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

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Basic information

Entry
Database: PDB / ID: 4zxw
TitleCrystal structure of SgcC5 protein from Streptomyces globisporus (complex with (R)-(-)-1-(2-naphthyl)-1,2-ethanediol and sucrose)
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 / sucrose / (1R)-1-(naphthalen-2-yl)ethane-1,2-diol / C-domain type II peptide synthetase
Function and homology information
Biological speciesStreptomyces globisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.187 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
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 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 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 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: C-domain type II peptide synthetase
B: C-domain type II peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,33212
Polymers101,5702
Non-polymers1,76310
Water4,738263
1
A: C-domain type II peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6046
Polymers50,7851
Non-polymers8195
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)51,7296
Polymers50,7851
Non-polymers9445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.397, 105.304, 108.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein C-domain type II peptide synthetase


Mass: 50784.863 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: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 271 molecules

#3: Chemical ChemComp-4T7 / (1R)-1-(naphthalen-2-yl)ethane-1,2-diol


Mass: 188.222 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C12H12O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 55.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2 M lithium sulfate, 0.1 M CAPS:NaOH, pH 10.5, 2 M ammonium sulfate, 4.06 mM (S)-beta-tyrosine-N-acetylethylenediamine, 4.06 mM (R)-(-)-1-(2-naphthyl)-1,2-ethanediol, cryo 28% sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 58829 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 2.36 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZNM

4znm


Resolution: 2.187→34.278 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.96 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 1204 2.05 %random
Rwork0.1606 ---
obs0.1615 58751 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.187→34.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6878 0 113 263 7254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137194
X-RAY DIFFRACTIONf_angle_d1.3869787
X-RAY DIFFRACTIONf_dihedral_angle_d14.6682655
X-RAY DIFFRACTIONf_chiral_restr0.0671071
X-RAY DIFFRACTIONf_plane_restr0.0071289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1875-2.27510.30921160.21785950X-RAY DIFFRACTION94
2.2751-2.37860.23941240.20016397X-RAY DIFFRACTION100
2.3786-2.50390.27221250.18266386X-RAY DIFFRACTION100
2.5039-2.66080.21171400.18036341X-RAY DIFFRACTION100
2.6608-2.86610.23351530.1746395X-RAY DIFFRACTION100
2.8661-3.15440.22661420.1716409X-RAY DIFFRACTION100
3.1544-3.61040.19251270.15376474X-RAY DIFFRACTION100
3.6104-4.5470.17121310.13116510X-RAY DIFFRACTION100
4.547-34.28260.18361460.14696685X-RAY DIFFRACTION99
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)
14.8149-0.25270.46912.9654-2.21393.5216-0.15070.5459-0.1784-0.36580.11390.13790.2542-0.06070.1340.4065-0.0466-0.0250.2547-0.0310.2449-29.963612.3852-8.363
21.63170.02390.03571.4953-0.62942.6254-0.07110.0385-0.02-0.14280.02640.02030.087-0.00090.03920.2667-0.02990.00110.1661-0.00360.2342-29.36767.05711.7761
35.5170.75624.37252.49890.45583.4476-0.0517-0.01730.28210.1915-0.0659-0.01930.25230.0801-0.06060.23660.00340.02140.1283-0.00510.2196-27.90045.138417.2083
40.9997-0.0850.18271.3597-0.71032.7438-0.07630.03530.11210.04730.07040.2497-0.1807-0.3012-0.05780.2322-0.01410.00460.2263-0.01880.2796-39.032515.188111.7787
53.67670.5218-0.27513.0341-1.04993.0406-0.02180.35010.7044-0.34310.22170.5212-0.2403-0.3421-0.20170.4605-0.005-0.07730.2410.07440.3255-33.198333.7307-13.5768
61.4748-0.5144-0.13183.5378-0.07681.72860.0751-00.15940.0583-0.0975-0.2018-0.27140.2108-0.00450.1774-0.0136-0.0070.23950.01480.2384-16.162230.45892.9355
73.60111.918-2.01483.2464-1.71932.5317-0.09720.03860.1927-0.23110.16640.1850.0799-0.0619-0.12440.25150.0306-0.04870.18550.00210.2121-29.670528.2676-1.1552
82.14890.75490.08753.17840.00161.7167-0.07110.15640.3275-0.51050.07140.2259-0.1233-0.017-0.04390.2982-0.014-0.02240.18770.0560.3068-27.06936.9887-7.2003
91.60050.6178-1.17561.6034-1.78762.00710.10370.05030.08380.0565-0.0244-0.1282-0.1019-0.08-0.06530.26420.002-0.00750.191-0.01930.2356-22.364521.06786.0912
101.56870.6799-0.01555.47311.13652.2030.0558-0.09640.12410.0137-0.1602-0.2289-0.06130.1870.02040.2162-0.0002-0.01160.22040.02360.2622-11.618730.03953.4952
115.0664-2.58180.93025.84310.10971.7610.06250.34150.2477-0.4572-0.0358-0.7169-0.10380.32770.04190.2221-0.00720.04780.2773-0.01240.2781-7.216-16.29291.1773
121.4905-0.5789-0.19771.08020.57341.31720.0061-0.06310.0590.08780.0446-0.0681-0.02360.0634-0.0550.2477-0.036-0.0020.2063-0.00220.2232-22.6199-12.210117.2645
134.5962-2.6828-2.01354.5961.76950.9933-0.0719-0.70360.22850.2050.5974-0.60120.51620.9014-0.27710.32540.1357-0.08550.4447-0.03550.3060.0738-26.094517.3048
144.0076-0.99621.10274.1325-0.59987.02290.0144-0.0935-0.24220.17960.1237-0.4010.32370.3612-0.22970.20290.0368-0.01410.2792-0.02490.3540.8931-40.8020.8114
150.8041-1.00730.02421.9620.00911.43040.07050.2117-0.0909-0.2921-0.12650.1056-0.0423-0.1190.05990.2207-0.0258-0.02510.2894-0.00020.2187-20.2974-24.4186-8.6033
168.1464-5.77761.3064.1983-1.63975.4467-0.1701-0.6463-0.9260.44030.21410.93990.184-0.7759-0.1390.2959-0.04630.08680.2431-0.00040.4707-31.5892-44.50237.7655
172.45750.1136-1.24373.4872-2.37059.4709-0.09040.1029-0.1921-0.0543-0.05270.14610.1336-0.0868-0.03570.198-0.025-0.00330.1678-0.02140.2458-21.7092-40.7192-3.0286
181.1070.2214-0.03352.79780.58331.0463-0.00660.0031-0.1480.21060.0856-0.16180.24830.0771-0.07830.23560.0362-0.02270.21270.00990.2426-13.4362-38.02184.5856
190.9179-0.6643-0.28380.97490.5211.11860.0111-0.0519-0.05570.08710.0157-0.03710.02470.1110.0260.2194-0.01950.00090.19930.00090.2208-17.5784-27.23754.5981
201.40630.37-0.18844.0483-0.77111.8652-0.02250.0461-0.21550.05830.01620.34820.1375-0.2918-0.05460.2059-0.0038-0.00290.2676-0.01520.2646-28.2796-33.5625-4.0718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 15:43)
2X-RAY DIFFRACTION2(chain A and resid 44:129)
3X-RAY DIFFRACTION3(chain A and resid 130:144)
4X-RAY DIFFRACTION4(chain A and resid 145:198)
5X-RAY DIFFRACTION5(chain A and resid 199:226)
6X-RAY DIFFRACTION6(chain A and resid 227:278)
7X-RAY DIFFRACTION7(chain A and resid 279:308)
8X-RAY DIFFRACTION8(chain A and resid 309:354)
9X-RAY DIFFRACTION9(chain A and resid 355:412)
10X-RAY DIFFRACTION10(chain A and resid 413:457)
11X-RAY DIFFRACTION11(chain B and resid 15:43)
12X-RAY DIFFRACTION12(chain B and resid 44:185)
13X-RAY DIFFRACTION13(chain B and resid 186:205)
14X-RAY DIFFRACTION14(chain B and resid 206:218)
15X-RAY DIFFRACTION15(chain B and resid 219:247)
16X-RAY DIFFRACTION16(chain B and resid 248:261)
17X-RAY DIFFRACTION17(chain B and resid 262:283)
18X-RAY DIFFRACTION18(chain B and resid 284:335)
19X-RAY DIFFRACTION19(chain B and resid 336:412)
20X-RAY DIFFRACTION20(chain B and resid 413:457)

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