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- PDB-6nci: Crystal structure of CDP-Chase: Vector data collection -

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Basic information

Entry
Database: PDB / ID: 6nci
TitleCrystal structure of CDP-Chase: Vector data collection
ComponentsPhosphohydrolase (MutT/nudix family protein)
KeywordsHYDROLASE / nudix / CDP-chase / CDP-choline hydrolase / ADP-ribose / vector data collection
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
DI(HYDROXYETHYL)ETHER / 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: 2.08 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)48,36511
Polymers47,4382
Non-polymers9289
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-133 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.771, 67.008, 111.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#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
#5: 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

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Non-polymers , 4 types, 263 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 49.4 %
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: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.08→29.47 Å / Num. obs: 28297 / % possible obs: 98.8 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.039 / Rrim(I) all: 0.142 / Net I/σ(I): 14.4
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.942 / Num. unique obs: 1769 / CC1/2: 0.818 / Rpim(I) all: 0.28 / Rrim(I) all: 0.985 / % possible all: 84.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.503
Highest resolutionLowest resolution
Rotation29.45 Å3.5 Å

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Processing

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

3q1p


Resolution: 2.08→29.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.656 / SU ML: 0.125 / SU R Cruickshank DPI: 0.1962 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.173
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 1502 5.3 %RANDOM
Rwork0.1712 ---
obs0.1741 26741 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.64 Å2 / Biso mean: 33.807 Å2 / Biso min: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.85 Å2
Refinement stepCycle: final / Resolution: 2.08→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 52 255 3581
Biso mean--77.99 40.91 -
Num. residues----401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133407
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173122
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.6444603
X-RAY DIFFRACTIONr_angle_other_deg1.4361.5827292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48824.912171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88115624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.055158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023710
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02678
LS refinement shellResolution: 2.078→2.132 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 84 -
Rwork0.241 1683 -
all-1767 -
obs--84.34 %

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