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

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Basic information

Entry
Database: PDB / ID: 4fht
TitleCrystal Structure of the PcaV transcriptional regulator from Streptomyces coelicolor in complex with its natural ligand
ComponentsPcaV transcriptional regulator
KeywordsTRANSCRIPTION / MarR family / winged helix-turn-helix / transcription factor / protocatechuate binding
Function / homology
Function and homology information


response to stress / 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
ACETATE ION / 3,4-DIHYDROXYBENZOIC ACID / Transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionJun 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 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 / struct_ref_seq_dif / struct_sheet / 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_sheet.number_strands / _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
B: PcaV transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9915
Polymers34,6232
Non-polymers3673
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-40 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.357, 63.965, 73.009
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 PcaV transcriptional regulator


Mass: 17311.734 Da / Num. of mol.: 2
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-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.2 M lithium acetate, 20% w/v PEG 3350, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2010
RadiationMonochromator: Double silicon(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 16473 / Num. obs: 16472 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Biso Wilson estimate: 30.26 Å2 / Net I/σ(I): 49.7
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 795 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NNN

2nnn


Resolution: 2.15→44.651 Å / SU ML: 0.63 / σ(F): 0 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 1621 10.03 %random
Rwork0.1971 ---
all0.2018 16435 --
obs0.2018 16161 98.33 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.588 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3197 Å20 Å2-0 Å2
2--2.2978 Å20 Å2
3----0.9781 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 26 168 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032284
X-RAY DIFFRACTIONf_angle_d0.6923090
X-RAY DIFFRACTIONf_dihedral_angle_d12.454867
X-RAY DIFFRACTIONf_chiral_restr0.045353
X-RAY DIFFRACTIONf_plane_restr0.004411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1502-2.21350.26971270.1961138X-RAY DIFFRACTION94
2.2135-2.28490.29941260.191166X-RAY DIFFRACTION96
2.2849-2.36660.28371280.20281172X-RAY DIFFRACTION97
2.3666-2.46130.27911280.20891197X-RAY DIFFRACTION98
2.4613-2.57330.30391390.21431177X-RAY DIFFRACTION98
2.5733-2.7090.28311330.2181219X-RAY DIFFRACTION99
2.709-2.87870.25691310.21541197X-RAY DIFFRACTION99
2.8787-3.10090.27791400.22321217X-RAY DIFFRACTION99
3.1009-3.41290.25671380.20021225X-RAY DIFFRACTION100
3.4129-3.90650.21661380.19161251X-RAY DIFFRACTION100
3.9065-4.92070.20791440.16961254X-RAY DIFFRACTION100
4.9207-44.66030.21551490.19411327X-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)
10.44380.0413-0.3650.41090.47430.73520.09140.0770.0019-0.1673-0.0396-0.0342-0.18680.03740.00020.230.02-0.01310.15460.02910.174228.61637.618322.4237
20.6926-0.1530.36480.1224-0.17080.3349-0.0779-0.0312-0.3956-0.3971-0.04440.09350.1956-0.0643-0.01790.22390.0180.00750.1537-0.0520.192740.242129.019620.6742
30.0316-0.0084-0.00630.0097-0.00930.01390.0347-0.2695-0.40490.03110.07780.00580.2733-0.0399-0.00010.25120.0287-0.04550.350.0650.394752.217422.674927.7504
40.6152-0.1245-0.32840.37190.76721.6340.15860.41640.4052-0.3623-0.0094-0.2098-0.68770.1564-0.0320.2917-0.09480.1560.18650.00110.307442.976143.83616.5289
50.1748-0.1117-0.15630.08920.11820.16360.2063-0.173-0.106-0.0341-0.0625-0.23910.06820.37460.04070.31390.0288-0.0370.22340.01580.271925.693446.79532.1206
60.1168-0.09820.1720.1096-0.22330.5988-0.17120.0416-0.2431-0.06310.208-0.1344-0.1015-0.1410.0970.1249-0.00690.02290.1171-0.0580.196232.350339.520727.0291
70.82770.00470.19160.5312-0.24790.54660.04060.471-0.1879-0.0096-0.22750.1391-0.2294-0.5392-0.61670.17640.1465-0.02710.4052-0.0390.16688.924231.916619.4468
81.07890.876-0.02911.0026-0.0310.2219-0.08210.59080.1228-0.41720.16550.21940.196-0.04840.42810.31080.1067-0.18130.9172-0.32350.3036-0.922529.54779.8659
90.32640.21780.23540.43470.08910.17450.04440.0683-0.38440.0114-0.25520.36570.1823-0.4531-0.10440.17130.0034-0.01410.3947-0.1180.35134.289225.53929.2898
100.16470.16510.04470.230.00910.0470.0394-0.11310.08260.25720.04650.343-0.2134-0.2723-0.01010.21650.03490.00280.17280.0390.192517.290844.366432.9521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:55)
2X-RAY DIFFRACTION2(chain A and resid 56:80)
3X-RAY DIFFRACTION3(chain A and resid 81:93)
4X-RAY DIFFRACTION4(chain A and resid 94:114)
5X-RAY DIFFRACTION5(chain A and resid 115:141)
6X-RAY DIFFRACTION6(chain B and resid 0:22)
7X-RAY DIFFRACTION7(chain B and resid 23:70)
8X-RAY DIFFRACTION8(chain B and resid 71:94)
9X-RAY DIFFRACTION9(chain B and resid 95:114)
10X-RAY DIFFRACTION10(chain B and resid 115:141)

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