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- PDB-5d50: Crystal structure of Rep-Ant complex from Salmonella-temperate phage -

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Basic information

Entry
Database: PDB / ID: 5d50
TitleCrystal structure of Rep-Ant complex from Salmonella-temperate phage
Components
  • Anti-repressor protein
  • Repressor
KeywordsDNA BINDING PROTEIN / Repressor / Anti-repressor / complex
Function / homologylambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Orthogonal Bundle / Mainly Alpha / Repressor / Anti-repressor protein
Function and homology information
Biological speciesSalmonella phage SPC32H (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.49 Å
AuthorsSon, S.H. / Yoon, H.J. / Ryu, S. / Lee, H.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Noncanonical DNA-binding mode of repressor and its disassembly by antirepressor
Authors: Kim, M. / Kim, H.J. / Son, S.H. / Yoon, H.J. / Lim, Y. / Lee, J.W. / Seok, Y.-J. / Jin, K.S. / Yu, Y.G. / Kim, S.K. / Ryu, S. / Lee, H.H.
History
DepositionAug 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Repressor
B: Repressor
C: Repressor
D: Repressor
E: Anti-repressor protein
G: Anti-repressor protein
I: Repressor
J: Repressor
K: Repressor
L: Repressor
M: Anti-repressor protein
O: Anti-repressor protein
F: Anti-repressor protein
H: Anti-repressor protein
N: Anti-repressor protein
P: Anti-repressor protein


Theoretical massNumber of molelcules
Total (without water)260,44816
Polymers260,44816
Non-polymers00
Water1,15364
1
A: Repressor
B: Repressor
C: Repressor
D: Repressor
E: Anti-repressor protein
G: Anti-repressor protein
F: Anti-repressor protein
H: Anti-repressor protein


Theoretical massNumber of molelcules
Total (without water)130,2248
Polymers130,2248
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24240 Å2
ΔGint-211 kcal/mol
Surface area43710 Å2
MethodPISA
2
I: Repressor
J: Repressor
K: Repressor
L: Repressor
M: Anti-repressor protein
O: Anti-repressor protein
N: Anti-repressor protein
P: Anti-repressor protein


Theoretical massNumber of molelcules
Total (without water)130,2248
Polymers130,2248
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25520 Å2
ΔGint-216 kcal/mol
Surface area44110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.612, 86.612, 337.031
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Repressor


Mass: 22560.760 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage SPC32H (virus) / Gene: rep, SPC32H_041 / Production host: Escherichia coli (E. coli) / References: UniProt: T1S9Z0
#2: Protein
Anti-repressor protein


Mass: 9995.278 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage SPC32H (virus) / Gene: ant, SPC32H_020 / Production host: Escherichia coli (E. coli) / References: UniProt: T1SA45
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: Sodium citrate, Sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 96551 / % possible obs: 99.3 % / Redundancy: 3.8 % / Net I/σ(I): 27.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
DENZOdata reduction
RefinementResolution: 2.49→36.61 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.376 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21006 4743 4.9 %RANDOM
Rwork0.20087 ---
obs0.20131 92085 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.732 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.49→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13261 0 0 64 13325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01913476
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213091
X-RAY DIFFRACTIONr_angle_refined_deg0.981.95118195
X-RAY DIFFRACTIONr_angle_other_deg0.769330020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16651638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76324.492650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.332152432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1381595
X-RAY DIFFRACTIONr_chiral_restr0.0580.22077
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023048
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3856.4186648
X-RAY DIFFRACTIONr_mcbond_other2.3856.4186647
X-RAY DIFFRACTIONr_mcangle_it3.8519.6118254
X-RAY DIFFRACTIONr_mcangle_other3.8519.6118255
X-RAY DIFFRACTIONr_scbond_it2.2276.5576828
X-RAY DIFFRACTIONr_scbond_other2.2276.5576829
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6429.7629942
X-RAY DIFFRACTIONr_long_range_B_refined6.34150.53715979
X-RAY DIFFRACTIONr_long_range_B_other6.3450.52915972
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.493→2.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 293 -
Rwork0.132 5559 -
obs--80.34 %

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