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- PDB-4znm: Crystal structure of SgcC5 protein from Streptomyces globisporus ... -

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Basic information

Entry
Database: PDB / ID: 4znm
TitleCrystal structure of SgcC5 protein from Streptomyces globisporus (apo form)
ComponentsC-domain type II peptide synthetase
KeywordsLIGASE / C-1027 synthesis / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homologyCondensation domain / Condensation domain / lipid biosynthetic process / Chloramphenicol acetyltransferase-like domain superfamily / catalytic activity / C-domain type II peptide synthetase
Function and homology information
Biological speciesStreptomyces globisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.998 Å
AuthorsMichalska, K. / Bigelow, L. / Jedrzejczak, R. / Babnigg, G. / Lohman, J. / Ma, M. / Rudolf, J. / Chang, C.-Y. / Shen, B. / Joachimiak, A. ...Michalska, K. / Bigelow, L. / Jedrzejczak, R. / Babnigg, G. / Lohman, J. / Ma, M. / Rudolf, J. / Chang, C.-Y. / Shen, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098248 United States
CitationJournal: To Be Published
Title: Crystal structure of SgcC5 protein from Streptomyces globisporus (apo form)
Authors: Michalska, K. / Bigelow, L. / Jedrzejczak, R. / Babnigg, G. / Lohman, J. / Ma, M. / Rudolf, J. / Chang, C.-Y. / Shen, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / ...Authors: Michalska, K. / Bigelow, L. / Jedrzejczak, R. / Babnigg, G. / Lohman, J. / Ma, M. / Rudolf, J. / Chang, C.-Y. / Shen, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Source and taxonomy
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-domain type II peptide synthetase
B: C-domain type II peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,5867
Polymers102,4462
Non-polymers1405
Water8,071448
1
A: C-domain type II peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3044
Polymers51,2231
Non-polymers813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C-domain type II peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2813
Polymers51,2231
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.596, 104.542, 108.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein C-domain type II peptide synthetase


Mass: 51222.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces globisporus (bacteria) / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8GMG2
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M sodium citrate, 0.1 M Na cacodylate/HCl, pH 6.5, cryo 1.4 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2012 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.998→30 Å / Num. obs: 77045 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 15.84
Reflection shellResolution: 1.998→2.03 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.11 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
HKL-3000phasing
HKL-3000data scaling
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.998→29.74 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.42 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 1532 1.99 %random
Rwork0.1643 ---
obs0.1648 76966 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6887 0 5 448 7340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137151
X-RAY DIFFRACTIONf_angle_d1.2819714
X-RAY DIFFRACTIONf_dihedral_angle_d14.6852630
X-RAY DIFFRACTIONf_chiral_restr0.0571057
X-RAY DIFFRACTIONf_plane_restr0.0071305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.998-2.06250.29271170.23556545X-RAY DIFFRACTION96
2.0625-2.13620.26441360.21386787X-RAY DIFFRACTION100
2.1362-2.22170.22391460.18796822X-RAY DIFFRACTION100
2.2217-2.32280.23831500.17486791X-RAY DIFFRACTION100
2.3228-2.44520.17391490.1666808X-RAY DIFFRACTION100
2.4452-2.59830.20681310.17116861X-RAY DIFFRACTION100
2.5983-2.79880.23331340.18846838X-RAY DIFFRACTION100
2.7988-3.08010.21761240.18926919X-RAY DIFFRACTION100
3.0801-3.52520.20491380.16496918X-RAY DIFFRACTION100
3.5252-4.4390.16471360.13466962X-RAY DIFFRACTION100
4.439-29.73830.14911710.13797183X-RAY DIFFRACTION100
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)
10.62630.3573-0.00440.85920.23880.53460.01050.35070.0971-0.48230.0078-0.0168-0.29580.0815-0.01240.31170.00120.01040.3268-0.00950.280679.202440.1433-8.047
21.0687-0.1402-0.39280.79320.53952.755-0.05810.0589-0.05970.06610.05290.0401-0.04650.0749-00.1855-0.02150.00610.16040.00570.187182.718741.586712.0907
30.23320.08510.1440.3953-0.43750.7820.20940.1344-0.2295-0.36110.0908-0.37470.35030.2440.08240.36150.0633-0.00770.3535-0.13390.451183.145716.9987-15.0137
41.17-0.0033-0.23851.65950.76720.63080.0254-0.0552-0.22270.29710.03810.12920.1438-0.0788-0.00010.2527-0.0096-0.01920.25760.02910.29265.466321.58611.9652
50.4785-0.1263-0.67361.670.0220.9589-0.0761-0.1887-0.3915-0.14420.1209-0.15080.0699-0.05980.00020.26410.03420.01950.21530.02040.268979.110823.7385-2.0637
61.7213-0.0965-0.37641.75670.45381.27150.09780.0263-0.1175-0.14620.025-0.0818-0.03810.053700.31510.0043-0.02860.2367-0.01450.272574.487818.7541-6.8519
70.31090.0522-0.19350.23010.09180.33090.1017-0.1245-0.27330.0497-0.04670.14430.3483-0.29190.00050.3677-0.0160.03160.3261-0.01880.289373.562134.050818.0756
81.15380.4882-0.04851.63080.7250.84640.0565-0.0827-0.24810.19780.00360.1630.0647-0.1003-00.1912-0.00650.00690.27870.01790.306863.03324.19852.2558
90.6058-0.0435-0.14781.4495-0.14490.63940.0320.0753-0.1202-0.5877-0.01640.5601-0.0035-0.2338-0.00430.3039-0.0045-0.05880.29990.01830.327357.504567.721.8806
101.9647-0.69340.35150.8958-0.24181.44660.0079-0.049-0.02660.0510.05030.0254-0.0649-0.1438-00.2139-0.01750.01470.17450.01730.184269.66565.147517.8415
110.9682-0.9207-0.00872.1635-0.27421.37180.0053-0.00580.1578-0.04290.00710.0457-0.1233-0.1318-0.0030.2167-0.0168-0.01810.2189-0.00720.217360.512681.6764-4.1012
121.0747-0.15330.10612.5297-0.66261.3314-0.07880.00580.19970.19280.0548-0.1601-0.27710.0455-0.00020.27170.0123-0.03650.2145-0.01650.250866.3490.53192.6139
131.6239-0.0519-0.92711.6647-0.33930.7847-0.0224-0.22940.08720.28950.05890.10290.1654-0.4165-0.00950.32530.0499-0.04080.2912-0.00280.271760.305180.8134-1.9469
140.4492-0.1799-0.18030.4003-0.20840.3577-0.0944-0.05210.2008-0.1446-0.1818-0.0222-0.28080.28150.00030.37570.0020.02020.32160.03110.334180.027772.745714.913
151.2336-0.5158-0.11611.9001-1.06230.8878-0.0426-0.00980.10540.0292-0.0176-0.4718-0.00920.16230.00010.22110.0201-0.01520.24150.01130.280874.851578.6876-3.4636
162.118-0.9251-0.12221.06540.13940.31720.15890.84270.1599-0.62140.1108-0.3061-0.03740.203-0.00810.4865-0.1128-0.0160.37480.06220.673179.3146100.1556-6.3356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 15:44)
2X-RAY DIFFRACTION2(chain A and resid 45:201)
3X-RAY DIFFRACTION3(chain A and resid 202:224)
4X-RAY DIFFRACTION4(chain A and resid 225:278)
5X-RAY DIFFRACTION5(chain A and resid 279:311)
6X-RAY DIFFRACTION6(chain A and resid 312:377)
7X-RAY DIFFRACTION7(chain A and resid 378:399)
8X-RAY DIFFRACTION8(chain A and resid 400:457)
9X-RAY DIFFRACTION9(chain B and resid 15:46)
10X-RAY DIFFRACTION10(chain B and resid 47:201)
11X-RAY DIFFRACTION11(chain B and resid 202:247)
12X-RAY DIFFRACTION12(chain B and resid 248:345)
13X-RAY DIFFRACTION13(chain B and resid 346:377)
14X-RAY DIFFRACTION14(chain B and resid 378:399)
15X-RAY DIFFRACTION15(chain B and resid 400:447)
16X-RAY DIFFRACTION16(chain B and resid 448:458)

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