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- PDB-3tr3: Structure of a bolA protein homologue from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3tr3
TitleStructure of a bolA protein homologue from Coxiella burnetii
ComponentsBolA
KeywordsUNKNOWN FUNCTION / Cellular processes / stress-induced
Function / homology
Function and homology information


DNA-templated transcription / cytosol
Similarity search - Function
: / BolA-like / BolA protein / BolA-like superfamily / BolA-like protein / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.456 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 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BolA
B: BolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6424
Polymers18,5242
Non-polymers1182
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BolA
hetero molecules

B: BolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6424
Polymers18,5242
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+y+1,-x,z-1/31
Buried area1430 Å2
ΔGint-22 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.245, 66.245, 118.009
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-104-

HOH

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Components

#1: Protein BolA


Mass: 9261.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: bolA, CBU_0582 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83DW0
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.04 Å3/Da / Density % sol: 69.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH 6.5 1.8M ammonium sulphate 0.010M cobalt chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X4C10.979
ROTATING ANODERIGAKU MICROMAX-007 HF21.5418
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJul 29, 2011
RIGAKU SATURN 9442CCDJul 14, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2VARIMAX HFSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.54181
ReflectionRedundancy: 4.3 % / Av σ(I) over netI: 19.03 / Number: 35908 / Rmerge(I) obs: 0.063 / Χ2: 1.27 / D res high: 2.7 Å / D res low: 30 Å / Num. obs: 8436 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.33099.810.0361.8384.2
5.87.399.810.0591.7644.5
5.075.899.810.0541.4364.7
4.615.0799.810.0461.4484.7
4.284.6110010.0461.6384.7
4.034.2810010.0471.3574.8
3.834.0310010.0521.2134.8
3.663.8310010.0541.1964.7
3.523.6610010.0571.1624.7
3.43.5210010.0711.1424.8
3.293.410010.0831.114.7
3.23.2910010.1151.2044.8
3.123.210010.1091.0474.8
3.043.1210010.1391.014.8
2.973.0410010.1541.0254.4
2.912.979910.1481.0793.6
2.852.919810.1730.9983
2.82.8595.510.1940.9962.7
2.752.888.710.2351.2042.6
2.72.7584.110.2560.9852.3
ReflectionResolution: 2.45→50 Å / Num. all: 11441 / Num. obs: 11190 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.088 / Χ2: 1.208 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.45-2.492.50.4024730.7811,288.2
2.49-2.5430.415330.8071,294.5
2.54-2.593.40.3435130.9711,295.5
2.59-2.643.90.3615720.8221,297.1
2.64-2.74.30.3645401.1481,299.1
2.7-2.7650.3255720.8151,299.5
2.76-2.835.50.2825380.8921,299.4
2.83-2.95.80.2675640.9081,299.5
2.9-2.9960.225780.8711,299.5
2.99-3.096.10.2085460.9231,299.5
3.09-3.260.1655640.9481,298.9
3.2-3.326.30.1385670.9621,299.5
3.32-3.486.10.15691.1111,299
3.48-3.666.10.0815761.1531,299.5
3.66-3.896.20.0665601.3271,298.6
3.89-4.1960.0595661.3851,298.6
4.19-4.616.10.0495681.5051,298.3
4.61-5.2860.055811.4271,298.5
5.28-6.6560.0585951.721,297.5
6.65-505.50.0466152.661,294.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.456→41.132 Å / Occupancy max: 1 / Occupancy min: 0.68 / FOM work R set: 0.8563 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 537 4.8 %RANDOM
Rwork0.1864 ---
all0.1881 11973 --
obs0.1881 11183 97.88 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.442 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 271.57 Å2 / Biso mean: 45.1491 Å2 / Biso min: 22.68 Å2
Baniso -1Baniso -2Baniso -3
1-7.8379 Å2-0 Å2-0 Å2
2--7.8379 Å2-0 Å2
3----15.6759 Å2
Refinement stepCycle: LAST / Resolution: 2.456→41.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 2 77 1337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141286
X-RAY DIFFRACTIONf_angle_d1.3641745
X-RAY DIFFRACTIONf_chiral_restr0.081196
X-RAY DIFFRACTIONf_plane_restr0.005225
X-RAY DIFFRACTIONf_dihedral_angle_d13.847458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4559-2.7030.31761150.26162508262395
2.703-3.0940.25331570.20032650280799
3.094-3.89760.21641310.17682697282899
3.8976-41.13810.18851340.17012791292598
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)
11.5121-0.87060.32940.7628-0.36011.0443-0.0933-0.13660.9775-0.2025-0.2664-0.0615-0.7934-0.08430.09670.53940.0329-0.04490.2895-0.06070.337337.8174-11.322-1.004
20.280.2274-0.09430.3122-0.2450.28310.0659-0.0240.08020.1409-0.14950.36150.0077-0.506-0.06570.35650.2413-0.11640.5776-0.09170.39329.4153-14.26152.5516
30.07880.25420.0450.75250.12630.6625-0.132-0.08030.07490.02580.0312-0.0588-0.1429-0.30290.03920.31340.0876-0.01090.499-0.03560.304528.4593-18.4447-5.2919
40.39860.0306-0.32610.1777-0.07080.3193-0.13890.1766-0.31670.0423-0.0311-0.186-0.16930.16120.0754-0.0202-0.06890.07470.6558-0.06020.235534.6114-19.9054-5.4097
50.0859-0.05340.04850.07860.04250.15680.0688-0.3740.13520.165-0.08110.07260.0127-0.2180.01970.5912-0.08470.20261.0709-0.2270.455119.3006-20.17948.22
60.16180.11270.16880.17120.13570.1822-0.1251-0.0703-0.0862-0.0347-0.16480.00110.0190.1530.10050.34640.17060.0010.47360.04940.19445.4944-33.95986.6137
70.749-0.0219-0.28430.38390.48660.7772-0.0646-0.0968-0.12990.02220.10450.12130.10330.0408-0.00620.35760.05760.00740.2693-0.00390.243140.922-20.638516.7283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:14)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 15:25)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 26:59)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 60:71)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 72:78)A0
6X-RAY DIFFRACTION6chain 'B' and (resseq -1:3)B0
7X-RAY DIFFRACTION7chain 'B' and (resseq 4:79)B0

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