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- PDB-1ui6: Crystal structure of gamma-butyrolactone receptor (ArpA-like protein) -

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Basic information

Entry
Database: PDB / ID: 1ui6
TitleCrystal structure of gamma-butyrolactone receptor (ArpA-like protein)
ComponentsA-factor receptor homolog
KeywordsANTIBIOTIC / helix-turn-helix / alpha-helix bundle
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
: / : / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family ...: / : / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNatsume, R. / Senda, T. / Horinouchi, S.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of a gamma-butyrolactone autoregulator receptor protein in Streptomyces coelicolor A3(2)
Authors: Natsume, R. / Ohnishi, Y. / Senda, T. / Horinouchi, S.
History
DepositionJul 15, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / 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

Downloads & links

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Assembly

Deposited unit
A: A-factor receptor homolog
B: A-factor receptor homolog


Theoretical massNumber of molelcules
Total (without water)47,4392
Polymers47,4392
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-11 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.792, 69.562, 148.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is a dimer that is contained in the asymmetric unit.

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Components

#1: Protein A-factor receptor homolog / CprB / bacterial autoregulator receptor protein / gamma-butyrolactone receptor


Mass: 23719.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Production host: Escherichia coli (E. coli) / References: UniProt: O66122
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.27 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 6000, lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 18, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 31849 / Num. obs: 31849 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3591 / Rsym value: 0.205 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UI5

1ui5


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.869 / SU B: 13.834 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.782 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28401 751 5.1 %RANDOM
Rwork0.22493 ---
all0.22787 15231 --
obs0.22787 13950 91.59 %-
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: 21.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2---0.68 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 0 57 3082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213079
X-RAY DIFFRACTIONr_bond_other_d0.0010.022970
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9564171
X-RAY DIFFRACTIONr_angle_other_deg0.81836795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2643382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.0915551
X-RAY DIFFRACTIONr_chiral_restr0.0850.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023413
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02685
X-RAY DIFFRACTIONr_nbd_refined0.260.3794
X-RAY DIFFRACTIONr_nbd_other0.2190.32848
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5106
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0020.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.358
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2970.512
X-RAY DIFFRACTIONr_mcbond_it0.8741.51921
X-RAY DIFFRACTIONr_mcangle_it1.66823085
X-RAY DIFFRACTIONr_scbond_it2.69431158
X-RAY DIFFRACTIONr_scangle_it4.7054.51086
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 63
Rwork0.214 993
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)
11.4497-1.19952.10363.02711.52063.92950.156-0.0224-0.274-0.1825-0.0612-0.03270.3488-0.2806-0.09480.1078-0.02410.04740.06720.00010.12356.21766.806-8.409
20.4153-0.2445-0.49441.4544-0.2392.63110.0080.01-0.01230.14480.00040.0825-0.0186-0.0149-0.00850.05860.0205-0.00860.1156-0.01790.095260.34387.47215.191
34.53610.64481.33933.13040.98223.02980.0121-0.15680.0807-0.3695-0.04660.17930.00790.01980.03460.17-0.0178-0.0390.1047-0.04070.072350.96749.62922.398
41.28920.28790.39392.38661.00172.0333-0.12960.01620.02-0.18080.10650.096-0.07960.01920.02310.1193-0.0023-0.05810.08340.05840.067648.04679.25731.019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 534 - 53
2X-RAY DIFFRACTION2AA75 - 21275 - 212
3X-RAY DIFFRACTION3BB6 - 536 - 53
4X-RAY DIFFRACTION4BB75 - 21275 - 212

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