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- PDB-5v7o: Crystal Structure of NosK from Streptomyces actuosus -

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Basic information

Entry
Database: PDB / ID: 5v7o
TitleCrystal Structure of NosK from Streptomyces actuosus
ComponentsNosK
KeywordsTRANSFERASE / alpha/beta hydrolase fold / nosiheptide / acyltransferase
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / NosK
Function and homology information
Biological speciesStreptomyces actuosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsBooker, S.J. / Boal, A.K. / Grove, T.L. / Badding, E.D.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Rerouting the Pathway for the Biosynthesis of the Side Ring System of Nosiheptide: The Roles of NosI, NosJ, and NosK.
Authors: Badding, E.D. / Grove, T.L. / Gadsby, L.K. / LaMattina, J.W. / Boal, A.K. / Booker, S.J.
History
DepositionMar 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Structure summary
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NosK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1262
Polymers34,0301
Non-polymers961
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-9 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.290, 75.290, 110.121
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein NosK


Mass: 34030.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces actuosus (bacteria) / Gene: nosK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6FX50
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.6 M (NH4)2SO4, 0.1 M NaCl, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→28.053 Å / Num. obs: 16566 / % possible obs: 99.9 % / Redundancy: 10.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.3-2.3811.11.1550.9211100
8.91-28.0590.0440.972197.1

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementResolution: 2.3→28.053 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.35
RfactorNum. reflection% reflection
Rfree0.2627 1649 10.02 %
Rwork0.2188 --
obs0.2232 16451 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.66 Å2 / Biso mean: 41.8926 Å2 / Biso min: 18.24 Å2
Refinement stepCycle: final / Resolution: 2.3→28.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 5 91 1858
Biso mean--35.19 43.34 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071810
X-RAY DIFFRACTIONf_angle_d0.8632464
X-RAY DIFFRACTIONf_chiral_restr0.049268
X-RAY DIFFRACTIONf_plane_restr0.006327
X-RAY DIFFRACTIONf_dihedral_angle_d14.0821051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3004-2.36810.32951600.25511801340100
2.3681-2.44450.32861290.259112131342100
2.4445-2.53180.35631220.260712261348100
2.5318-2.63310.28741280.254812211349100
2.6331-2.75290.38861240.34841199132397
2.7529-2.89790.2811380.229712331371100
2.8979-3.07920.25171400.228312141354100
3.0792-3.31660.29271380.231712251363100
3.3166-3.64970.29461340.24421238137299
3.6497-4.17640.26461470.218512561403100
4.1764-5.25610.1831430.153812531396100
5.2561-28.05490.19731460.169813441490100
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)
10.58610.5123-0.38140.32660.22132.7793-0.17720.19350.02980.04790.0651-0.0164-0.40930.64530.25690.28860.0172-0.03940.28660.00950.27259.94644.207935.1932
23.5789-0.8475-0.60712.5268-0.86826.04990.0966-0.13470.7061-0.5370.1784-0.2136-0.3110.2671-0.39990.3992-0.02560.03850.3329-0.00430.352213.90247.587928.8059
31.8992-0.23080.69270.83211.67453.7433-0.1055-0.09720.0695-0.0891-0.08970.1393-0.2983-0.76480.16720.2830.0631-0.00080.3452-0.02030.2201-0.839843.598340.9537
41.77020.5418-0.86161.22720.76281.2952-0.0520.0258-0.08130.218-0.01350.06740.093-0.28760.09110.21570.02360.01080.31020.00760.25545.134134.093234.0231
52.24520.8730.81914.32052.55831.9540.02820.42750.66460.80210.25340.3620.75090.1439-0.24030.4347-0.0059-0.00570.37960.01220.532511.263528.010750.525
61.32630.76860.35232.04370.75312.0219-0.2179-0.0916-0.1156-0.01950.2265-0.1912-0.2227-0.0317-0.02230.31470.07820.0330.33580.02950.25399.087544.281155.0283
70.315-0.04360.92280.73570.6993.50650.2719-0.0169-0.29440.2056-0.05440.23660.3875-1.0507-0.31040.44480.04680.00030.31930.03410.32553.298225.012939.9945
82.57550.00120.97781.8783-0.13053.1348-0.14190.1356-0.4-0.0340.1891-0.20470.00180.78890.02590.38970.0913-0.01980.4331-0.05850.34219.176328.652735.7697
93.50070.35341.71314.04050.65684.3332-0.06310.44960.2187-0.6746-0.1289-0.6044-0.36470.48410.13910.33150.0310.04480.5198-0.00290.335718.700536.515925.503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 46 )A28 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 62 )A47 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 95 )A63 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 126 )A96 - 126
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 144 )A127 - 144
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 179 )A145 - 179
7X-RAY DIFFRACTION7chain 'A' and (resid 180 through 197 )A180 - 197
8X-RAY DIFFRACTION8chain 'A' and (resid 198 through 240 )A198 - 240
9X-RAY DIFFRACTION9chain 'A' and (resid 241 through 257 )A241 - 257

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