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- PDB-5d4z: Crystal structure of Repressor from Salmonella-temperate phage -

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Basic information

Entry
Database: PDB / ID: 5d4z
TitleCrystal structure of Repressor from Salmonella-temperate phage
ComponentsRepressor
KeywordsDNA BINDING PROTEIN / Repressor
Function / homologyHelix-turn-helix / lambda 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
Function and homology information
Biological speciesSalmonella phage SPC32H (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsKim, H.J. / 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 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_reflns_twin / 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_reflns_twin.operator / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Repressor
B: Repressor
C: Repressor
D: Repressor
E: Repressor
F: Repressor
G: Repressor
H: Repressor
I: Repressor
J: Repressor
K: Repressor
L: Repressor
M: Repressor
N: Repressor
O: Repressor
P: Repressor
Q: Repressor
R: Repressor
T: Repressor
U: Repressor
V: Repressor
W: Repressor
X: Repressor
Y: Repressor
Z: Repressor
1: Repressor
2: Repressor
3: Repressor
4: Repressor
5: Repressor
6: Repressor
7: Repressor


Theoretical massNumber of molelcules
Total (without water)376,30532
Polymers376,30532
Non-polymers00
Water9,494527
1
A: Repressor
B: Repressor
I: Repressor
J: Repressor


Theoretical massNumber of molelcules
Total (without water)47,0384
Polymers47,0384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Repressor
D: Repressor
K: Repressor
L: Repressor


Theoretical massNumber of molelcules
Total (without water)47,0384
Polymers47,0384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Repressor
F: Repressor
4: Repressor
5: Repressor


Theoretical massNumber of molelcules
Total (without water)47,0384
Polymers47,0384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Repressor
H: Repressor
6: Repressor
7: Repressor


Theoretical massNumber of molelcules
Total (without water)47,0384
Polymers47,0384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: Repressor
N: Repressor
V: Repressor
W: Repressor


Theoretical massNumber of molelcules
Total (without water)47,0384
Polymers47,0384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
O: Repressor
P: Repressor
X: Repressor
Y: Repressor


Theoretical massNumber of molelcules
Total (without water)47,0384
Polymers47,0384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
Q: Repressor
R: Repressor
Z: Repressor
1: Repressor


Theoretical massNumber of molelcules
Total (without water)47,0384
Polymers47,0384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
T: Repressor
U: Repressor
2: Repressor
3: Repressor


Theoretical massNumber of molelcules
Total (without water)47,0384
Polymers47,0384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.599, 62.497, 267.896
Angle α, β, γ (deg.)89.99, 89.97, 72.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
Repressor /


Mass: 11759.522 Da / Num. of mol.: 32 / Fragment: UNP residues 92-198
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 15%(w/v) PEG 4000, 0.1M magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.509
11-h,-k,l20.491
ReflectionResolution: 2.98→50 Å / Num. obs: 75973 / % possible obs: 98.6 % / Redundancy: 1.6 % / Net I/σ(I): 22.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D50

5d50


Resolution: 2.98→49.13 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.887 / SU B: 19.355 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27324 3813 5 %RANDOM
Rwork0.21564 ---
obs0.21855 72158 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.309 Å2
Baniso -1Baniso -2Baniso -3
1-7.69 Å235.58 Å20.29 Å2
2--20.99 Å216.14 Å2
3----28.68 Å2
Refinement stepCycle: LAST / Resolution: 2.98→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25435 0 0 527 25962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01925878
X-RAY DIFFRACTIONr_bond_other_d0.0020.0225423
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.94934960
X-RAY DIFFRACTIONr_angle_other_deg0.842358496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46553281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5824.5771053
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.795154603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1615128
X-RAY DIFFRACTIONr_chiral_restr0.0680.24017
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02128976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025580
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_it2.837.83713220
X-RAY DIFFRACTIONr_mcbond_other2.8297.83713219
X-RAY DIFFRACTIONr_mcangle_it4.78911.75116469
X-RAY DIFFRACTIONr_mcangle_other4.78911.75116470
X-RAY DIFFRACTIONr_scbond_it2.1427.84612658
X-RAY DIFFRACTIONr_scbond_other2.1427.84612659
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.74611.73518492
X-RAY DIFFRACTIONr_long_range_B_refined8.90762.7733426
X-RAY DIFFRACTIONr_long_range_B_other8.86662.88633283
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.979→3.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 241 -
Rwork0.256 4542 -
obs--83.68 %

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