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- PDB-3of5: Crystal Structure of a Dethiobiotin Synthetase from Francisella t... -

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Basic information

Entry
Database: PDB / ID: 3of5
TitleCrystal Structure of a Dethiobiotin Synthetase from Francisella tularensis subsp. tularensis SCHU S4
ComponentsDethiobiotin synthetase
KeywordsLIGASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Dethiobiotin synthetase
Function / homology
Function and homology information


dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Dethiobiotin synthase BioD / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ATP-dependent dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsBrunzelle, J.S. / Skarina, T. / Gordon, E. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of a Dethiobiotin Synthetase from Francisella tularensis subsp. tularensis SCHU S4
Authors: Brunzelle, J.S. / Skarina, T. / Gordon, E. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases
History
DepositionAug 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dethiobiotin synthetase
B: Dethiobiotin synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,36210
Polymers51,0702
Non-polymers2928
Water10,557586
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-138 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.278, 93.177, 62.732
Angle α, β, γ (deg.)90.00, 95.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dethiobiotin synthetase / Dethiobiotin synthase / DTB synthetase / DTBS


Mass: 25535.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: bioD, FTT_0934c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5NGB5, dethiobiotin synthase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8K 18%, CaAcetate 0.2M, NaCacod. 0.1M pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9755 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2009 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. all: 136170 / Num. obs: 136170 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 33.8
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.77 / % possible all: 100

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHENIX(phenix.autosol)model building
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→26.22 Å / Cor.coef. Fo:Fc: 0.9602 / Cor.coef. Fo:Fc free: 0.9475 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 3485 5.06 %RANDOM
Rwork0.1692 ---
obs0.1706 68887 --
all-68887 --
Displacement parametersBiso mean: 22.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.266 Å20 Å2-0.453 Å2
2--0.2562 Å20 Å2
3---1.0098 Å2
Refine analyzeLuzzati coordinate error obs: 0.171 Å
Refinement stepCycle: LAST / Resolution: 1.52→26.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 17 586 4030
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093946HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055400HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1443SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes576HARMONIC5
X-RAY DIFFRACTIONt_it3946HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion16.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5635
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact55094
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2077 236 4.67 %
Rwork0.1736 4822 -
all0.1753 5058 -
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)
1-0.0676-0.21840.31941.3530.27390.2832-0.0568-0.0046-0.0247-0.01190.00440.0249-0.02250.06670.0524-0.0435-0.01260.0023-0.0307-0.0326-0.019920.694354.631661.9824
21.4412-0.4624-0.51431.28460.53781.5772-0.02670.01440.0415-0.0582-0.0930.21580.0015-0.13420.1197-0.0392-0.0095-0.0026-0.0118-0.04770.024812.49548.747659.4816
30.3760.74330.07493.9964-0.33653.5354-0.11210.01390.0453-0.2356-0.0140.20570.1303-0.20880.1261-0.0483-0.02430.0052-0.0184-0.04260.032412.210343.424354.938
40.555-0.0292-0.53150.63820.5832.0285-0.04790.0151-0.12460.0799-0.05910.0660.2094-0.06990.107-0.0264-0.00680.0245-0.0265-0.0225-0.009619.315842.474769.2536
50.6056-0.17340.14790.59910.29850.9642-0.04480.0216-0.07050.02210.00920.00630.00650.05370.0356-0.0191-0.00140.0043-0.0004-0.00780.002125.675354.552172.5652
62.0432-0.88120.49462.28352.80153.9734-0.10730.1328-0.0080.11960.2745-0.1935-0.03180.3916-0.1672-0.0169-0.00860.00260.0476-0.02890.019233.960858.484872.9711
72.1319-0.4471.12152.84610.88532.597-0.24830.09510.1884-0.2024-0.01760.1412-0.34170.01690.26590.0186-0.0289-0.0468-0.04020.0234-0.012123.028671.539666.0134
81.88180.997-1.50872.33111.11755.1002-0.04710.3537-0.0006-0.4336-0.00860.002-0.2603-0.33210.0557-0.0017-0.0274-0.02150.01320.0064-0.0922.803165.000554.4202
90.4350.8973-0.53862.48770.42861.8814-0.00370.03720.04810.11560.03650.1237-0.1032-0.0431-0.0328-0.02540.0220.0025-0.0379-0.0113-0.025721.540371.352593.4429
104.66861.6498-1.73242.201-0.51694.6880.138-0.04110.24350.3522-0.03330.3157-0.1646-0.1118-0.1046-0.00260.02280.0471-0.0787-0.02650.000220.444178.132899.4493
116.4615-1.7971-0.3123.7034-0.47142.03660.14290.23770.6360.13130.04310.364-0.3981-0.2403-0.186-0.02610.06730.095-0.06430.03570.134714.898383.744695.7661
121.3099-0.0769-0.32422.0079-0.54842.334-0.04120.27560.4343-0.0322-0.03940.57810.0445-0.24620.0806-0.0726-0.0074-0.0101-0.07110.05320.082321.290184.751484.9626
130.6041-2.86724.20112.4058-3.96119.84940.2785-0.0982-0.0209-0.17390.03930.25770.1986-0.1047-0.3177-0.027-0.0409-0.035-0.01040.02340.002130.046284.259779.523
140.58850.65610.07760.98850.35550.7936-0.0228-0.0260.04990.01640.00940.0193-0.08440.02940.0133-0.04190.0169-0.021-0.0345-0.0112-0.030127.47969.335588.7598
151.4383-0.53830.45111.71771.08112.4427-0.0116-0.1577-0.12150.2176-0.08030.08790.1853-0.17420.0920.006-0.01040.0155-0.0003-0.0026-0.009617.247254.228591.5762
161.8544-1.414-1.83383.5778-3.84915.6861-0.0213-0.00840.10850.11130.04210.0298-0.1732-0.2911-0.02090.07070.03740.00580.0161-0.0126-0.103217.888263.2376104.4887

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