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- PDB-9f14: The crystal structure of full length tetramer CysB from Klebsiell... -

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Basic information

Entry
Database: PDB / ID: 9f14
TitleThe crystal structure of full length tetramer CysB from Klebsiella aerogenes in complex with N-acetylserine
ComponentsHTH-type transcriptional regulator CysB
KeywordsTRANSCRIPTION / CysB / cysteine biosynthesis / LysR family / transcriptional regulator
Function / homology
Function and homology information


cysteine biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytoplasm
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
N-ACETYL-SERINE / HTH-type transcriptional regulator CysB
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVerschueren, K.H.G. / Dodson, E.J. / Wilkinson, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BO4808 United Kingdom
Citation
Journal: Eur.Biophys.J. / Year: 2024
Title: The Structure of the LysR-type Transcriptional Regulator, CysB, Bound to the Inducer, N-acetylserine.
Authors: Verschueren, K.H.G. / Dodson, E.J. / Wilkinson, A.J.
#1: Journal: Structure / Year: 1997
Title: The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement.
Authors: Tyrrell, R. / Verschueren, K.H. / Dodson, E.J. / Murshudov, G.N. / Addy, C. / Wilkinson, A.J.
History
DepositionApr 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator CysB
B: HTH-type transcriptional regulator CysB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3104
Polymers72,0162
Non-polymers2942
Water4,360242
1
A: HTH-type transcriptional regulator CysB
B: HTH-type transcriptional regulator CysB
hetero molecules

A: HTH-type transcriptional regulator CysB
B: HTH-type transcriptional regulator CysB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6218
Polymers144,0324
Non-polymers5894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area12460 Å2
ΔGint-60 kcal/mol
Surface area54750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.864, 185.864, 113.043
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

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Components

#1: Protein HTH-type transcriptional regulator CysB / Cys regulon transcriptional activator


Mass: 36008.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: cysB / Plasmid: pKKCysB / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P45600
#2: Chemical ChemComp-SAC / N-ACETYL-SERINE


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 53 % / Description: Chunky
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12 -17% PEG 8000, 0.2M sodium tartrate and 0.1M Tris-HCl pH 8.5, 0.2M KSCN, 10 mM N-acetylserine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.3→19.817 Å / Num. obs: 33205 / % possible obs: 99.8 % / Redundancy: 11.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.029 / Rrim(I) all: 0.072 / Net I/σ(I): 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.91-19.819.90.0315570.9990.0150.034
2.3-2.3811.60.52212510.960.2330.572

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
HKL-3000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.817 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.314 / WRfactor Rwork: 0.236 / Average fsc free: 0.935 / Average fsc work: 0.9665 / Cross valid method: FREE R-VALUE / ESU R: 0.357 / ESU R Free: 0.279
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2898 1681 5.062 %
Rwork0.2106 31524 -
all0.215 --
obs-33205 99.799 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.806 Å2
Baniso -1Baniso -2Baniso -3
1-1.333 Å20.666 Å2-0 Å2
2--1.333 Å20 Å2
3----4.324 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5062 0 20 242 5324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125198
X-RAY DIFFRACTIONr_bond_other_d00.0164968
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.8227062
X-RAY DIFFRACTIONr_angle_other_deg0.5281.75111419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.654540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14510872
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.79110225
X-RAY DIFFRACTIONr_chiral_restr0.0750.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026099
X-RAY DIFFRACTIONr_gen_planes_other0.010.021185
X-RAY DIFFRACTIONr_nbd_refined0.2270.21115
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2280.24747
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22553
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22683
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0520.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.231
X-RAY DIFFRACTIONr_nbd_other0.1710.2155
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.219
X-RAY DIFFRACTIONr_mcbond_it6.7126.2142597
X-RAY DIFFRACTIONr_mcbond_other6.7026.2152597
X-RAY DIFFRACTIONr_mcangle_it9.44811.1523241
X-RAY DIFFRACTIONr_mcangle_other9.44711.1523242
X-RAY DIFFRACTIONr_scbond_it6.4126.6762601
X-RAY DIFFRACTIONr_scbond_other6.4116.6762602
X-RAY DIFFRACTIONr_scangle_it9.46112.063821
X-RAY DIFFRACTIONr_scangle_other9.4612.063822
X-RAY DIFFRACTIONr_lrange_it12.59560.4135821
X-RAY DIFFRACTIONr_lrange_other12.60659.55784
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.3590.3421170.27422950.27724120.9150.951000.285
2.359-2.4230.3981010.25322570.25923580.9090.9591000.262
2.423-2.4920.3431080.23521610.2422690.9390.9641000.24
2.492-2.5670.335950.23721310.24122260.9280.9651000.24
2.567-2.650.3981100.26720460.27421560.9120.9551000.272
2.65-2.7410.3181190.23319660.23720850.9290.9651000.238
2.741-2.8430.3331090.24319230.24820320.9260.9611000.246
2.843-2.9560.3551110.24618120.25219230.9110.961000.249
2.956-3.0850.3451050.21917770.22518820.9280.971000.226
3.085-3.2310.285920.21616890.2217810.9440.9721000.224
3.231-3.4010.2561050.22416130.22617180.9520.9691000.235
3.401-3.6010.289790.21515250.21916040.9430.9721000.23
3.601-3.840.283850.20714490.21115340.9610.9751000.223
3.84-4.1350.282710.20113630.20514340.9490.9751000.231
4.135-4.510.225670.1812590.18313260.9670.9781000.216
4.51-5.010.248640.17411350.17812000.9670.98199.91670.214
5.01-5.7240.296550.18910290.19410840.9460.9791000.232
5.724-6.8690.329360.2368860.249220.9360.9691000.29
6.869-9.1790.234260.1717300.1737560.9650.9811000.223
9.179-19.8170.227260.1824780.1845060.9680.97499.60470.248

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