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- PDB-8a2n: Structure of crocagin biosynthetic protein CgnD -

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Basic information

Entry
Database: PDB / ID: 8a2n
TitleStructure of crocagin biosynthetic protein CgnD
ComponentsCgnD
KeywordsHYDROLASE / crocagin / RiPP / Protease
Function / homologySGNH hydrolase superfamily / SGNH hydrolase-type esterase domain-containing protein
Function and homology information
Biological speciesChondromyces crocatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsAdam, S. / Koehnke, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO 4116/3-2 Germany
CitationJournal: Nat.Chem. / Year: 2023
Title: Unusual peptide-binding proteins guide pyrroloindoline alkaloid formation in crocagin biosynthesis.
Authors: Adam, S. / Zheng, D. / Klein, A. / Volz, C. / Mullen, W. / Shirran, S.L. / Smith, B.O. / Kalinina, O.V. / Muller, R. / Koehnke, J.
History
DepositionJun 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: CgnD
A: CgnD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3734
Polymers78,1812
Non-polymers1922
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.480, 102.060, 150.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein CgnD


Mass: 39090.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein underwent reductive lysine methylation prior to crystallization.
Source: (gene. exp.) Chondromyces crocatus (bacteria) / Gene: CMC5_025550 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K1EC25
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM ammonium sulfate, 100 mM MES pH 6.5 and 30% PEG 5000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97833 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97833 Å / Relative weight: 1
ReflectionResolution: 2.35→39.56 Å / Num. obs: 30717 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 28.42 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.2
Reflection shellResolution: 2.35→2.41 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 8 / Num. unique obs: 2158 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
SCALAdata scaling
PHENIXAutosolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→39.56 Å / SU ML: 0.2177 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2237 1576 5.14 %
Rwork0.1715 29082 -
obs0.1742 30658 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.07 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4820 0 10 251 5081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01454956
X-RAY DIFFRACTIONf_angle_d1.53146705
X-RAY DIFFRACTIONf_chiral_restr0.0724728
X-RAY DIFFRACTIONf_plane_restr0.0122845
X-RAY DIFFRACTIONf_dihedral_angle_d14.719772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.26771290.18732558X-RAY DIFFRACTION98.17
2.43-2.510.24571510.17662565X-RAY DIFFRACTION99.63
2.51-2.610.25981350.17252630X-RAY DIFFRACTION99.78
2.61-2.730.2691370.1772634X-RAY DIFFRACTION99.96
2.73-2.880.23471410.17882602X-RAY DIFFRACTION99.96
2.88-3.060.20941230.18522628X-RAY DIFFRACTION99.96
3.06-3.290.26471660.17742636X-RAY DIFFRACTION100
3.29-3.620.21511230.1642663X-RAY DIFFRACTION99.93
3.62-4.150.1681430.14952663X-RAY DIFFRACTION100
4.15-5.220.18721740.1492673X-RAY DIFFRACTION99.96
5.22-39.560.24721540.19792830X-RAY DIFFRACTION99.8
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)
11.11459550499-0.273375947741-0.3109108857761.19766972069-0.543475759390.7775855230020.086957639846-0.1019690063490.418115329201-0.394463541114-0.07564558393270.0710495360452-0.610911737204-0.01957673155620.08882100513360.2958988846850.009769714120260.02021308186860.206770806421-0.05793027723180.342886848189102.260503416131.724574381177.66988451
22.250956341720.5570011593230.2076195454863.037182433020.1220408743222.6476013963-0.0476457935662-0.164681529469-0.1344200705690.1929542992910.0843213996689-0.3433758824150.2640470609820.40471814338-0.01393622740730.1566207290130.0695389628173-0.00489558641740.262801357713-0.01729499849580.14509198308106.484864397113.837988057184.271266492
31.00686467591-0.528880748211-0.05546097869750.9746340089340.386212365921.510245589540.07303977716970.0504942627063-0.0184713341693-0.113375094032-0.06738829552740.09256358719030.124011611891-0.257769082690.03556645894890.2376737360570.01705503257890.01877988846370.2420380755620.001249096732420.26006478258886.7534893334113.51679123175.258031476
42.412731571342.917617109721.262828794614.68515665412.6740128511.86115128109-0.3779191003890.1665158867920.648830800242-0.7262689957620.0245743324780.555592500486-0.731593773066-0.3974731505810.3434763128920.3574781639580.0438554679331-0.010450098410.331617218989-0.001750330209850.4415401451385.0396903238132.705442458183.439471044
52.512006118170.6339017478870.6345550768012.655716647380.159952379651.67715057616-0.0482636433661-0.374344085677-0.01290969489790.112901987038-0.01186983342-0.03991700752770.13987875023-0.2373995866970.06866936654320.191181138424-0.01203910322240.03824705054970.267648309324-0.02784323202090.14154331286388.3994325819117.280360418190.871285455
61.553844028-0.8452305339210.3031219847342.612144922831.046909760522.905467093980.05018027874880.145666822972-0.2023560544220.0313654808808-0.2111018600390.3598672686070.299330731037-0.4974434302510.06809707026670.136362122214-0.05007781822940.02855025837090.210905691277-0.05295094461970.18684569161490.765340627997.3010927465152.700223612
71.683694237931.04487670069-0.5889264040762.245403888270.6987096527492.347376873830.02279243501370.04678507178650.1120219179170.05187121336820.133203179854-0.159922043442-0.03839192272740.169898390141-0.1521526247790.2000787140250.07124166612630.02530152779030.212570303678-0.04343251479330.255951665176108.246170999105.165927428161.816757637
81.33602680786-0.06829615872250.5110424959691.774198696580.8396358957223.480530194280.003893621344250.168669201965-0.1790814247960.0794529395630.138664721139-0.2454816590020.1969561000550.377644276577-0.1683391795410.2167962935040.06753638724790.01541902706740.239112902065-0.06696567987830.274554748002108.94638030391.2240075981148.898249689
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 34 )BA1 - 341 - 34
22chain 'B' and (resid 35 through 140 )BA35 - 14035 - 140
33chain 'B' and (resid 141 through 256 )BA141 - 256141 - 219
44chain 'B' and (resid 257 through 283 )BA257 - 283220 - 237
55chain 'B' and (resid 284 through 347 )BA284 - 347238 - 301
66chain 'A' and (resid 7 through 128 )AB7 - 1281 - 124
77chain 'A' and (resid 129 through 236 )AB129 - 236125 - 199
88chain 'A' and (resid 237 through 347 )AB237 - 347200 - 301

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