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- PDB-6nch: Crystal structure of CDP-Chase: Raster data collection -

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Basic information

Entry
Database: PDB / ID: 6nch
TitleCrystal structure of CDP-Chase: Raster data collection
ComponentsPhosphohydrolase (MutT/nudix family protein)
KeywordsHYDROLASE / nudix / CDPChase / CDP-choline hydrolase / CDP / ADP-ribose
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1120 / Hydrolase of X-linked nucleoside diphosphate N terminal / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1120 / Hydrolase of X-linked nucleoside diphosphate N terminal / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Helix non-globular / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / D-ribose / Phosphohydrolase (MutT/nudix family protein)
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMiller, M.S. / Shi, W. / Gabelli, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA062924 United States
CitationJournal: Molecules / Year: 2019
Title: Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II.
Authors: Miller, M.S. / Maheshwari, S. / Shi, W. / Gao, Y. / Chu, N. / Soares, A.S. / Cole, P.A. / Amzel, L.M. / Fuchs, M.R. / Jakoncic, J. / Gabelli, S.B.
History
DepositionDec 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 1, 2020Group: Atomic model / Category: atom_site / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphohydrolase (MutT/nudix family protein)
B: Phosphohydrolase (MutT/nudix family protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8756
Polymers47,4382
Non-polymers4374
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-92 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.711, 67.201, 111.286
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphohydrolase (MutT/nudix family protein)


Mass: 23718.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_2032 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q81EE8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-RB5 / D-ribose


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.2 to 0.3 M Lithium sulfate, 26 to 29% PEG-4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→19.76 Å / Num. obs: 30674 / % possible obs: 96.6 % / Redundancy: 7 % / CC1/2: 0.941 / Rmerge(I) obs: 0.357 / Rpim(I) all: 0.137 / Rrim(I) all: 0.385 / Net I/σ(I): 4.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 7 % / Rmerge(I) obs: 1.105 / Num. unique obs: 2248 / CC1/2: 0.608 / Rpim(I) all: 0.425 / Rrim(I) all: 1.192 / % possible all: 96.8
Serial crystallography sample deliveryMethod: fixed target

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.505
Highest resolutionLowest resolution
Rotation19.75 Å3.5 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.5.21data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q1P

3q1p


Resolution: 2→19.76 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.614 / SU ML: 0.155 / SU R Cruickshank DPI: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.192
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 1461 4.8 %RANDOM
Rwork0.2 ---
obs0.2029 29211 95.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.49 Å2 / Biso mean: 26.155 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2---0.15 Å20 Å2
3----1.53 Å2
Refinement stepCycle: final / Resolution: 2→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 25 366 3660
Biso mean--51.77 34.66 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133414
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173124
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.6454624
X-RAY DIFFRACTIONr_angle_other_deg1.4111.5827311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03225.085177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04115631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.996158
X-RAY DIFFRACTIONr_chiral_restr0.070.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02682
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 101 -
Rwork0.276 2146 -
all-2247 -
obs--96.23 %

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