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- PDB-3fya: Crystal Structure of an R35A mutant of the Restriction-Modificati... -

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Basic information

Entry
Database: PDB / ID: 3fya
TitleCrystal Structure of an R35A mutant of the Restriction-Modification Controller Protein C.Esp1396I
ComponentsRegulatory protein
KeywordsTRANSCRIPTION REGULATOR / transcriptional regulator / helix-turn-helix / Restriction-modification
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsBall, N.J. / McGeehan, J.E. / Thresh, S.J. / Streeter, S.D. / Kneale, G.G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the restriction-modification controller protein C.Esp1396I.
Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E.
#1: Journal: Nucleic Acids Res. / Year: 2008
Title: Structural analysis of the genetic switch that regulates the expression of restriction-modification genes
Authors: McGeehan, J.E. / Streeter, S.D. / Thresh, S. / Ball, N. / Ravelli, R.B. / Kneale, G.G.
History
DepositionJan 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein
B: Regulatory protein


Theoretical massNumber of molelcules
Total (without water)22,6482
Polymers22,6482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-21 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.435, 48.435, 135.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHRAA3 - 3623 - 56
21SERSERTHRTHRBB3 - 3623 - 56
12ILEILEARGARGAA38 - 4358 - 63
22ILEILEARGARGBB38 - 4358 - 63
13ASNASNILEILEAA47 - 7567 - 95
23ASNASNILEILEBB47 - 7567 - 95

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Components

#1: Protein Regulatory protein


Mass: 11324.147 Da / Num. of mol.: 2 / Mutation: R35A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. (bacteria) / Strain: RFL1396 / Gene: esp1396IC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q8GGH0

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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: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 277 K / Method: precipitation / pH: 8
Details: 150 mM NaCl, 40 mM Tris-HCl, 5 % w/v glycerol, 2.5 mM CaCl2, pH 8.0, precipitation, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.952→41.959 Å / Num. all: 3840 / Num. obs: 3839 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 86 Å2 / Rmerge(I) obs: 0.263 / Rsym value: 0.263 / Net I/σ(I): 1.394
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.95-3.115.50.4121.930415530.412100
3.11-3.35.50.2293.229225280.229100
3.3-3.535.60.1475.127604960.147100
3.53-3.815.50.1056.825554660.105100
3.81-4.1780.31.533084140.3100
4.17-4.6610.90.3881.342443880.388100
4.66-5.39110.3881.438443480.388100
5.39-6.610.70.3391.531042890.339100
6.6-9.339.90.2431.722512270.243100
9.33-41.9280.1044.310401300.10498.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CLC

3clc


Resolution: 3→35.69 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.248 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.811 / SU B: 50.745 / SU ML: 0.406 / SU R Cruickshank DPI: 0.453 / SU Rfree: 0.486 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 164 4.5 %RANDOM
Rwork0.248 ---
obs0.249 3615 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.28 Å2 / Biso mean: 56.744 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 3→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 0 0 1208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221207
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9981614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.24924.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.61315256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.701156
X-RAY DIFFRACTIONr_chiral_restr0.1260.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02824
X-RAY DIFFRACTIONr_nbd_refined0.2610.2643
X-RAY DIFFRACTIONr_nbtor_refined0.3260.2840
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4090.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.25
X-RAY DIFFRACTIONr_mcbond_it0.4011.5781
X-RAY DIFFRACTIONr_mcangle_it0.62321213
X-RAY DIFFRACTIONr_scbond_it0.8033478
X-RAY DIFFRACTIONr_scangle_it1.2644.5401
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 524 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.080.05
TIGHT THERMAL0.090.5
LS refinement shellResolution: 3.001→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 17 -
Rwork0.305 239 -
all-256 -
obs--100 %
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)
112.33080.12785.936.6956-4.375315.8733-0.5287-0.3370.25070.680.04570.1607-1.08820.12070.483-0.32890.0324-0.01440.2140.0742-0.163711.81084.50726.9148
29.5146-3.06020.33862.0107-0.33084.5993-0.1236-0.0358-0.1526-0.5419-0.3265-0.2928-0.27440.19710.4502-0.0936-0.1471-0.0450.41620.15370.248729.90815.9774-2.2473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 75
2X-RAY DIFFRACTION2B3 - 79

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