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- PDB-4mo1: Crystal structure of antitermination protein Q from bacteriophage... -

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Basic information

Entry
Database: PDB / ID: 4mo1
TitleCrystal structure of antitermination protein Q from bacteriophage lambda. Northeast Structural Genomics Consortium target OR18A.
ComponentsAntitermination protein Q
KeywordsTranscription regulator / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Antitermination protein Q / DNA binding
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / DNA binding / zinc ion binding
Similarity search - Function
Enzyme I; Chain A, domain 2 - #110 / Antitermination protein Q / Antitermination protein Q superfamily / Antitermination protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / Enzyme I; Chain A, domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Antitermination protein Q
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.099 Å
AuthorsVorobiev, S. / Su, M. / Nickels, B. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Kogan, S. / Maglaqui, M. / Wang, D. / Everett, J.K. ...Vorobiev, S. / Su, M. / Nickels, B. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Kogan, S. / Maglaqui, M. / Wang, D. / Everett, J.K. / Acton, T.B. / Ebright, R.H. / Montelione, G.T. / Hunt, J. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of antitermination protein Q from bacteriophage lambda.
Authors: Vorobiev, S. / Su, M. / Nickels, B. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Kogan, S. / Maglaqui, M. / Wang, D. / Everett, J.K. / Acton, T.B. / Ebright, R.H. / Montelione, G.T. / Hunt, J. / Tong, L.
History
DepositionSep 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitermination protein Q
B: Antitermination protein Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,42510
Polymers39,9482
Non-polymers4778
Water2,918162
1
A: Antitermination protein Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1554
Polymers19,9741
Non-polymers1813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Antitermination protein Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2706
Polymers19,9741
Non-polymers2965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.474, 54.474, 109.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Detailsmonomer according to gel-filtration

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Components

#1: Protein Antitermination protein Q /


Mass: 19974.064 Da / Num. of mol.: 2 / Mutation: truncation: 1-37; C-terminus tag: LEHHHHHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: Q / Plasmid: pET21_NESG, OR18A-39-207-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P03047
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 10
Details: 12% PEG 20000, 0.1M ammonium bromide, 0.1M CAPS, pH 10.0, Microbatch crystallization under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. all: 42628 / Num. obs: 42458 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 32.06 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.3 / Num. unique all: 4027 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.099→43.348 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.05 / Phase error: 25.7 / Stereochemistry target values: ML
Details: CYS108 SIDE CHAIN IS COVALENTLY MODIFIED BASED ON THE ELECTRON DENSITY. HOWEVER, THE IDENTITY OF THE MODIFYING GROUP IS NOT KNOWN.THE EXTRA ELECTRON DENSITY IS CURRENTLY MODELED BY WATERS 605, 640, 668 AND 669.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2172 5.14 %RANDOM
Rwork0.214 ---
obs0.216 42280 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.938 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 113.7 Å2 / Biso mean: 39.773 Å2 / Biso min: 13.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.372 Å20 Å20 Å2
2---1.372 Å20 Å2
3---2.743 Å2
Refinement stepCycle: LAST / Resolution: 2.099→43.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 8 162 2372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062242
X-RAY DIFFRACTIONf_angle_d1.3083032
X-RAY DIFFRACTIONf_chiral_restr0.09341
X-RAY DIFFRACTIONf_plane_restr0.006387
X-RAY DIFFRACTIONf_dihedral_angle_d15.107824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.099-2.1450.3491240.3382363248795
2.145-2.1950.3361270.3092523265099
2.195-2.250.3261210.3582444256598
2.25-2.310.3751520.3342509266199
2.31-2.3780.2691540.24425362690100
2.378-2.4550.2921500.23425042654100
2.455-2.5430.2741240.2325062630100
2.543-2.6450.251280.21625002628100
2.645-2.7650.2381480.21425582706100
2.765-2.9110.3071140.21625302644100
2.911-3.0930.2881440.23825022646100
3.093-3.3320.3251320.22925642696100
3.332-3.6670.2661400.21124902630100
3.667-4.1970.1861300.18325682698100
4.197-5.2870.1671380.15125022640100
5.287-43.3570.1931460.1762509265599
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0335-0.04750.04390.0220.00740.02110.0812-0.00950.0135-0.0499-0.0503-0.10240.08430.0350.15340.03730.01950.12010.00520.152233.777631.444981.236
20.00880.02980.03460.05830.00840.0023-0.03830.05750.06630.03190.02830.08550.1049-0.05880.1512-0.01980.00580.1527-0.0210.134211.816847.889461.9525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA62 - 206
2X-RAY DIFFRACTION2chain BB62 - 204

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