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- PDB-1iz1: CRYSTAL STRUCTURE OF CBNR, A LYSR FAMILY TRANSCRIPTIONAL REGULATOR -

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Basic information

Entry
Database: PDB / ID: 1iz1
TitleCRYSTAL STRUCTURE OF CBNR, A LYSR FAMILY TRANSCRIPTIONAL REGULATOR
ComponentsLysR-type regulatory protein
KeywordsDNA BINDING PROTEIN / LONG ALPHA HELIX CONNECTING DNA BINDING AND REGULATORY DOMAINS
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity
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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LysR-type regulatory protein
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMuraoka, S. / Okumura, R. / Ogawa, N. / Miyashita, K. / Senda, T.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of a Full-length LysR-type Transcriptional Regulator, CbnR: Unusual Combination of Two Subunit Forms and Molecular Bases for Causing and Changing DNA Bend
Authors: Muraoka, S. / Okumura, R. / Ogawa, N. / Nonaka, T. / Miyashita, K. / Senda, T.
History
DepositionSep 18, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LysR-type regulatory protein
B: LysR-type regulatory protein
P: LysR-type regulatory protein
Q: LysR-type regulatory protein


Theoretical massNumber of molelcules
Total (without water)128,3414
Polymers128,3414
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-70 kcal/mol
Surface area50020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.271, 124.477, 166.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
LysR-type regulatory protein / CbnR


Mass: 32085.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9WXC7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.66 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Magnesium sulfate, Sodium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Muraoka, S., (2003) Protein Pept. Lett., 10, 325.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2001
RadiationMonochromator: FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR SI(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.5→43.5 Å / Num. all: 46950 / Num. obs: 46835 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 1.8 / Num. unique all: 284 / Rsym value: 0.389 / % possible all: 73.9
Reflection
*PLUS
Num. obs: 44422 / % possible obs: 97.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.19refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IXC

1ixc


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.857 / SU B: 12.429 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.607 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28616 2374 5.1 %RANDOM
Rwork0.22218 ---
all0.22545 47875 --
obs0.22545 44422 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.719 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.05 Å2
Refine analyzeLuzzati coordinate error free: 0.332 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8982 0 0 115 9097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0219161
X-RAY DIFFRACTIONr_bond_other_d0.0020.028866
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.95912394
X-RAY DIFFRACTIONr_angle_other_deg0.819320379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78751166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.21426
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210214
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022010
X-RAY DIFFRACTIONr_nbd_refined0.1980.21837
X-RAY DIFFRACTIONr_nbd_other0.2210.29877
X-RAY DIFFRACTIONr_nbtor_other0.0860.26037
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6241.55826
X-RAY DIFFRACTIONr_mcangle_it1.17729336
X-RAY DIFFRACTIONr_scbond_it1.56833335
X-RAY DIFFRACTIONr_scangle_it2.824.53058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.409 138
Rwork0.328 2848
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.441

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