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- PDB-7jvt: Crystal structure of a lambda-186 hybrid repressor -

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Basic information

Entry
Database: PDB / ID: 7jvt
TitleCrystal structure of a lambda-186 hybrid repressor
Components
  • OL1 bottom
  • OL1 top
  • Repressor protein CI
KeywordsGENE REGULATION/DNA / DNA binding transcriptional regulator / GENE REGULATION / GENE REGULATION-DNA complex
Function / homology
Function and homology information


maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / core promoter sequence-specific DNA binding / protein complex oligomerization / negative regulation of DNA-templated transcription / DNA binding / identical protein binding
Similarity search - Function
Bacteriophage CI repressor, N-terminal / Bacteriophage CI repressor, C-terminal / Bacteriophage CI repressor helix-turn-helix domain / Bacteriophage CI repressor C-terminal domain / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins ...Bacteriophage CI repressor, N-terminal / Bacteriophage CI repressor, C-terminal / Bacteriophage CI repressor helix-turn-helix domain / Bacteriophage CI repressor C-terminal domain / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Repressor protein cI / Repressor protein CI
Similarity search - Component
Biological speciesEscherichia phage lambda (virus)
Escherichia phage 186 (virus)
Escherichia virus Lambda
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsTruong, J.Q. / Bruning, J.B. / Shearwin, K.E.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150103009 Australia
Australian Research Council (ARC)DP160101450 Australia
CitationJournal: To Be Published
Title: Crystal structure of a hybrid lambda-186 repressor
Authors: Truong, J.Q. / Pukala, T. / Bruning, J.B. / Shearwin, K.S.
History
DepositionAug 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
C: Repressor protein CI
D: Repressor protein CI
E: OL1 bottom
F: OL1 top


Theoretical massNumber of molelcules
Total (without water)59,6194
Polymers59,6194
Non-polymers00
Water91951
1
C: Repressor protein CI
D: Repressor protein CI
E: OL1 bottom
F: OL1 top

C: Repressor protein CI
D: Repressor protein CI
E: OL1 bottom
F: OL1 top


Theoretical massNumber of molelcules
Total (without water)119,2398
Polymers119,2398
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area19300 Å2
ΔGint-119 kcal/mol
Surface area47710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.338, 177.338, 108.607
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Repressor protein CI


Mass: 23676.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus), (gene. exp.) Escherichia phage 186 (virus)
Gene: cI, lambdap88, CI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03034, UniProt: P08707
#2: DNA chain OL1 bottom


Mass: 6158.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus Lambda
#3: DNA chain OL1 top


Mass: 6108.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus Lambda
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.08 M sodium chloride, 0.012 M potassium chloride, 0.04 sodium cacodylate trihydrate pH 8.0, 30% w/v (+/-)-2-methyl-2,4-pentadiol, 0.012 M spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.16→44.34 Å / Num. obs: 11372 / % possible obs: 99.8 % / Redundancy: 14.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.037 / Rrim(I) all: 0.14 / Net I/σ(I): 14.6 / Num. measured all: 165170
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.16-3.3814.30.7382929920450.910.20.7653.199.4
8.93-44.3413.20.03370505330.9990.0090.03450.899.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSMarch2015data reduction
Aimless0.3.11data scaling
PHASER2.7.17phasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FJR,3BDN

2fjr

3bdn


Resolution: 3.16→36.2 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2814 1142 10.06 %
Rwork0.2282 10211 -
obs0.2336 11353 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 229.8 Å2 / Biso mean: 84.9896 Å2 / Biso min: 29.47 Å2
Refinement stepCycle: final / Resolution: 3.16→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 779 0 51 3882
Biso mean---56.47 -
Num. residues----435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.16-3.30.3481450.28821293143899
3.3-3.480.35211420.296812441386100
3.48-3.690.38841420.286912741416100
3.7-3.980.35241370.27611230136799
3.98-4.380.24251400.205412791419100
4.38-5.010.25661490.194512911440100
5.03-6.30.28871480.222312661414100
6.32-36.20.2131390.190713341473100
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)
13.23971.236-1.69366.82782.252.65520.3281-0.4079-0.69661.9653-0.0544-1.2560.88231.6767-0.04651.370.2083-0.36091.66070.35970.884914.685863.155711.1407
23.6012-0.4434-2.11367.6686-0.10497.71260.4835-1.1281-0.51650.6521-0.1309-0.72170.3091.0977-0.35620.8835-0.2139-0.32870.8370.16410.95239.018863.18063.8504
33.016-1.32461.19024.4241-3.80134.9338-0.40210.07650.74110.74730.1772-0.4519-0.9920.510.07470.7307-0.1342-0.05090.6963-0.10710.72581.203339.60747.642
42.52240.2579-0.28014.6595-3.29045.1726-0.0515-0.42170.18440.25720.0737-0.2005-0.39450.342-0.06920.48690.0164-0.10730.3867-0.06790.45720.521425.194315.8014
55.17170.1107-0.42954.8391-1.83891.64580.0991-0.0087-0.18390.564-0.29550.11010.8277-0.71270.14091.0403-0.42620.03690.6568-0.01780.5445-15.668163.19160.1047
61.7999-0.9807-0.05886.19262.5174.08020.08430.08480.4002-0.2592-0.064-0.4406-0.46460.404-0.00220.60390.08840.00820.45070.03640.4008-1.877930.0035-13.8722
75.4727-2.9223-0.63712.02361.36139.04490.13-0.6981-0.77920.7036-0.3582-2.0063-0.38441.97350.51440.8522-0.1784-0.35861.15630.39731.637220.342876.95428.088
82.23412.3941-4.22813.6311-5.81619.5509-1.05240.3732-0.24310.54220.3466-0.67170.0936-0.29790.73151.0169-0.06250.07630.8246-0.03631.0813-5.32179.87628.4264
99.23090.8736-1.9744.53126.27589.8116-1.92860.3884-2.0929-0.96541.68960.1991-0.4745-0.402-0.04631.523-0.25850.38681.3353-0.2081.8018-30.677979.475310.492
104.98860.0712-1.34983.26440.26715.1345-0.1108-0.39761.10230.2586-0.00241.12320.0265-0.7035-0.15411.1272-0.32740.24861.3545-0.09141.095-19.581478.10098.005
114.9788-0.0337-5.07742.43791.27115.8098-1.291-0.9945-0.03330.4187-0.2396-2.2617-0.09281.41941.06371.2157-0.3866-0.35341.28540.42941.584512.983381.08956.1198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 4 through 29 )C4 - 29
2X-RAY DIFFRACTION2chain 'C' and (resid 30 through 88 )C30 - 88
3X-RAY DIFFRACTION3chain 'C' and (resid 89 through 132 )C89 - 132
4X-RAY DIFFRACTION4chain 'C' and (resid 133 through 201 )C133 - 201
5X-RAY DIFFRACTION5chain 'D' and (resid 3 through 88 )D3 - 88
6X-RAY DIFFRACTION6chain 'D' and (resid 89 through 201 )D89 - 201
7X-RAY DIFFRACTION7chain 'E' and (resid 2 through 6 )E2 - 6
8X-RAY DIFFRACTION8chain 'E' and (resid 7 through 16 )E7 - 16
9X-RAY DIFFRACTION9chain 'E' and (resid 17 through 20 )E17 - 20
10X-RAY DIFFRACTION10chain 'F' and (resid 22 through 31 )F22 - 31
11X-RAY DIFFRACTION11chain 'F' and (resid 32 through 40 )F32 - 40

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