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- PDB-4bnq: The structure of the Staphylococcus aureus Ham1 protein -

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Basic information

Entry
Database: PDB / ID: 4bnq
TitleThe structure of the Staphylococcus aureus Ham1 protein
ComponentsNON-CANONICAL PURINE NTP PYROPHOSPHATASE
KeywordsHYDROLASE / HAM / INOSINE TRIPHOSPHATE PYROPHOSPHATASE
Function / homology
Function and homology information


XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / XTP diphosphatase activity / dITP diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / metal ion binding
Similarity search - Function
dITP/XTP pyrophosphatase / Ham1-like protein / Ham1 family / Maf protein - #10 / Inosine triphosphate pyrophosphatase-like / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / dITP/XTP pyrophosphatase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.279 Å
AuthorsAbergel, C. / Claverie, J.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Molecular Replacement: Tricks and Treats.
Authors: Abergel, C.
History
DepositionMay 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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

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Assembly

Deposited unit
A: NON-CANONICAL PURINE NTP PYROPHOSPHATASE
B: NON-CANONICAL PURINE NTP PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4498
Polymers42,8822
Non-polymers5676
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-38.3 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.403, 101.542, 102.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NON-CANONICAL PURINE NTP PYROPHOSPHATASE / NON-STANDARD PURINE NTP PYROPHOSPHATASE / NUCLEOSIDE-TRIPHOS PHATE DIPHOSPHATASE / NUCLEOSIDE- ...NON-STANDARD PURINE NTP PYROPHOSPHATASE / NUCLEOSIDE-TRIPHOS PHATE DIPHOSPHATASE / NUCLEOSIDE-TRIPHOSPHATE PYROPHOSPHATASE / NTPASE


Mass: 21441.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria)
Strain: N315 / Plasmid: IN HOUSE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P99094, nucleoside-triphosphate diphosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLACK OF INITIAL MET

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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: 3.31 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growDetails: 20% AMSO4, PH 6

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97974
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97974 Å / Relative weight: 1
ReflectionResolution: 2.28→43.4 Å / Num. obs: 26528 / % possible obs: 85.7 % / Observed criterion σ(I): 1.34 / Redundancy: 4.1 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.8
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.4 / % possible all: 85.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.279→43.398 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 25.46 / Stereochemistry target values: ML / Details: THE TWO MONOMERS ADOPT DIFFERENT CONFORMATIONS
RfactorNum. reflection% reflection
Rfree0.2383 1143 5.1 %
Rwork0.1882 --
obs0.1908 22550 85.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.279→43.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 0 31 193 3207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083054
X-RAY DIFFRACTIONf_angle_d1.1374114
X-RAY DIFFRACTIONf_dihedral_angle_d14.5921139
X-RAY DIFFRACTIONf_chiral_restr0.079449
X-RAY DIFFRACTIONf_plane_restr0.005543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2791-2.38280.27141110.21441756X-RAY DIFFRACTION58
2.3828-2.50840.30281190.22822589X-RAY DIFFRACTION83
2.5084-2.66560.30261420.23022882X-RAY DIFFRACTION92
2.6656-2.87130.26781490.2252856X-RAY DIFFRACTION92
2.8713-3.16020.28391670.21272825X-RAY DIFFRACTION91
3.1602-3.61730.24131640.17782834X-RAY DIFFRACTION90
3.6173-4.55670.20141520.15582803X-RAY DIFFRACTION89
4.5567-43.40610.20511390.18122862X-RAY DIFFRACTION85

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