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- PDB-1utx: Regulation of Cytolysin Expression by Enterococcus faecalis: Role... -

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Basic information

Entry
Database: PDB / ID: 1utx
TitleRegulation of Cytolysin Expression by Enterococcus faecalis: Role of CylR2
ComponentsCYLR2
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / TRANSCRIPTIONAL REPRESSOR / REGULATION OF CYTOLYSIN OPERON / HELIX-TURN-HELIX
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / 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 speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.9 Å
AuthorsRazeto, A. / Rumpel, S. / Pillar, C.M. / Gilmore, M.S. / Becker, S. / Zweckstetter, M.
CitationJournal: Embo J. / Year: 2004
Title: Structure and DNA-Binding Properties of the Cytolysin Regulator CylR2 from Enterococcus Faecalis
Authors: Rumpel, S. / Razeto, A. / Pillar, C.M. / Vijayan, V. / Taylor, A. / Giller, K. / Gilmore, M.S. / Becker, S. / Zweckstetter, M.
History
DepositionDec 12, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYLR2
B: CYLR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,61512
Polymers15,4502
Non-polymers1,16510
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.679, 63.679, 41.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.721, -0.212, 0.659), (-0.213, -0.838, -0.502), (0.659, -0.502, 0.56)
Vector: 42.92585, 18.76443, -11.67423)

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Components

#1: Protein CYLR2


Mass: 7724.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: FA2-2(PAM714) / Description: DSM 20478, NCDO 581, NCIB 775, NCTC 775 / Plasmid: PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VL32
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.7 Å3/Da / Density % sol: 54.3 %
Crystal growpH: 7
Details: SALTING-IN BY DIALYSIS AGAINST 0.2 M NAI, 10 % GLYCEROL, 50 MM HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS M18X / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 15, 2003 / Details: COSMIC MIRRORS CMF12-38CU6
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 13086 / % possible obs: 99.2 % / Redundancy: 14.8 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 19
Reflection shellResolution: 1.9→2 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 5.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.9→19.76 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.982 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 651 5 %RANDOM
Rwork0.153 ---
obs0.155 13208 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 10 193 1274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221090
X-RAY DIFFRACTIONr_bond_other_d0.0020.021020
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9811475
X-RAY DIFFRACTIONr_angle_other_deg0.81232392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8575130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02184
X-RAY DIFFRACTIONr_nbd_refined0.2310.2328
X-RAY DIFFRACTIONr_nbd_other0.2460.21178
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1210.2739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3840.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3330.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7251.5664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32721078
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0283426
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2844.5397
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: 1.9→1.94 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 42
Rwork0.22 896

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