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- PDB-1p92: Crystal Structure of (H79A)DtxR -

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Basic information

Entry
Database: PDB / ID: 1p92
TitleCrystal Structure of (H79A)DtxR
ComponentsDiphtheria toxin repressor
KeywordsDNA BINDING PROTEIN / Diphtheria toxin repressor / DtxR / DNA-binding protein / Helix-turn-helix / SH3-like / metal ion binding site
Function / homology
Function and homology information


transition metal ion binding / SH3 domain binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / Ferrous iron transport protein A (FeoA) / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / Diphtheria Toxin Repressor; domain 2 / DtxR-type HTH domain profile. ...Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / Ferrous iron transport protein A (FeoA) / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / Diphtheria Toxin Repressor; domain 2 / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Transcriptional repressor, C-terminal / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Diphtheria toxin repressor / Diphtheria toxin repressor
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsD'Aquino, J.A. / Ringe, D.
CitationJournal: J.Bacteriol. / Year: 2003
Title: Determinants of the SRC homology domain 3-like fold.
Authors: D'Aquino, J.A. / Ringe, D.
History
DepositionMay 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphtheria toxin repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3612
Polymers25,2831
Non-polymers781
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Diphtheria toxin repressor
hetero molecules

A: Diphtheria toxin repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7224
Polymers50,5652
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area2740 Å2
ΔGint-22 kcal/mol
Surface area22840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.390, 63.390, 109.872
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-618-

HOH

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Components

#1: Protein Diphtheria toxin repressor / Iron-dependent diphtheria tox regulatory element / Tox regulatory factor


Mass: 25282.727 Da / Num. of mol.: 1 / Mutation: H79A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DTXR / Production host: Escherichia coli (E. coli) / References: UniProt: P33120, UniProt: P0DJL7*PLUS
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.54 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 5, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 15278 / Num. obs: 15278 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.24 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1BYM, 2TDX

1bym

2tdx


Resolution: 2.1→27.45 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 272961.01 / Data cutoff high rms absF: 272961.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 716 4.9 %RANDOM
Rwork0.243 ---
all0.243 15278 --
obs0.243 14509 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.949 Å2 / ksol: 0.327259 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å21.16 Å20 Å2
2---1.3 Å20 Å2
3---2.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.1→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 4 99 1791
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.191.5
X-RAY DIFFRACTIONc_mcangle_it4.442
X-RAY DIFFRACTIONc_scbond_it5.092
X-RAY DIFFRACTIONc_scangle_it6.772.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 108 5 %
Rwork0.278 2066 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BME.PARAM
X-RAY DIFFRACTION3WATER.PARAM

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