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- PDB-6k2h: structural characterization of mutated NreA protein in nitrate bi... -

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Basic information

Entry
Database: PDB / ID: 6k2h
Titlestructural characterization of mutated NreA protein in nitrate binding site from staphylococcus aureus.
ComponentsNreA
KeywordsSIGNALING PROTEIN / Complex
Function / homologyGAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / GAF domain-containing protein / GAF domain-containing protein
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSangare, L. / Chen, W. / Wang, C. / Chen, X. / Wu, M. / Zhang, X. / Zang, J.
CitationJournal: Biotechnol.Lett. / Year: 2020
Title: Structural insights into the conformational change of Staphylococcus aureus NreA at C-terminus.
Authors: Sangare, L. / Chen, W. / Wang, C. / Chen, X. / Wu, M. / Zhang, X. / Zang, J.
History
DepositionMay 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NreA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2694
Polymers17,0831
Non-polymers1863
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.000, 106.302, 33.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NreA


Mass: 17082.742 Da / Num. of mol.: 1 / Mutation: Y94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Gene: QU38_07700 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1FZV0, UniProt: Q2FVM5*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.83 Å3/Da / Density % sol: 32.66 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG monomethyl ether 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 12171 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 4.5
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.455 / Num. unique obs: 150995

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PAU

4pau


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.557 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22195 600 4.9 %RANDOM
Rwork0.17523 ---
obs0.17766 11531 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å2-0 Å2-0 Å2
2---2.32 Å20 Å2
3---1.37 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 12 64 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191125
X-RAY DIFFRACTIONr_bond_other_d0.0020.021102
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9781510
X-RAY DIFFRACTIONr_angle_other_deg1.02832551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31123.26952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02315208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7611510
X-RAY DIFFRACTIONr_chiral_restr0.1330.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211224
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02234
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_it3.1122.906541
X-RAY DIFFRACTIONr_mcbond_other3.12.898540
X-RAY DIFFRACTIONr_mcangle_it4.1714.331675
X-RAY DIFFRACTIONr_mcangle_other4.1694.34676
X-RAY DIFFRACTIONr_scbond_it4.3643.563584
X-RAY DIFFRACTIONr_scbond_other4.3593.563584
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3635.094835
X-RAY DIFFRACTIONr_long_range_B_refined8.62635.151228
X-RAY DIFFRACTIONr_long_range_B_other8.62335.1831229
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 40 -
Rwork0.196 726 -
obs--87.44 %

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