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- PDB-1al3: COFACTOR BINDING FRAGMENT OF CYSB FROM KLEBSIELLA AEROGENES -

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Basic information

Entry
Database: PDB / ID: 1al3
TitleCOFACTOR BINDING FRAGMENT OF CYSB FROM KLEBSIELLA AEROGENES
ComponentsCYS REGULON TRANSCRIPTIONAL ACTIVATOR CYSB
KeywordsTRANSCRIPTION REGULATION / LYSR FAMILY / CYSTEINE BIOSYNTHESIS
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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator CysB
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsVerschueren, K.H.G. / Tyrrell, R. / Wilkinson, A.J.
CitationJournal: 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
DepositionJun 10, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: CYS REGULON TRANSCRIPTIONAL ACTIVATOR CYSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1042
Polymers36,0081
Non-polymers961
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.380, 107.530, 32.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

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Components

#1: Protein CYS REGULON TRANSCRIPTIONAL ACTIVATOR CYSB


Mass: 36008.109 Da / Num. of mol.: 1 / Fragment: COFACTOR BINDING FRAGMENT, RESIDUES 88 - 324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria)
Description: KLEBSIELLA AEROGENES NCTC 418. CHYMOTRYPTIC C-TERMINAL COFACTOR BINDING FRAGMENT OF CYSB
Gene: CYSB / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P45600
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: COFACTOR BINDING DOMAIN WAS CRYSTALLISED IN HANGING DROPS AT 18 DEGREES CELSIUS FROM 14% MONO-METHYLETHER PEG750, 100MM MES PH 6.5, vapor diffusion - hanging drop, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %mono-methylether PEG7501reservoir
20.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 22479 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 1.6 / % possible all: 84.9
Reflection
*PLUS
Num. obs: 20911 / % possible obs: 93 %
Reflection shell
*PLUS
% possible obs: 84.9 %

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Processing

Software
NameClassification
DENZOdata reduction
CCP4data reduction
MLPHAREphasing
REFMACrefinement
CCP4data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1054 5 %RANDOM
Rwork0.179 ---
obs-22479 94.1 %-
Displacement parametersBiso mean: 29.8 Å2
Refine analyzeLuzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 5 253 2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.382
X-RAY DIFFRACTIONp_mcangle_it4.453
X-RAY DIFFRACTIONp_scbond_it4.172
X-RAY DIFFRACTIONp_scangle_it5.883
X-RAY DIFFRACTIONp_plane_restr0.030.04
X-RAY DIFFRACTIONp_chiral_restr0.130.15
X-RAY DIFFRACTIONp_singtor_nbd0.210.3
X-RAY DIFFRACTIONp_multtor_nbd0.320.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.270.3
X-RAY DIFFRACTIONp_planar_tor57
X-RAY DIFFRACTIONp_staggered_tor21.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 20911 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.014

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