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- PDB-3tyr: Crystal structure of transcriptional regulator VanUg, Form I -

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Basic information

Entry
Database: PDB / ID: 3tyr
TitleCrystal structure of transcriptional regulator VanUg, Form I
ComponentsTranscriptional 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 / SAD / Resolution: 1.699 Å
AuthorsStogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Dong, A. / Depardieu, F. / Courvalin, P. / Shabalin, I. / Chruszcz, M. / Minor, W. / Savchenko, A. ...Stogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Dong, A. / 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 I
Authors: Stogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Dong, A. / Depardieu, F. / Courvalin, P. / Shabalin, I. / Chruszcz, M. / Minor, W. / Savchenko, A. / Anderson, W.F. / Center for Structural ...Authors: Stogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Dong, A. / 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
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
SupersessionOct 19, 2011ID: 3T75
Revision 1.1Oct 19, 2011Group: Other / Structure summary
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Apr 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)20,3462
Polymers20,3462
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-23 kcal/mol
Surface area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.246, 53.022, 55.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulator / VanU


Mass: 10173.168 Da / Num. of mol.: 2 / Fragment: UNP residues 1-67
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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.025 M MGCL2, 0.1 M KCL, 50 MM NA CACODYLATE PH 6, 15% ISOPROPANOL, 1 MM RHAMNOSE, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT22.29
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 27, 2010
RIGAKU RAXIS IV2IMAGE PLATESep 21, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1C(111)SINGLE WAVELENGTHMx-ray1
2GraphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
22.291
ReflectionResolution: 1.699→50 Å / Num. all: 17618 / Num. obs: 17248 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rsym value: 0.053 / Net I/σ(I): 30.2
Reflection shellResolution: 1.699→1.73 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.334 / % possible all: 96.1

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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: SAD / Resolution: 1.699→38.365 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 1643 5.11 %random
Rwork0.1574 ---
obs0.1595 17221 97.89 %-
all-17618 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.476 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9506 Å20 Å20 Å2
2--5.9386 Å2-0 Å2
3---0.6233 Å2
Refinement stepCycle: LAST / Resolution: 1.699→38.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 0 221 1405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161250
X-RAY DIFFRACTIONf_angle_d1.471689
X-RAY DIFFRACTIONf_dihedral_angle_d11.183492
X-RAY DIFFRACTIONf_chiral_restr0.115192
X-RAY DIFFRACTIONf_plane_restr0.007213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.699-1.76020.27881520.23743003X-RAY DIFFRACTION95
1.7602-1.83060.24591690.21172983X-RAY DIFFRACTION97
1.8306-1.91390.22041620.17163022X-RAY DIFFRACTION97
1.9139-2.01480.22551680.15393022X-RAY DIFFRACTION97
2.0148-2.14110.22191630.14343059X-RAY DIFFRACTION99
2.1411-2.30640.22271530.15133103X-RAY DIFFRACTION99
2.3064-2.53840.21581580.14943089X-RAY DIFFRACTION99
2.5384-2.90560.21781710.16873086X-RAY DIFFRACTION99
2.9056-3.66030.18261660.14693096X-RAY DIFFRACTION99
3.6603-38.37440.15311810.14693059X-RAY DIFFRACTION98
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)
12.4454-0.308-0.01131.84180.35192.0139-0.0212-0.12390.12720.1646-0.06430.0434-0.05520.09120.0330.0298-0.001-0.00010.05930.00750.051818.690216.134936.2714
22.2089-0.24720.09621.88490.41642.30540.0152-0.01030.16490.0885-0.0498-0.1343-0.01990.06340.03640.0445-0.0086-0.00120.02830.00830.087515.710916.131437.4616
32.67430.0185-0.12042.1424-0.43451.44550.02720.0197-0.22220.0441-0.14090.15950.1699-0.1252-0.00330.011-0.00830.02950.00950.02460.05773.95114.724532.6578
41.8956-0.07620.25662.62590.20212.02560.03030.0182-0.1175-0.0923-0.0604-0.03870.0492-0.0510.0260.0429-0.0097-0.00230.03530.01080.075810.68246.524530.9428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 14:50
2X-RAY DIFFRACTION2chain A and resi 51:88
3X-RAY DIFFRACTION3chain B and resi 15:62
4X-RAY DIFFRACTION4chain B and resi 63:88

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