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- PDB-5v30: Crystal structure of the sensor domain of the transcriptional reg... -

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Basic information

Entry
Database: PDB / ID: 5v30
TitleCrystal structure of the sensor domain of the transcriptional regulator HcpR from Porphyromonas Gingivalis
ComponentsTranscriptional regulatorTranscriptional regulation
KeywordsTRANSCRIPTION / Beta barrel / Dimerization helix / Transcriptional regulator / Heme binding protein
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
: / Transcriptional regulator, putative
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3.15 Å
AuthorsMusayev, F.N. / Belvin, B.R. / Escalante, C.R. / Turner, J. / Lewis, J.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)1R01DE023304 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)1F31DE025158 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.
Authors: Belvin, B.R. / Musayev, F.N. / Burgner, J. / Scarsdale, J.N. / Escalante, C.R. / Lewis, J.P.
History
DepositionMar 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 2.0Apr 24, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.auth_seq_id / _citation.journal_abbrev ..._atom_site.auth_seq_id / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9599
Polymers34,3022
Non-polymers6577
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-73 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.970, 144.970, 77.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsDimer as determined by native gel electrophoresis

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Components

#1: Protein Transcriptional regulator / Transcriptional regulation


Mass: 17151.102 Da / Num. of mol.: 2 / Fragment: residues 2-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: AT291_03060 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A134DM59, UniProt: Q7MVK4*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 5.97 Å3/Da / Density % sol: 79.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Na Acetate (pH 4.5), 1-2-1.4M Ammonium sulfate, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 24, 2016 / Details: Rigaku varimax confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.15→29.93 Å / Num. obs: 14801 / % possible obs: 99.5 % / Redundancy: 6.22 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.9
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.367 / Num. unique obs: 1429 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.15→28.994 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.33
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 756 5.11 %RANDOM
Rwork0.1948 ---
obs0.1971 14781 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→28.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 39 22 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012399
X-RAY DIFFRACTIONf_angle_d1.2923229
X-RAY DIFFRACTIONf_dihedral_angle_d15.911891
X-RAY DIFFRACTIONf_chiral_restr0.046374
X-RAY DIFFRACTIONf_plane_restr0.005405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
3.15-3.39290.35841404.860.279274099
3.3929-3.73370.28751505.140.24142769100
3.7337-4.27250.24391414.830.17882781100
4.2725-5.37730.18771755.880.16992805100

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