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- PDB-3trb: Structure of an addiction module antidote protein of a HigA (higA... -

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Basic information

Entry
Database: PDB / ID: 3trb
TitleStructure of an addiction module antidote protein of a HigA (higA) family from Coxiella burnetii
ComponentsVirulence-associated protein I
KeywordsDNA BINDING PROTEIN / Mobile and extrachromosomal element functions
Function / homology
Function and homology information


plasmid maintenance / toxic substance binding / response to toxic substance / DNA binding
Similarity search - Function
Toxin-antitoxin system, antidote protein, HigA / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Virulence-associated protein I
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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 / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
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
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virulence-associated protein I
B: Virulence-associated protein I


Theoretical massNumber of molelcules
Total (without water)23,3502
Polymers23,3502
Non-polymers00
Water2,486138
1
A: Virulence-associated protein I
B: Virulence-associated protein I

A: Virulence-associated protein I
B: Virulence-associated protein I


Theoretical massNumber of molelcules
Total (without water)46,6994
Polymers46,6994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7930 Å2
ΔGint-46 kcal/mol
Surface area18770 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-17 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.669, 44.669, 221.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

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Components

#1: Protein Virulence-associated protein I


Mass: 11674.853 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_1490, higA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83BL4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 7.5
Details: 0.2M calcium chloride 20% PEG 3350, pH 7.5, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 1, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 16259 / Num. obs: 15412 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.035 / Χ2: 1.022 / Net I/σ(I): 20.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.032.40.2097040.647188
2.03-2.073.10.1916920.678190.6
2.07-2.114.10.1667260.68190.3
2.11-2.154.10.1347080.698191.5
2.15-2.24.20.1297130.685192.8
2.2-2.254.10.1067470.708192.6
2.25-2.314.10.0977210.732192.1
2.31-2.374.10.0877530.732193.9
2.37-2.444.10.0747520.765194.5
2.44-2.524.10.0637540.789195
2.52-2.614.20.0597600.833195.5
2.61-2.714.10.0497590.818195.2
2.71-2.844.20.0427730.828195.8
2.84-2.994.20.0417950.93196.5
2.99-3.174.40.0388081.198199.8
3.17-3.424.70.0338151.254199.8
3.42-3.764.70.038201.311199.4
3.76-4.3150.0278301.353198.9
4.31-5.436.30.0278621.309198.6
5.43-508.40.0319201.535194.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CEC

3cec


Resolution: 2.001→34.777 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8664 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 778 5.06 %RANDOM
Rwork0.199 ---
all0.2011 16984 --
obs0.2011 15371 95.08 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.4 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 111.34 Å2 / Biso mean: 34.1258 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.6931 Å20 Å2-0 Å2
2--2.6931 Å2-0 Å2
3----5.3862 Å2
Refinement stepCycle: LAST / Resolution: 2.001→34.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 0 138 1582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021502
X-RAY DIFFRACTIONf_angle_d0.52032
X-RAY DIFFRACTIONf_chiral_restr0.032232
X-RAY DIFFRACTIONf_plane_restr0.002259
X-RAY DIFFRACTIONf_dihedral_angle_d10.797572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0009-2.12620.28231350.22032238237390
2.1262-2.29030.22681250.19392257238292
2.2903-2.52080.20761230.20282390251394
2.5208-2.88540.29111250.20092415254096
2.8854-3.63470.23341440.20832540268499
3.6347-34.78230.24011260.18952753287998
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)
11.60870.5742-0.86660.2834-0.27961.87390.5930.20090.9775-0.0403-0.50590.1015-0.70310.3615-0.05210.28360.00790.0420.21980.03650.460521.233729.162323.0414
21.0074-0.0581-0.20440.9220.19630.1280.0095-0.17420.05890.0920.07530.0473-0.9495-0.217-0.05990.41340.05470.03630.2747-0.01440.1859.288229.743528.2145
30.6892-0.01850.10150.42550.17950.33990.1258-0.33010.14430.7401-0.68581.11350.1064-0.85110.11510.39660.07390.12490.2993-0.11160.26031.309924.393334.1222
43.39750.1517-1.31921.5482-1.7173.0638-0.0936-0.4114-0.75890.5742-0.1351-0.1396-0.06480.36770.18640.36810.04510.07630.21920.01120.22918.638416.76132.6318
51.5524-0.0433-0.38460.2451-0.04760.1046-0.2623-0.0089-0.09950.16840.17710.1125-0.42390.7650.19680.33620.0111-0.04130.3477-0.00380.183714.946416.766527.8292
60.7858-0.2029-0.01241.1121-0.8091.0813-0.0042-0.0002-0.03190.1913-0.0232-0.1522-0.1362-0.154-0.00270.22770.02140.04620.2262-0.04950.22882.203120.132421.7177
71.26130.008-0.57640.47370.22230.6468-0.23660.3580.4845-0.11590.2513-0.1322-0.21280.2775-0.12750.2005-0.06830.06090.3291-0.06340.218324.358520.606714.3558
80.18150.27390.63672.2719-0.60493.5939-0.1175-0.0110.0583-0.015-0.05370.35310.2635-0.63760.19190.2147-0.0253-0.00150.2535-0.04010.292715.86578.76820.1256
91.6353-0.00681.81345.12940.11222.24420.31920.3495-0.4361-0.71140.32790.2960.90041.1226-0.6540.50130.0219-0.04880.487-0.01620.348728.29485.6951-6.1412
101.6174-0.2207-0.80110.52830.75351.12790.3397-0.2994-0.15090.1943-0.2079-0.07130.71110.4711-0.04590.29590.1120.01940.29140.01040.280428.6825.09296.3522
112.27720.0490.13153.32840.97441.54610.2239-0.21950.24080.1255-0.51340.4310.44530.00930.2850.2726-0.03410.02970.23820.01630.213919.12846.278811.5224
120.3556-0.0791-0.14910.13960.49091.49190.0387-0.03660.4482-0.0093-0.0849-0.41450.12340.0094-0.00420.15750.03730.01310.20660.04470.198326.255316.91546.1427
131.0078-0.5190.02640.5556-0.50040.6146-0.12490.2205-0.2055-0.167-0.11560.15720.2386-0.23330.19450.2199-0.03990.04780.1986-0.08330.23726.593112.799113.8833
140.8444-0.0937-0.78710.00660.0810.7156-0.4194-0.24560.50970.1238-0.43160.091-0.5292-0.3958-0.188-0.77550.99810.4798-0.2602-0.36390.5978-5.435524.426526.2719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:10)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 11:21)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 22:34)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 35:45)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 46:52)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 53:66)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 67:97)A0
8X-RAY DIFFRACTION8chain 'B' and (resseq 7:21)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 22:26)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 27:45)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 46:52)B0
12X-RAY DIFFRACTION12chain 'B' and (resseq 53:66)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 67:93)B0
14X-RAY DIFFRACTION14chain 'B' and (resseq 94:98)B0

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