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

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Basic information

Entry
Database: PDB / ID: 9fdd
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionMay 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator CysB
B: HTH-type transcriptional regulator CysB
C: HTH-type transcriptional regulator CysB
D: HTH-type transcriptional regulator CysB
E: HTH-type transcriptional regulator CysB
F: HTH-type transcriptional regulator CysB
G: HTH-type transcriptional regulator CysB
H: HTH-type transcriptional regulator CysB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,24216
Polymers288,0658
Non-polymers1,1778
Water37821
1
A: HTH-type transcriptional regulator CysB
B: HTH-type transcriptional regulator CysB
C: HTH-type transcriptional regulator CysB
D: 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
Buried area12470 Å2
ΔGint-67 kcal/mol
Surface area54660 Å2
MethodPISA
2
E: HTH-type transcriptional regulator CysB
F: HTH-type transcriptional regulator CysB
G: HTH-type transcriptional regulator CysB
H: 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
Buried area12690 Å2
ΔGint-66 kcal/mol
Surface area54220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.436, 187.436, 224.662
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 36008.109 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella (bacteria) / Gene: cysB / Production host: Escherichia coli (E. coli) / References: UniProt: P45600
#2: Chemical
ChemComp-SAC / N-ACETYL-SERINE


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12-17% PEG 8000, 0.2 M sodium tartrate, 0.1 M Tris-HCl

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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: 2.8→41.462 Å / Num. obs: 72415 / % possible obs: 99.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.9

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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: 2.8→41.462 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.897 / SU B: 15.672 / SU ML: 0.302 / Cross valid method: FREE R-VALUE / ESU R Free: 0.382
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2456 3626 5.011 %
Rwork0.18 68742 -
all0.183 --
obs-72368 99.916 %
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: 45.469 Å2
Baniso -1Baniso -2Baniso -3
1-0.862 Å20.431 Å2-0 Å2
2--0.862 Å20 Å2
3----2.797 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20288 0 80 21 20389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01220832
X-RAY DIFFRACTIONr_bond_other_d0.0010.01619924
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.82228300
X-RAY DIFFRACTIONr_angle_other_deg0.5871.75245800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23452592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.415160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.357103504
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.24510900
X-RAY DIFFRACTIONr_chiral_restr0.0790.23276
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024744
X-RAY DIFFRACTIONr_nbd_refined0.2230.24399
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.218366
X-RAY DIFFRACTIONr_nbtor_refined0.1820.210137
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.210948
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2386
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.225
X-RAY DIFFRACTIONr_nbd_other0.1960.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.23
X-RAY DIFFRACTIONr_mcbond_it3.984.40610404
X-RAY DIFFRACTIONr_mcbond_other3.984.40610404
X-RAY DIFFRACTIONr_mcangle_it6.357.92312984
X-RAY DIFFRACTIONr_mcangle_other6.3497.92312985
X-RAY DIFFRACTIONr_scbond_it4.0464.75610428
X-RAY DIFFRACTIONr_scbond_other4.0464.75610429
X-RAY DIFFRACTIONr_scangle_it6.5638.57815316
X-RAY DIFFRACTIONr_scangle_other6.5638.57815317
X-RAY DIFFRACTIONr_lrange_it9.30942.09522573
X-RAY DIFFRACTIONr_lrange_other9.30842.09522574
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
2.8-2.8730.3642580.26850480.27353070.9160.96199.98120.238
2.873-2.9510.3111940.22650050.22951990.9410.9721000.193
2.951-3.0360.3281530.23148880.23450410.9340.9681000.2
3.036-3.1290.3212580.21546900.2249490.9340.97299.97980.186
3.129-3.2310.2792720.20844930.21247650.9470.9741000.182
3.231-3.3440.3232580.20343310.20945890.9320.9751000.176
3.344-3.4690.2762530.20942220.21244750.9450.9741000.187
3.469-3.610.2582350.18540300.18842650.9550.981000.165
3.61-3.7690.2861520.19839690.20141210.9450.9771000.179
3.769-3.9510.2612140.17237070.17739210.9590.9821000.155
3.951-4.1630.2212250.15935180.16237430.9680.9841000.141
4.163-4.4120.2082270.15532980.15935250.970.9861000.142
4.412-4.7130.2291730.1531470.15433200.9670.9871000.138
4.713-5.0850.1931830.14229200.14531030.9770.9891000.131
5.085-5.5620.181910.15927490.1628400.9780.9871000.145
5.562-6.2050.2381210.16924870.17326080.9680.9861000.153
6.205-7.1380.236970.14721770.1522740.9710.9891000.133
7.138-8.6790.158960.11918490.12119450.9850.9921000.113
8.679-12.0130.1641310.13113880.13415190.9860.9931000.132
12.013-41.4620.327350.2348260.2378970.9790.97595.98660.229

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