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- PDB-4iuk: Crystal structure of NreA of Staphylococcus carnosus with bound n... -

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Basic information

Entry
Database: PDB / ID: 4iuk
TitleCrystal structure of NreA of Staphylococcus carnosus with bound nitrate
ComponentsNreA protein
KeywordsNitrate-binding protein / GAF domain / Nitrate sensor / Staphylococcus / Nitrate binding / Nitrate / Cytosolic
Function / homologyGAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / NITRATE ION / NreA protein
Function and homology information
Biological speciesStaphylococcus carnosus subsp. carnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsStehle, T. / Niemann, V.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The NreA Protein Functions as a Nitrate Receptor in the Staphylococcal Nitrate Regulation System.
Authors: Niemann, V. / Koch-Singenstreu, M. / Neu, A. / Nilkens, S. / Gotz, F. / Unden, G. / Stehle, T.
History
DepositionJan 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NreA protein
B: NreA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8334
Polymers37,7092
Non-polymers1242
Water70339
1
A: NreA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9162
Polymers18,8541
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NreA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9162
Polymers18,8541
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.660, 85.660, 91.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-321-

HOH

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Components

#1: Protein NreA protein


Mass: 18854.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus carnosus subsp. carnosus (bacteria)
Strain: TM300 / Gene: nreA, Sca_1890, SCA_1890 / Production host: Escherichia coli (E. coli) / References: UniProt: B9DL91
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12.5 % (w/v) PEG 1.000, 12.5 % (w/v) PEG 3350, 12.5 % (v/v) 2-methyl-2,4-pentanediol, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, 0.1 M bicine/Trizma ...Details: 12.5 % (w/v) PEG 1.000, 12.5 % (w/v) PEG 3350, 12.5 % (v/v) 2-methyl-2,4-pentanediol, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, 0.1 M bicine/Trizma base, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 9, 2011
RadiationMonochromator: toroidal focused Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→42.83 Å / Num. obs: 14713 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 1
Reflection shellResolution: 2.35→2.41 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
BsxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→42.83 Å / SU ML: 0.35 / σ(F): 1.99 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 1470 9.99 %
Rwork0.2128 --
obs0.2168 14713 99.95 %
all-14712 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 8 39 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052211
X-RAY DIFFRACTIONf_angle_d0.8542997
X-RAY DIFFRACTIONf_dihedral_angle_d14.486808
X-RAY DIFFRACTIONf_chiral_restr0.059340
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.42590.36241280.34271174X-RAY DIFFRACTION100
2.4259-2.51260.33441300.2971172X-RAY DIFFRACTION100
2.5126-2.61320.33391330.28141188X-RAY DIFFRACTION100
2.6132-2.73210.30381300.28841172X-RAY DIFFRACTION100
2.7321-2.87610.29491320.24851189X-RAY DIFFRACTION100
2.8761-3.05620.25321330.22441195X-RAY DIFFRACTION100
3.0562-3.29210.2511320.21731193X-RAY DIFFRACTION100
3.2921-3.62330.28381330.21151192X-RAY DIFFRACTION100
3.6233-4.14720.23161350.18021214X-RAY DIFFRACTION100
4.1472-5.22350.20981370.16931238X-RAY DIFFRACTION100
5.2235-42.83710.221470.19991316X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6714-0.048-0.36534.0671.0255.32180.1125-0.0492-0.243-0.0477-0.1404-0.42920.12390.04670.02220.28770.07380.04260.32970.08560.2587-28.3306-13.3923-12.545
24.11060.0109-0.07864.60870.57395.33050.01270.15260.39650.0672-0.0963-0.3444-0.3691-0.28730.02970.3076-0.0881-0.02390.28230.07230.3105-38.361519.13738.7059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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