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- PDB-4g9y: Crystal Structure of the PcaV transcriptional regulator from Stre... -

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Basic information

Entry
Database: PDB / ID: 4g9y
TitleCrystal Structure of the PcaV transcriptional regulator from Streptomyces coelicolor
ComponentsPcaV transcriptional regulator
KeywordsTRANSCRIPTION / MarR family / winged helix-turn-helix / transcription factor
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
MarR family / : / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
AuthorsBrown, B.L. / Davis, J.R. / Sello, J.K. / Page, R.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Study of PcaV from Streptomyces coelicolor yields new insights into ligand-responsive MarR family transcription factors.
Authors: Davis, J.R. / Brown, B.L. / Page, R. / Sello, J.K.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PcaV transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4042
Polymers17,3121
Non-polymers921
Water2,378132
1
A: PcaV transcriptional regulator
hetero molecules

A: PcaV transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8084
Polymers34,6232
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x,-y-1/2,-z-3/41
Buried area3740 Å2
ΔGint-31 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.771, 102.771, 100.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-201-

GOL

21A-325-

HOH

31A-388-

HOH

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Components

#1: Protein PcaV transcriptional regulator


Mass: 17311.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO6704 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Gold / References: UniProt: Q9XAM6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.82 Å3/Da / Density % sol: 67.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.2 M ammonium chloride, 20% w/v PEG 3350 , pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2012
RadiationMonochromator: Double silicon(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 17151 / Num. obs: 17150 / % possible obs: 99.99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 24.7 % / Biso Wilson estimate: 32.5 Å2 / Net I/σ(I): 52.7
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 23.3 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 819 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4FHT

4fht


Resolution: 2.051→41.277 Å / SU ML: 0.16 / σ(F): 1.38 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1724 10.06 %random
Rwork0.1751 ---
all0.1773 17134 --
obs0.1773 17131 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.051→41.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 6 132 1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081101
X-RAY DIFFRACTIONf_angle_d1.1151489
X-RAY DIFFRACTIONf_dihedral_angle_d11.852423
X-RAY DIFFRACTIONf_chiral_restr0.07170
X-RAY DIFFRACTIONf_plane_restr0.005198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0511-2.11140.28071460.27331241X-RAY DIFFRACTION100
2.1114-2.17950.26781480.23521255X-RAY DIFFRACTION100
2.1795-2.25740.24331380.2171260X-RAY DIFFRACTION100
2.2574-2.34780.22231460.19541253X-RAY DIFFRACTION100
2.3478-2.45470.2431430.19431276X-RAY DIFFRACTION100
2.4547-2.58410.2471420.18231269X-RAY DIFFRACTION100
2.5841-2.74590.20951410.17491277X-RAY DIFFRACTION100
2.7459-2.95790.19831370.181289X-RAY DIFFRACTION100
2.9579-3.25540.19891460.17251282X-RAY DIFFRACTION100
3.2554-3.72620.20671380.16161291X-RAY DIFFRACTION100
3.7262-4.69360.15721510.14311319X-RAY DIFFRACTION100
4.6936-41.28540.15741480.17421395X-RAY DIFFRACTION100
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)
10.22320.02110.00360.2012-0.00810.1353-0.10580.3485-0.0452-0.40740.2675-0.19940.03660.36510.01210.1975-0.0557-0.02640.2272-0.01780.1676-16.0012-18.8193-41.0216
20.39580.1821-0.33980.6429-0.09350.6249-0.1178-0.3053-0.43280.2066-0.198-0.3750.04140.2919-0.3440.1785-0.12390.01980.25580.09270.3003-2.7256-12.3401-20.3855
30.77630.5415-0.02810.41910.21690.5499-0.1482-0.06840.4333-0.09870.02140.1574-0.21030.0004-0.03130.12760.0116-0.00750.15210.00830.122-23.7944-15.5954-32.571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:34)
2X-RAY DIFFRACTION2(chain A and resid 35:97)
3X-RAY DIFFRACTION3(chain A and resid 98:143)

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