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- PDB-3tys: Crystal structure of transcriptional regulator VanUg, Form II -

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Basic information

Entry
Database: PDB / ID: 3tys
TitleCrystal structure of transcriptional regulator VanUg, Form II
ComponentsPredicted transcriptional regulator
KeywordsTRANSCRIPTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / HELIX-TURN-HELIX / TRANSCRIPTION REGULATOR / VANCOMYCIN RESISTANCE / VANG PHENOTYPE / DNA / cytoplasmic
Function / homologyCro/C1-type HTH DNA-binding domain / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Predicted transcriptional regulator
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.121 Å
AuthorsStogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Depardieu, F. / Courvalin, P. / Shabalin, I. / Chruszcz, M. / Minor, W. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of transcriptional regulator VanUg, Form II
Authors: Stogios, P.J. / Evdokimova, E. / WAWRZAK, Z. / Depardieu, F. / Courvalin, P. / Shabalin, I. / Chruszcz, M. / Minor, W. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of ...Authors: Stogios, P.J. / Evdokimova, E. / WAWRZAK, Z. / Depardieu, F. / Courvalin, P. / Shabalin, I. / Chruszcz, M. / Minor, W. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 26, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionOct 12, 2011ID: 3T76
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)10,1731
Polymers10,1731
Non-polymers00
Water2,360131
1
A: Predicted transcriptional regulator

A: Predicted transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)20,3462
Polymers20,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area2900 Å2
ΔGint-22 kcal/mol
Surface area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.499, 39.307, 61.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-151-

HOH

21A-162-

HOH

31A-170-

HOH

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Components

#1: Protein Predicted transcriptional regulator / VanU


Mass: 10173.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: BM4518 / Gene: vanU, vanUG / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WRY9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.7 Å3/Da / Density % sol: 27.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M CA NITRATE, 20% PEG3350, PH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.121→50 Å / Num. all: 27492 / Num. obs: 27437 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rsym value: 0.049 / Net I/σ(I): 32.33
Reflection shellResolution: 1.121→1.14 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.49 / Rsym value: 0.324 / % possible all: 97.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_842)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TYR

3tyr


Resolution: 1.121→33.188 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1628 1338 4.99 %random
Rwork0.1404 ---
obs0.1415 26804 97.69 %-
all-27438 --
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.109 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.8727 Å2-0 Å2
3---1.1127 Å2
Refinement stepCycle: LAST / Resolution: 1.121→33.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms603 0 0 131 734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025659
X-RAY DIFFRACTIONf_angle_d1.967894
X-RAY DIFFRACTIONf_dihedral_angle_d12.055269
X-RAY DIFFRACTIONf_chiral_restr0.116100
X-RAY DIFFRACTIONf_plane_restr0.01115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.121-1.16120.19931190.18852400X-RAY DIFFRACTION93
1.1612-1.20760.19071300.16562421X-RAY DIFFRACTION95
1.2076-1.26260.1951330.15142484X-RAY DIFFRACTION97
1.2626-1.32920.15631340.13742489X-RAY DIFFRACTION97
1.3292-1.41250.1681310.1362532X-RAY DIFFRACTION98
1.4125-1.52150.1731320.12932557X-RAY DIFFRACTION99
1.5215-1.67460.14661370.11842589X-RAY DIFFRACTION99
1.6746-1.91690.13351370.12282598X-RAY DIFFRACTION100
1.9169-2.4150.15261400.12032647X-RAY DIFFRACTION100
2.415-33.20210.16981450.15732749X-RAY DIFFRACTION99
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)
12.55460.5399-0.23641.1197-0.6151.93130.00680.11650.0504-0.08040.00690.04360.01660.0545-0.01160.09020.00240.00630.0320.00190.0148-12.23121.0203-16.9283
20.64310.1742-0.05620.5712-0.60261.5629-0.00430.0089-0.0191-0.03380.01350.00040.0644-0.0714-0.00520.0975-0.0024-0.00150.04330.00270.0022-13.570619.7006-5.6093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 11:37
2X-RAY DIFFRACTION2chain A and resi 38:88

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