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- PDB-4i4k: Streptomyces globisporus C-1027 9-membered enediyne conserved pro... -

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Basic information

Entry
Database: PDB / ID: 4i4k
TitleStreptomyces globisporus C-1027 9-membered enediyne conserved protein SgcE6
Componentsuncharacterized protein SgcJ
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / alpha-beta sandwich
Function / homology
Function and homology information


Domain of unknown function DUF4440 / Domain of unknown function (DUF4440) / Steroid delta5-4-isomerase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / SgcJ/EcaC family oxidoreductase
Similarity search - Component
Biological speciesStreptomyces globisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKim, Y. / Bigelow, L. / Clancy, S. / Babnigg, J. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...Kim, Y. / Bigelow, L. / Clancy, S. / Babnigg, J. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: J Antibiot (Tokyo) / Year: 2016
Title: Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027.
Authors: Huang, T. / Chang, C.Y. / Lohman, J.R. / Rudolf, J.D. / Kim, Y. / Chang, C. / Yang, D. / Ma, M. / Yan, X. / Crnovcic, I. / Bigelow, L. / Clancy, S. / Bingman, C.A. / Yennamalli, R.M. / ...Authors: Huang, T. / Chang, C.Y. / Lohman, J.R. / Rudolf, J.D. / Kim, Y. / Chang, C. / Yang, D. / Ma, M. / Yan, X. / Crnovcic, I. / Bigelow, L. / Clancy, S. / Bingman, C.A. / Yennamalli, R.M. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.
History
DepositionNov 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Other
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Dec 7, 2016Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein SgcJ
B: uncharacterized protein SgcJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0408
Polymers30,0362
Non-polymers1,0046
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-12 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.715, 86.901, 55.265
Angle α, β, γ (deg.)90.00, 121.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

CIT

21A-204-

PO4

31A-380-

HOH

41A-416-

HOH

51B-320-

HOH

61B-375-

HOH

Detailsdimer is in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein uncharacterized protein SgcJ


Mass: 15018.234 Da / Num. of mol.: 2 / Fragment: SgcJ
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces globisporus (bacteria) / Strain: C-1027 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold / References: UniProt: Q8GMG4

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Non-polymers , 6 types, 216 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M disodium hydrogen phosphate citric acid pH 4.2, 40 %(w/v) PEG300, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 31922 / Num. obs: 31922 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3 / Num. unique all: 1594 / Rsym value: 0.498 / % possible all: 98.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
ARP/wARPmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→27.683 Å / SU ML: 0.16 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 19.79 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1564 5.07 %random
Rwork0.168 ---
all0.169 30859 --
obs0.169 30859 95.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 66 210 2252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012194
X-RAY DIFFRACTIONf_angle_d1.3252986
X-RAY DIFFRACTIONf_dihedral_angle_d18.058801
X-RAY DIFFRACTIONf_chiral_restr0.1314
X-RAY DIFFRACTIONf_plane_restr0.006405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7001-1.7550.25891100.21131936204671
1.755-1.81770.26141150.1922523263891
1.8177-1.89050.19861410.18092742288398
1.8905-1.97650.1951610.16932692285399
1.9765-2.08070.18051390.16062760289999
2.0807-2.2110.18271510.15852744289599
2.211-2.38160.19141350.163227762911100
2.3816-2.62110.23341420.173427622904100
2.6211-30.21871600.180227742934100
3-3.77810.20041630.167627812944100
3.7781-27.68620.1561470.1542805295299
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)
14.5283-1.0954-0.00520.20160.11340.1056-0.2977-0.0574-0.5954-0.04370.34110.27320.0331-0.48410.02970.1460.0018-0.0380.39770.07940.21775.962472.67028.6683
21.6544-0.5394-0.00491.4201-0.24781.9469-0.05440.0465-0.2024-0.14450.0356-0.00960.1615-0.13690.01390.0962-0.01490.00210.0856-0.01530.113722.939872.285.4542
32.2932-0.63430.8242.5481-1.51213.41670.07120.2936-0.22730.0351-0.0558-0.03280.13830.1803-0.03350.06030.02560.02060.1277-0.02060.119621.440175.412812.8327
43.5717-0.2344-0.45472.8322-0.91872.76340.09050.0376-0.397-0.02540.05770.1312-0.0312-0.1363-0.12740.05240.02920.00820.10140.01250.09318.848677.96838.5877
57.05282.86243.75493.10632.88123.9210.00920.9632-0.2452-0.8840.14130.2704-0.38260.3865-0.16030.53560.1219-0.08920.2422-0.03680.228218.123698.4552-1.822
65.34931.98311.07578.1886-0.20173.8292-0.06950.1190.622-0.2775-0.28580.5824-0.8748-0.42710.18640.33340.1255-0.00360.2062-0.02210.169615.6992101.481310.0243
74.563-2.68420.20414.38420.65614.1917-0.1132-0.19070.21760.1259-0.04910.0701-0.1438-0.42250.15480.12090.0094-0.00260.1267-0.02660.090319.213390.115315.1317
86.53191.8986-1.4174.29030.88523.76750.1026-0.43660.25460.1276-0.12680.1183-0.4772-0.14980.0430.31920.06650.01940.1254-0.0110.115521.6572100.817216.2384
96.28184.13112.59596.29914.15185.57560.03740.39340.2028-0.08660.1976-0.0107-0.4110.0314-0.19150.18430.01340.03280.08420.03140.086226.155893.3348-1.6367
106.14972.42271.70673.55941.30463.60520.19970.0695-0.0749-0.02470.0645-0.0255-0.245-0.4012-0.14160.14910.01660.00910.1192-00.06620.566990.0943-0.6359
117.38340.25410.57611.8848-0.46030.17060.4078-1.07830.16560.6401-0.18670.0574-0.39930.3454-0.18350.3094-0.08590.06580.1961-0.05340.250939.177298.87836.2632
128.6503-0.54481.26924.0547-0.47822.8413-0.2219-0.451-0.0851-0.15810.10750.2562-0.3591-0.43190.10380.15440.0363-0.00810.1201-0.01580.042121.126390.72923.7611
131.73740.51270.63573.474-0.10693.9305-0.03110.29480.3948-0.356-0.10510.0992-0.8497-0.34720.0370.2240.1186-0.01590.1636-0.0040.12820.463491.134.3456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 140 )
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 45 )
7X-RAY DIFFRACTION7chain 'B' and (resid 46 through 56 )
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 75 )
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 86 )
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 101 )
11X-RAY DIFFRACTION11chain 'B' and (resid 102 through 109 )
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 123 )
13X-RAY DIFFRACTION13chain 'B' and (resid 124 through 140 )

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