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- PDB-4k39: Native anSMEcpe with bound AdoMet and Cp18Cys peptide -

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Basic information

Entry
Database: PDB / ID: 4k39
TitleNative anSMEcpe with bound AdoMet and Cp18Cys peptide
Components
  • Anaerobic sulfatase-maturating enzyme
  • Cp18Cys peptide
KeywordsOXIDOREDUCTASE / AdoMet radical fold
Function / homology
Function and homology information


cysteine-type anaerobic sulfatase-maturating enzyme / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Anaerobic Cys-type sulfatase-maturating enzyme / : / Anaerobic sulphatase maturase, radical SAM / 4Fe4S-binding SPASM domain / Iron-sulfur cluster-binding domain / 4Fe-4S single cluster domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I ...Anaerobic Cys-type sulfatase-maturating enzyme / : / Anaerobic sulphatase maturase, radical SAM / 4Fe4S-binding SPASM domain / Iron-sulfur cluster-binding domain / 4Fe-4S single cluster domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Cysteine-type anaerobic sulfatase-maturating enzyme
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.783 Å
AuthorsGoldman, P.J. / Drennan, C.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: X-ray structure of an AdoMet radical activase reveals an anaerobic solution for formylglycine posttranslational modification.
Authors: Goldman, P.J. / Grove, T.L. / Sites, L.A. / McLaughlin, M.I. / Booker, S.J. / Drennan, C.L.
History
DepositionApr 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anaerobic sulfatase-maturating enzyme
B: Anaerobic sulfatase-maturating enzyme
D: Cp18Cys peptide
C: Cp18Cys peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,34415
Polymers90,5244
Non-polymers2,82011
Water8,431468
1
A: Anaerobic sulfatase-maturating enzyme
C: Cp18Cys peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9008
Polymers45,2622
Non-polymers1,6386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-76 kcal/mol
Surface area15950 Å2
MethodPISA
2
B: Anaerobic sulfatase-maturating enzyme
D: Cp18Cys peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4457
Polymers45,2622
Non-polymers1,1825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-84 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.031, 91.915, 91.004
Angle α, β, γ (deg.)90.000, 91.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABDC

#1: Protein Anaerobic sulfatase-maturating enzyme / AnSME / Cys-type sulfatase-activating enzyme


Mass: 43393.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / NCTC 8237 / Type A / Gene: CPF_0616 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0TTH1, EC: 1.8.98.-
#2: Protein/peptide Cp18Cys peptide


Mass: 1868.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: standard Fmoc chemistry

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Non-polymers , 5 types, 479 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 29% PEG 4000, 150 mM ammonium acetate, 100 mM sodium acetate, pH 4.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 69024 / Biso Wilson estimate: 24.41 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
APEXdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.783→41.022 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8336 / SU ML: 0.19 / σ(F): 1.35 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 3361 4.95 %
Rwork0.1797 --
obs0.1815 67935 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.25 Å2 / Biso mean: 26.7309 Å2 / Biso min: 12.4 Å2
Refinement stepCycle: LAST / Resolution: 1.783→41.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6016 0 94 468 6578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126290
X-RAY DIFFRACTIONf_angle_d1.3468503
X-RAY DIFFRACTIONf_chiral_restr0.096876
X-RAY DIFFRACTIONf_plane_restr0.0061062
X-RAY DIFFRACTIONf_dihedral_angle_d23.2792363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7834-1.80890.2995950.26221834192967
1.8089-1.83590.27441500.24062713286399
1.8359-1.86460.2721350.224526642799100
1.8646-1.89510.24261410.21427472888100
1.8951-1.92780.24151460.207627332879100
1.9278-1.96290.241570.202926902847100
1.9629-2.00060.23761400.200827392879100
2.0006-2.04150.27061300.18527162846100
2.0415-2.08590.23071330.186127252858100
2.0859-2.13440.22991440.18427032847100
2.1344-2.18780.2521610.186727242885100
2.1878-2.24690.28081330.182727062839100
2.2469-2.3130.23181350.179327662901100
2.313-2.38770.22911410.179326872828100
2.3877-2.4730.22321260.183527622888100
2.473-2.5720.2131410.186527192860100
2.572-2.6890.23631500.184127292879100
2.689-2.83080.25051490.189827362885100
2.8308-3.00810.2321170.189827482865100
3.0081-3.24020.21531400.186527372877100
3.2402-3.56610.20191490.178427292878100
3.5661-4.08180.18171580.167327482906100
4.0818-5.1410.16241420.150327482890100
5.141-41.03250.19581480.16612771291999

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