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- PDB-4k37: Native anSMEcpe with bound AdoMet -

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Basic information

Entry
Database: PDB / ID: 4k37
TitleNative anSMEcpe with bound AdoMet
ComponentsAnaerobic sulfatase-maturating enzyme
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: 1.62 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_comp_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_comp_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_comp_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.ptnr3_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,12628
Polymers86,7882
Non-polymers4,33826
Water15,493860
1
A: Anaerobic sulfatase-maturating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,56314
Polymers43,3941
Non-polymers2,16913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anaerobic sulfatase-maturating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,56314
Polymers43,3941
Non-polymers2,16913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.414, 92.405, 94.099
Angle α, β, γ (deg.)90.000, 93.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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.-

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Non-polymers , 5 types, 886 molecules

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


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


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


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 860 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
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-E / 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: 1.62→50 Å / Num. obs: 96411 / Biso Wilson estimate: 13.29 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: 1.62→41.462 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8667 / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 4773 4.98 %
Rwork0.1718 --
obs0.1731 95895 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.75 Å2 / Biso mean: 18.1692 Å2 / Biso min: 4.88 Å2
Refinement stepCycle: LAST / Resolution: 1.62→41.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5977 0 190 860 7027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136357
X-RAY DIFFRACTIONf_angle_d1.3828579
X-RAY DIFFRACTIONf_chiral_restr0.092878
X-RAY DIFFRACTIONf_plane_restr0.0061058
X-RAY DIFFRACTIONf_dihedral_angle_d17.5852403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.63750.27441360.24642776291291
1.6375-1.65680.25691580.22812987314598
1.6568-1.6770.26341750.22482974314999
1.677-1.69820.2641690.215130203189100
1.6982-1.72060.25471640.221630073171100
1.7206-1.74420.23451460.211530643210100
1.7442-1.76910.25031500.202730633213100
1.7691-1.79550.21971670.192230113178100
1.7955-1.82350.2141560.181130213177100
1.8235-1.85340.19641660.175831013267100
1.8534-1.88540.1981690.169529903159100
1.8854-1.91970.21091500.189530573207100
1.9197-1.95660.21621720.173830083180100
1.9566-1.99650.18121690.166130493218100
1.9965-2.03990.21341550.167730543209100
2.0399-2.08740.18971530.171730423195100
2.0874-2.13960.23451480.163830793227100
2.1396-2.19740.211700.154130153185100
2.1974-2.26210.19651520.170530373189100
2.2621-2.33510.17711570.159830873244100
2.3351-2.41860.18611480.162730543202100
2.4186-2.51540.19781500.165630463196100
2.5154-2.62980.19681570.173630713228100
2.6298-2.76850.19181680.166930513219100
2.7685-2.94190.20271600.177330723232100
2.9419-3.1690.19011440.178330773221100
3.169-3.48770.18241570.167930373194100
3.4877-3.9920.16561810.157530743255100
3.992-5.02820.16911540.144130903244100
5.0282-41.47530.20981720.170731083280100

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