826305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73415967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8451510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214680
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
Rfree0.33 68 -
Rwork0.265 5344 -
obs--94.22 %
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)
11.61020.2034-0.32170.67990.11621.02020.02350.18020.0134-0.0755-0.041-0.0808-0.0042-0.05830.01750.09410.01790.00310.0299-0.00690.130.1574-5.9617-4.8028
22.9658-0.1012-0.65720.6770.1552.30650.0728-0.13020.06230.0387-0.021-0.1515-0.13470.2813-0.05180.0727-0.0337-0.02190.044-0.00940.104639.4078-4.01510.4126
31.5046-0.5369-0.28081.0326-0.280.61210.1005-0.2190.19370.1556-0.0163-0.1041-0.21680.2002-0.08420.1609-0.0663-0.0010.0799-0.0540.085925.01725.582619.7136
41.58490.25720.32030.85670.07590.74920.01740.26230.0339-0.12690.0010.0876-0.03820.0663-0.01850.10640.01670.01220.05090.02070.0891-4.84547.4893-6.7771
51.6615-0.14740.23310.9652-0.31211.62960.01720.00180.14730.00470.0290.2106-0.0187-0.1534-0.04620.06130.00010.02250.01490.00540.0959-16.4933.71226.2393
60.8831-0.31330.11271.07590.24930.29990.009-0.0688-0.02370.15550.00840.07560.008-0.0448-0.01740.1148-0.00940.02620.0140.01160.0419-3.1783-6.991316.7143
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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