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- PDB-6izj: Structural characterization of mutated NreA protein in nitrate bi... -

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Basic information

Entry
Database: PDB / ID: 6izj
TitleStructural characterization of mutated NreA protein in nitrate binding site from Staphylococcus aureus
ComponentsNreA
KeywordsSIGNALING PROTEIN / complex / Structural Genomics
Function / homology
Function and homology information


GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / GAF domain-containing protein / GAF domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionDec 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 1, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)17,2993
Polymers17,1751
Non-polymers1242
Water32418
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.914, 36.368, 36.545
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: 17174.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / Gene: ATCC 700699 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1FZV0, UniProt: A0A0H3JU14*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: sodium phosphate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→54.96 Å / Num. obs: 8537 / % possible obs: 93.4 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 20.35
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.377

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Processing

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

4pau


Resolution: 2.1→54.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.133 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26573 475 5.6 %RANDOM
Rwork0.20421 ---
obs0.20726 8031 93.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.315 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å20 Å2
2--0.1 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.1→54.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 8 18 1139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191151
X-RAY DIFFRACTIONr_bond_other_d0.0030.021115
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9771550
X-RAY DIFFRACTIONr_angle_other_deg0.96432581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1355139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.323.33354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9415211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3561510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211261
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02241
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_it4.8396.163553
X-RAY DIFFRACTIONr_mcbond_other4.8326.156552
X-RAY DIFFRACTIONr_mcangle_it6.9579.21690
X-RAY DIFFRACTIONr_mcangle_other6.9529.219691
X-RAY DIFFRACTIONr_scbond_it6.0096.886598
X-RAY DIFFRACTIONr_scbond_other5.6666.896595
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.62510.051857
X-RAY DIFFRACTIONr_long_range_B_refined11.4371.2761258
X-RAY DIFFRACTIONr_long_range_B_other11.42671.2991259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 19 -
Rwork0.359 472 -
obs--71.99 %

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