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- PDB-4q11: Crystal structure of Proteus mirabilis transcriptional regulator ... -

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Basic information

Entry
Database: PDB / ID: 4q11
TitleCrystal structure of Proteus mirabilis transcriptional regulator protein Crl at 1.95A resolution
ComponentsSigma factor-binding protein Crl
KeywordsTranscription regulator / sigma factor
Function / homology
Function and homology information


positive regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Sigma factor-binding protein Crl monomer / Sigma factor-binding transcriptional regulator Crl / Sigma factor-binding protein Crl superfamily / Sigma factor-binding transcriptional regulator Crl / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sigma factor-binding protein Crl
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNorel, F. / Mayer, C. / Saul, F.A. / Haouz, A.
CitationJournal: Biochem.J. / Year: 2014
Title: Structural and functional features of Crl proteins and identification of conserved surface residues required for interaction with the RpoS/ sigma S subunit of RNA polymerase.
Authors: Cavaliere, P. / Levi-Acobas, F. / Mayer, C. / Saul, F.A. / England, P. / Weber, P. / Raynal, B. / Monteil, V. / Bellalou, J. / Haouz, A. / Norel, F.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Sigma factor-binding protein Crl
B: Sigma factor-binding protein Crl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9434
Polymers31,5282
Non-polymers4152
Water2,072115
1
A: Sigma factor-binding protein Crl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9712
Polymers15,7641
Non-polymers2071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sigma factor-binding protein Crl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9712
Polymers15,7641
Non-polymers2071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-4 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.585, 36.195, 60.880
Angle α, β, γ (deg.)90.00, 115.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sigma factor-binding protein Crl


Mass: 15764.120 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: HI4320 / Gene: crl, PMI0368 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B4EUU9
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: 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: 1.82 Å3/Da / Density % sol: 32.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 100mM CHES-NaOH, PEG3000 30%(w/v), pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.95→30.25 Å / Num. all: 16783 / Num. obs: 16783 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1185 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RPJ

3rpj


Resolution: 1.95→30.25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.329 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23779 1309 7.8 %RANDOM
Rwork0.18549 ---
all0.18961 16778 --
obs0.18961 15469 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.639 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å2-6.34 Å2
2---13.77 Å2-0 Å2
3---11.03 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 26 115 2248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192190
X-RAY DIFFRACTIONr_bond_other_d0.0010.022074
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9522958
X-RAY DIFFRACTIONr_angle_other_deg0.76134778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6985250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70524.474114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40615387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7031512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212435
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.975 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.408 58 -
Rwork0.302 582 -
obs--99.22 %
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)
14.25380.19331.14241.65060.15221.2652-0.0832-0.11230.36340.19860.0383-0.08890.05150.13840.04490.13210.0049-0.04430.1929-0.00260.045910.47128.476-10.065
21.43460.03781.55012.45920.04824.47190.05650.0782-0.03790.05570.04110.31780.3873-0.0452-0.09760.15240.0154-0.01570.16040.00120.0455-4.563.937-25.797
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 132
2X-RAY DIFFRACTION2B5 - 130

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