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- PDB-3cu5: Crystal structure of a two component transcriptional regulator Ar... -

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Basic information

Entry
Database: PDB / ID: 3cu5
TitleCrystal structure of a two component transcriptional regulator AraC from Clostridium phytofermentans ISDg
ComponentsTwo component transcriptional regulator, AraC family
KeywordsTRANSCRIPTION REGULATOR / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / transcriptional regulator / AraC / PSI-2
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Homeobox-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Stage 0 sporulation protein A homolog
Similarity search - Component
Biological speciesClostridium phytofermentans ISDg (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMalashkevich, V.N. / Toro, R. / Wasserman, S.R. / Meyer, A. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a two component transcriptional regulator AraC from Clostridium phytofermentans ISDg.
Authors: Malashkevich, V.N. / Toro, R. / Wasserman, S.R. / Meyer, A. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Two component transcriptional regulator, AraC family
B: Two component transcriptional regulator, AraC family


Theoretical massNumber of molelcules
Total (without water)32,3212
Polymers32,3212
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Two component transcriptional regulator, AraC family


Theoretical massNumber of molelcules
Total (without water)16,1611
Polymers16,1611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Two component transcriptional regulator, AraC family


Theoretical massNumber of molelcules
Total (without water)16,1611
Polymers16,1611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.326, 87.038, 52.697
Angle α, β, γ (deg.)90.000, 106.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Two component transcriptional regulator, AraC family


Mass: 16160.503 Da / Num. of mol.: 2 / Fragment: Residues 2-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium phytofermentans ISDg (bacteria)
Species: Clostridium phytofermentans / Strain: ISDg / DSM 18823 / Gene: Cphy_0579 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A9KIW7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8 M Tri-ammonium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionRedundancy: 3.3 % / Av σ(I) over netI: 7.7 / Number: 55666 / Rmerge(I) obs: 0.101 / Χ2: 1.71 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 16975 / % possible obs: 85.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385099.310.0612.5123.8
4.275.3899.910.0782.683.9
3.734.2710010.1012.2023.9
3.393.7310010.1221.6143.9
3.153.3910010.1761.1323.7
2.963.1599.510.2180.9473.3
2.822.9692.810.2620.8012.7
2.692.8275.710.3220.8412.2
2.592.6955.310.3530.7471.7
2.52.5936.410.4070.8731.4
ReflectionResolution: 2.5→50 Å / Num. obs: 16975 / % possible obs: 85.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.101 / Χ2: 1.713 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.591.40.4077270.873136.4
2.59-2.691.70.35310880.747155.3
2.69-2.822.20.32215230.841175.7
2.82-2.962.70.26217830.801192.8
2.96-3.153.30.21819890.947199.5
3.15-3.393.70.17619811.1321100
3.39-3.733.90.12219831.6141100
3.73-4.273.90.10119662.2021100
4.27-5.383.90.07819642.68199.9
5.38-503.80.06119712.512199.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.873 / SU B: 29.312 / SU ML: 0.309 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.3 395 4.6 %RANDOM
Rwork0.183 ---
obs0.189 8565 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20.82 Å2
2--0.16 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 0 95 2115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222050
X-RAY DIFFRACTIONr_angle_refined_deg2.0981.9832774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.7495250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.3825.52196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.90615389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.9591512
X-RAY DIFFRACTIONr_chiral_restr0.1280.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211511
X-RAY DIFFRACTIONr_mcbond_it1.2273.51266
X-RAY DIFFRACTIONr_mcangle_it5.854502060
X-RAY DIFFRACTIONr_scbond_it14.25250784
X-RAY DIFFRACTIONr_scangle_it1.0614.5714
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 15 -
Rwork0.244 395 -
all-410 -
obs--100 %
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)
11.7511-0.0806-1.33925.8884-0.43264.56020.02890.24270.2684-0.13630.07040.0771-0.2744-0.2829-0.09930.1564-0.0104-0.03080.26830.04290.25119.915159.0816-8.68
23.15190.75560.09412.7321-0.16753.9482-0.01690.0113-0.0910.0884-0.00550.13880.1901-0.11490.02240.19280.0043-0.02080.1806-0.01260.1919-3.955446.770315.5149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1312 - 131
2X-RAY DIFFRACTION2BB2 - 1302 - 130

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