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- PDB-3lqk: Crystal structure of dipicolinate synthase subunit B from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 3lqk
TitleCrystal structure of dipicolinate synthase subunit B from Bacillus halodurans C
ComponentsDipicolinate synthase subunit B
KeywordsOXIDOREDUCTASE / dipicolinate synthase / Flavoprotein / PSI2 / MCSG / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / sporulation resulting in formation of a cellular spore / oxidoreductase activity
Similarity search - Function
Dipicolinic acid synthetase, subunit B / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Dipicolinate synthase subunit B
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsNocek, B. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of dipicolinate synthase subunit B from Bacillus halodurans C
Authors: Nocek, B. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionFeb 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipicolinate synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5863
Polymers22,3961
Non-polymers1902
Water1,51384
1
A: Dipicolinate synthase subunit B
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)135,51718
Polymers134,3776
Non-polymers1,14012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area16820 Å2
ΔGint-164 kcal/mol
Surface area42920 Å2
MethodPISA
2
A: Dipicolinate synthase subunit B
hetero molecules

A: Dipicolinate synthase subunit B
hetero molecules

A: Dipicolinate synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7589
Polymers67,1893
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5070 Å2
ΔGint-59 kcal/mol
Surface area24800 Å2
MethodPISA
3
A: Dipicolinate synthase subunit B
hetero molecules

A: Dipicolinate synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1726
Polymers44,7922
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Buried area2460 Å2
ΔGint-36 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.185, 110.185, 71.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-272-

HOH

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Components

#1: Protein Dipicolinate synthase subunit B


Mass: 22396.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: spoVFB, BH2402 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 / References: UniProt: Q9KA88
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.3 M 195NSBD, 2.0 M Ammonium dihydrogen phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 15060 / Num. obs: 14994 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.8 / Num. unique all: 742 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
DMmodel building
SHELXmodel building
MLPHAREphasing
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.987 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.16 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21296 749 5 %RANDOM
Rwork0.16658 ---
all0.17 14930 --
obs0.16882 14181 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.038 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 10 84 1554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221511
X-RAY DIFFRACTIONr_bond_other_d0.0020.02997
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9752058
X-RAY DIFFRACTIONr_angle_other_deg1.07732471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54925.27355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20215256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.912155
X-RAY DIFFRACTIONr_chiral_restr0.1230.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0941.5979
X-RAY DIFFRACTIONr_mcbond_other0.3011.5392
X-RAY DIFFRACTIONr_mcangle_it2.02121589
X-RAY DIFFRACTIONr_scbond_it3.2453532
X-RAY DIFFRACTIONr_scangle_it5.5414.5467
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 60 -
Rwork0.194 1029 -
obs--99 %
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)
11.2519-0.1598-0.54692.0684-0.05810.8456-0.03270.2485-0.1127-0.02750.0721-0.1268-0.011-0.0182-0.03940.15660.0038-0.00380.142-0.04160.13139.627841.8054-1.7784
23.8884-4.45110.60827.0889-1.96423.1194-0.01940.24820.1196-0.0497-0.0165-0.4956-0.09540.07730.03590.130.01390.03580.15490.00360.144617.488941.8877-2.9022
32.1807-1.11930.67464.4914-1.42860.53060.03830.2607-0.1278-0.0201-0.15090.05150.0142-0.00780.11260.14210.02470.00430.1821-0.0440.1117.416641.0005-5.2427
41.6418-5.44535.70212.4602-9.39218.7490.08910.1064-0.0068-0.4398-0.0151-0.00110.3940.0252-0.0740.4453-0.00890.01590.3230.01360.073610.050850.5485-19.4317
56.8588-3.42150.22574.2477-1.02460.6576-0.02330.4561-0.1093-0.2452-0.0280.05130.03480.0170.05130.14770.0137-0.00850.1951-0.04350.05364.960443.3046-11.0376
60.54360.445-0.181.33980.4620.35090.01250.0911-0.0279-0.0109-0.05860.0139-0.0135-0.07240.04610.14610.00830.01140.1668-0.00870.12911.243548.33111.5423
70.49240.20720.19510.26790.24960.31970.00350.02280.0516-0.0159-0.060.038-0.0245-0.03160.05650.15930.00890.00990.15120.00080.13054.038852.41175.9535
80.61650.7954-0.3863.02880.48791.4062-0.0564-0.0230.07790.05990.0765-0.08110.0786-0.0224-0.02010.14550.00520.01570.15080.00350.13223.220650.487114.7941
91.65221.06890.37361.83090.25580.16160.0233-0.0053-0.09930.0533-0.0532-0.09190.02470.09340.02990.14230.01010.01280.15580.00920.121816.316347.529810.0956
10-1.1217-0.32881.03692.4137-5.09979.37070.0282-0.0719-0.05390.0528-0.5352-0.3441-0.00580.76230.5070.13060.01190.0160.20520.0530.230818.695145.629614.9753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION2A20 - 28
3X-RAY DIFFRACTION3A29 - 43
4X-RAY DIFFRACTION4A44 - 59
5X-RAY DIFFRACTION5A60 - 75
6X-RAY DIFFRACTION6A76 - 104
7X-RAY DIFFRACTION7A105 - 141
8X-RAY DIFFRACTION8A142 - 150
9X-RAY DIFFRACTION9A151 - 185
10X-RAY DIFFRACTION10A186 - 195

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