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- PDB-5u7h: Ni-bound dihydroneopterin triphosphate pyrophosphohydrolase from ... -

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Basic information

Entry
Database: PDB / ID: 5u7h
TitleNi-bound dihydroneopterin triphosphate pyrophosphohydrolase from E. coli
ComponentsDihydroneopterin triphosphate diphosphatase
KeywordsHYDROLASE / Nudix hydrolase / Dihydroneopterin Triphosphate Pyrophosphohydrolase / Metal ion binding / tetranuclear
Function / homology
Function and homology information


dihydroneopterin triphosphate diphosphatase / dihydroneopterin triphosphate pyrophosphohydrolase activity / dATP diphosphatase activity / folic acid biosynthetic process / metal ion binding
Similarity search - Function
Dihydroneopterin triphosphate diphosphatase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Dihydroneopterin triphosphate diphosphatase
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNguyen, E. / Hill, S.E. / Lieberman, R.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Kimberly Clark United States
National Science Foundation (NSF, United States)0845445 United States
CitationJournal: PLoS ONE / Year: 2017
Title: Metal ion coordination in the E. coli Nudix hydrolase dihydroneopterin triphosphate pyrophosphatase: New clues into catalytic mechanism.
Authors: Hill, S.E. / Nguyen, E. / Ukachukwu, C.U. / Freeman, D.M. / Quirk, S. / Lieberman, R.L.
History
DepositionDec 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 16, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroneopterin triphosphate diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9099
Polymers17,3281
Non-polymers5828
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dihydroneopterin triphosphate diphosphatase
hetero molecules

A: Dihydroneopterin triphosphate diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,81918
Polymers34,6552
Non-polymers1,16316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2770 Å2
ΔGint-171 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.680, 42.980, 57.050
Angle α, β, γ (deg.)90.00, 91.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-326-

HOH

31A-376-

HOH

41A-414-

HOH

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Components

#1: Protein Dihydroneopterin triphosphate diphosphatase / Dihydroneopterin triphosphate pyrophosphatase / dATP pyrophosphohydrolase


Mass: 17327.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: nudB, Z2917, ECs2575 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AFC1, dihydroneopterin triphosphate diphosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Crystals were grown in 36% PEG 8000 and 0.05M Ammonium Sulfate. Crystals were soaked in 0.5mM dihydroneopterin and 10mM NiCl2.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.4938 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4938 Å / Relative weight: 1
ReflectionResolution: 2→33.55 Å / Num. obs: 8796 / % possible obs: 98.65 % / Redundancy: 6.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.1764 / Net I/σ(I): 11.56
Reflection shellHighest resolution: 2 Å / Rmerge(I) obs: 0.5763 / CC1/2: 0.917

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 201C

201c


Resolution: 2→33.547 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.39 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 1687 10.06 %
Rwork0.1678 --
obs0.1748 8795 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→33.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 20 128 1323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161239
X-RAY DIFFRACTIONf_angle_d0.7541654
X-RAY DIFFRACTIONf_dihedral_angle_d3.442722
X-RAY DIFFRACTIONf_chiral_restr0.052185
X-RAY DIFFRACTIONf_plane_restr0.005210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05880.30541380.2351220X-RAY DIFFRACTION95
2.0588-2.12530.31721490.22471258X-RAY DIFFRACTION97
2.1253-2.20120.3241310.2081239X-RAY DIFFRACTION97
2.2012-2.28930.29951470.20131236X-RAY DIFFRACTION96
2.2893-2.39350.33531390.21661243X-RAY DIFFRACTION97
2.3935-2.51960.29981370.20751256X-RAY DIFFRACTION98
2.5196-2.67740.25511390.19321288X-RAY DIFFRACTION98
2.6774-2.8840.26611460.17151264X-RAY DIFFRACTION99
2.884-3.17410.22971470.15981269X-RAY DIFFRACTION98
3.1741-3.63290.18651380.14711253X-RAY DIFFRACTION98
3.6329-4.57520.23571420.12621253X-RAY DIFFRACTION98
4.5752-33.55180.15391340.13451311X-RAY DIFFRACTION99

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