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- PDB-4iuh: Crystal structure of NreA of Staphylococcus carnosus with bound iodide -

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Basic information

Entry
Database: PDB / ID: 4iuh
TitleCrystal structure of NreA of Staphylococcus carnosus with bound iodide
ComponentsNreA proteinNational Rural Education Association
KeywordsNitrate-binding protein / GAF domain / Nitrate sensor / Staphylococcus / Nitrate binding / Iodide / Cytosolic
Function / homologyGAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / IODIDE ION / NreA protein
Function and homology information
Biological speciesStaphylococcus carnosus subsp. carnosus TM300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1971 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,9624
Polymers37,7092
Non-polymers2542
Water2,108117
1
A: NreA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9812
Polymers18,8541
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NreA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9812
Polymers18,8541
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.490, 85.490, 91.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein NreA protein / National Rural Education Association


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


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.54 %
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 fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base, 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 fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.92
SYNCHROTRONESRF ID14-420.92
SYNCHROTRONESRF ID14-430.92
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMar 12, 2011
ADSC QUANTUM 315r2CCDMar 12, 2011
ADSC QUANTUM 315r3CCDMar 12, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Single crystal Si(111)SINGLE WAVELENGTHMx-ray1
3Single crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.197→40.351 Å / Num. obs: 22412 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 1
Reflection shellResolution: 2.197→2.56 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
BsxCuBEdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1971→40.351 Å / SU ML: 0.3 / σ(F): 0.99 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 1633 4.99 %
Rwork0.2025 --
obs0.2049 32750 99.2 %
all-32751 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1971→40.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 2 117 2315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052242
X-RAY DIFFRACTIONf_angle_d0.8543036
X-RAY DIFFRACTIONf_dihedral_angle_d12.918834
X-RAY DIFFRACTIONf_chiral_restr0.059341
X-RAY DIFFRACTIONf_plane_restr0.003393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1971-2.26170.37171370.32592583X-RAY DIFFRACTION100
2.2617-2.33470.32051360.29482617X-RAY DIFFRACTION100
2.3347-2.41820.29511350.27082604X-RAY DIFFRACTION100
2.4182-2.5150.31711390.23612614X-RAY DIFFRACTION99
2.515-2.62940.27151390.23022571X-RAY DIFFRACTION99
2.6294-2.7680.25321420.24322624X-RAY DIFFRACTION99
2.768-2.94140.32841350.22092607X-RAY DIFFRACTION100
2.9414-3.16840.22911290.21042596X-RAY DIFFRACTION100
3.1684-3.48710.20421380.18522583X-RAY DIFFRACTION99
3.4871-3.99130.19981310.1692595X-RAY DIFFRACTION99
3.9913-5.02710.22261380.15062574X-RAY DIFFRACTION98
5.0271-40.35770.24591340.18092549X-RAY DIFFRACTION98
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)
13.61170.96910.33364.5713-0.30714.96030.06220.0740.1060.1163-0.0155-0.4259-0.16960.1658-0.05390.083-0.0989-0.02770.16760.04590.0964-28.221913.348-10.3726
23.68930.6486-0.25993.5831-0.15483.66730.0214-0.1138-0.4813-0.0544-0.0904-0.26170.3804-0.2704-0.0370.14540.05010.01860.10450.01880.1622-38.4637-19.1435-32.092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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