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- PDB-6on4: Crystal structure of the GntR-type sialoregulator NanR from Esche... -

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Basic information

Entry
Database: PDB / ID: 6on4
TitleCrystal structure of the GntR-type sialoregulator NanR from Escherichia coli, in complex with sialic acid
ComponentsHTH-type transcriptional repressor NanR
KeywordsDNA BINDING PROTEIN / Transcriptional Repressor / Bacterial Sialic Acid Catabolism
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA binding
Similarity search - Function
HTH-type transcriptional repressor NanR / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
polyethylene glycol / N-acetyl-beta-neuraminic acid / HTH-type transcriptional repressor NanR
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsHorne, C.R. / Panjikar, S. / North, R.A. / Dobson, R.C.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandUOC1506 New Zealand
CitationJournal: J. Bacteriol. / Year: 2013
Title: Control of the Escherichia coli sialoregulon by transcriptional repressor NanR.
Authors: Kalivoda, K.A. / Steenbergen, S.M. / Vimr, E.R.
History
DepositionApr 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional repressor NanR
B: HTH-type transcriptional repressor NanR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1705
Polymers59,1332
Non-polymers1,0373
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Used Sedimentation Velocity experiments in the analytical ultracentrifuge. When fitted to a continuous mass distribution [c(M)] model, the data is consistent ...Evidence: equilibrium centrifugation, Used Sedimentation Velocity experiments in the analytical ultracentrifuge. When fitted to a continuous mass distribution [c(M)] model, the data is consistent with a dimer., SAXS, The Porod Volume and analysis from online server SAXS MoW2 is consistent with a dimer., mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-71 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.771, 87.846, 73.869
Angle α, β, γ (deg.)90.000, 103.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 31 through 244)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 31 - 244 / Label seq-ID: 31 - 244

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 31 through 244)AA
2chain BBB

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Components

#1: Protein HTH-type transcriptional repressor NanR


Mass: 29566.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: nanR, yhcK, b3226, JW3195 / Variant: K-12 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8W0
#2: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID / N-Acetylneuraminic acid


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol / Polyethylene glycol


Mass: 662.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C30H62O15
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.33 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium HEPES, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo-Stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→43.92 Å / Num. obs: 28505 / % possible obs: 98.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 43.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.028 / Rrim(I) all: 0.053 / Net I/σ(I): 13.6 / Num. measured all: 96712
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.162.60.547526020240.6710.3910.6761.886.6
8.9-43.923.40.02313844020.9990.0140.02740.298.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.92 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.62
RfactorNum. reflection% reflection
Rfree0.2295 1391 4.88 %
Rwork0.1812 --
obs0.1834 28482 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.96 Å2 / Biso mean: 57.3052 Å2 / Biso min: 28.65 Å2
Refinement stepCycle: final / Resolution: 2.1→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 147 163 3733
Biso mean--78.17 51.52 -
Num. residues----431
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1886X-RAY DIFFRACTION19.675TORSIONAL
12B1886X-RAY DIFFRACTION19.675TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0966-2.17160.34011270.28692376250388
2.1716-2.25850.28591450.24452636278196
2.2585-2.36130.27331420.22012775291799
2.3613-2.48580.23341660.200627172883100
2.4858-2.64150.26391340.214227502884100
2.6415-2.84540.24491450.202227482893100
2.8454-3.13170.26561340.210127482882100
3.1317-3.58470.24531520.197527522904100
3.5847-4.51560.19371120.1592773288599
4.5156-43.93260.19271340.1432816295099
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)
10.66470.02170.14670.7924-0.02460.69250.3270.09280.1638-0.5642-0.3831-0.24270.24780.360600.56360.09660.07110.45730.13430.551214.806234.05941.339
22.76330.7565-0.35910.7261-0.27341.06530.0541-0.3867-0.07390.074-0.0143-0.07740.1316-0.08410.00010.3393-0.0242-0.03250.35290.04020.3098-1.93598.240927.6487
30.0936-0.0198-0.10170.01980.00270.11390.08130.1099-0.3084-0.004-0.343-0.90910.36660.3287-0.00080.71490.02010.03850.8747-0.05560.65997.711321.476648.7497
40.0657-0.0113-0.0165-0.00390.00950.04010.44270.2579-0.47710.197-0.2219-0.1002-0.0799-0.8181-0.00120.68970.0912-0.00531.1605-0.22120.5814-3.735424.700446.2601
50.17470.1208-0.11270.27520.24390.5102-0.063-0.28620.17040.5528-0.2110.0727-0.5501-0.7134-0.0010.76890.07010.0870.8152-0.15390.66062.252229.609450.9738
60.370.2185-0.16650.2284-0.30680.46940.01730.09520.1274-0.0398-0.0813-0.08060.15150.069400.3262-0.0044-0.00740.3369-0.02360.40911.970313.018319.8757
70.04270.01550.0380.0597-0.01390.04590.19880.3072-0.1987-0.5053-0.146-0.0224-0.0663-0.4040.00050.57310.023-0.01280.5975-0.04420.43322.0038.8767-3.8744
80.10840.1487-0.08470.3257-0.00260.07290.09930.41520.1607-0.43370.0246-0.0733-0.398-0.412-0.00010.53770.00780.0840.42570.03440.41212.077214.557-1.9477
90.07660.02340.05840.02880.03260.04460.05170.7129-0.2413-0.4665-0.0054-0.19840.02220.3143-0.00020.4022-0.00250.01940.49930.05580.443916.768319.023212.7758
100.06990.043-0.01480.0197-0.04770.16510.09670.1275-0.2505-0.2825-0.2716-0.9289-0.10430.4663-0.00060.5902-0.01850.12180.59210.03090.682917.70066.86630.7495
110.1026-0.0996-0.05580.09760.09330.10360.38580.6995-0.63980.3852-0.0796-0.09231.06270.46070.00310.5260.00870.01420.4427-0.10120.54478.3345-1.937.2087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 99 )A31 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 246 )A100 - 246
3X-RAY DIFFRACTION3chain 'B' and (resid 31 through 45 )B31 - 45
4X-RAY DIFFRACTION4chain 'B' and (resid 46 through 58 )B46 - 58
5X-RAY DIFFRACTION5chain 'B' and (resid 59 through 99 )B59 - 99
6X-RAY DIFFRACTION6chain 'B' and (resid 100 through 142 )B100 - 142
7X-RAY DIFFRACTION7chain 'B' and (resid 143 through 155 )B143 - 155
8X-RAY DIFFRACTION8chain 'B' and (resid 156 through 187 )B156 - 187
9X-RAY DIFFRACTION9chain 'B' and (resid 188 through 207 )B188 - 207
10X-RAY DIFFRACTION10chain 'B' and (resid 208 through 230 )B208 - 230
11X-RAY DIFFRACTION11chain 'B' and (resid 231 through 244 )B231 - 244

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