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

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Basic information

Entry
Database: PDB / ID: 6izk
TitleStructural characterization of mutated NreA protein in nitrate binding site from Staphylococcus aureus
ComponentsNreA
KeywordsSIGNALING PROTEIN / Complex
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
IMIDAZOLE / L(+)-TARTARIC ACID / GAF domain-containing protein / GAF domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSangare, L. / Chen, W. / Wang, C. / Chen, X. / Wu, M. / Zhang, X. / Zang, J.
CitationJournal: To Be Published
Title: Structural characterization of mutated NreA protein in nitrate binding site from Staphylococcus aureus
Authors: Sangare, L. / Cheng, W.
History
DepositionDec 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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
B: NreA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5257
Polymers34,1652
Non-polymers3595
Water59433
1
A: NreA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4065
Polymers17,0831
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area8060 Å2
MethodPISA
2
B: NreA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1182
Polymers17,0831
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.072, 38.782, 70.574
Angle α, β, γ (deg.)90.00, 91.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NreA


Mass: 17082.742 Da / Num. of mol.: 2 / 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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: K/Na tartrate, Imidazole, NaCl

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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: Jan 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.29→70.55 Å / Num. obs: 16671 / % possible obs: 95.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.7
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.294

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Processing

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

4pau


Resolution: 2.29→70.55 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.106 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24561 747 4.5 %RANDOM
Rwork0.18849 ---
obs0.19104 15916 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.017 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0.39 Å2
2---0.02 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.29→70.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 22 33 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192371
X-RAY DIFFRACTIONr_bond_other_d0.0020.022288
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9763192
X-RAY DIFFRACTIONr_angle_other_deg0.98935296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37623.393112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53915432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.131520
X-RAY DIFFRACTIONr_chiral_restr0.1060.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212608
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02512
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_it4.8855.6921138
X-RAY DIFFRACTIONr_mcbond_other4.8365.6871137
X-RAY DIFFRACTIONr_mcangle_it6.6998.5191420
X-RAY DIFFRACTIONr_mcangle_other6.7098.5231421
X-RAY DIFFRACTIONr_scbond_it6.0036.3791233
X-RAY DIFFRACTIONr_scbond_other6.0016.3791234
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.8789.2511771
X-RAY DIFFRACTIONr_long_range_B_refined11.02765.632587
X-RAY DIFFRACTIONr_long_range_B_other11.02565.6212588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.292→2.352 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 46 -
Rwork0.337 906 -
obs--76.28 %

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