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- PDB-5db5: Crystal structure of PLP-bound E. coli SufS (cysteine persulfide ... -

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Basic information

Entry
Database: PDB / ID: 5db5
TitleCrystal structure of PLP-bound E. coli SufS (cysteine persulfide intermediate) in space group P21
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / LYASE / cysteine desulfurase / pyridoxal 5'-phosphate (PLP) / NifS protein family / protein binding
Function / homology
Function and homology information


selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / cysteine desulfurase / cysteine desulfurase activity / sulfur compound metabolic process / cysteine metabolic process / iron-sulfur cluster assembly ...selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / cysteine desulfurase / cysteine desulfurase activity / sulfur compound metabolic process / cysteine metabolic process / iron-sulfur cluster assembly / pyridoxal phosphate binding / hydrolase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Cysteine desulfurase, SufS / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Cysteine desulfurase, SufS / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / CYSTEINE / PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli DH5[alpha] (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsArbing, M.A. / Shin, A. / Koo, C.W. / Medrano-Soto, A. / Eisenberg, D.
CitationJournal: To Be Published
Title: Crystal structure of PLP-bound E. coli SufS (cysteine persulfide intermediate) in space group P21
Authors: Arbing, M.A. / Shin, A. / Koo, C.W. / Medrano-Soto, A. / Eisenberg, D.
History
DepositionAug 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase
B: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1318
Polymers89,1992
Non-polymers9326
Water2,936163
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-33 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.680, 114.150, 63.110
Angle α, β, γ (deg.)90.000, 116.210, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: GLY / End label comp-ID: GLY

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PHEPHEchain AAA3 - 4064 - 407
2ILEILEchain BBB2 - 4063 - 407

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cysteine desulfurase / / Selenocysteine beta-lyase / SCL / Selenocysteine lyase / Selenocysteine reductase


Mass: 44599.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Strain: DH5[alpha] / Gene: sufS, csdB, ynhB, b1680, JW1670 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P77444, cysteine desulfurase, selenocysteine lyase

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Non-polymers , 5 types, 169 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1:1 or 1:2 protein to reservoir solution (4% PEG3350, 200 mM ammonium citrate), crystals grown over 3 days, cryoprotectant: reservoir solution + 10% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.75→50.73 Å / Num. all: 19720 / Num. obs: 19720 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.55 % / Biso Wilson estimate: 32.6 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.122 / Χ2: 0.941 / Net I/σ(I): 15.62 / Num. measured all: 148918
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.75-2.826.860.9080.4674.389283144913520.50493.3
2.82-2.90.9550.375.7610648141714110.39799.6
2.9-2.980.9650.3076.8210722141814160.32999.9
2.98-3.070.9750.2438.3210033133013230.26199.5
3.07-3.170.9760.2368.89976131413130.25399.9
3.17-3.280.9880.17711.069627126712630.1999.7
3.28-3.410.9890.15912.59177120412040.17100
3.41-3.550.9930.13514.218985119411810.14598.9
3.55-3.70.9940.10717.938618112811280.114100
3.7-3.880.9950.09819.038073106010590.10599.9
3.88-4.10.9960.09220.257889104310320.09998.9
4.1-4.340.9970.07722.3775079869820.08399.6
4.34-4.640.9980.0682568949159060.07399
4.64-5.020.9980.06824.4865368568530.07399.6
5.02-5.490.9970.07423.1959827807800.08100
5.49-6.140.9970.07921.8253847117040.08599
6.14-7.090.9970.07422.7948506366340.07999.7
7.09-8.690.9980.05531.0341035455410.05999.3
8.69-12.290.9980.04438.730524124080.04799
12.290.9980.04737.5415792392300.05196.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KMJ

1kmj


Resolution: 2.75→40.2 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 986 5 %Random selection
Rwork0.165 18732 --
obs0.1677 19718 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.86 Å2 / Biso mean: 37.9739 Å2 / Biso min: 15.53 Å2
Refinement stepCycle: final / Resolution: 2.75→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6226 0 96 163 6485
Biso mean--48.6 26.27 -
Num. residues----809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056436
X-RAY DIFFRACTIONf_angle_d0.918759
X-RAY DIFFRACTIONf_chiral_restr0.036982
X-RAY DIFFRACTIONf_plane_restr0.0041138
X-RAY DIFFRACTIONf_dihedral_angle_d12.5992294
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4721X-RAY DIFFRACTION11.133TORSIONAL
12B4721X-RAY DIFFRACTION11.133TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.890.29141350.22752567X-RAY DIFFRACTION96
2.8914-3.07250.30221410.20912679X-RAY DIFFRACTION100
3.0725-3.30970.23381410.20092681X-RAY DIFFRACTION100
3.3097-3.64250.25921420.18092693X-RAY DIFFRACTION100
3.6425-4.16910.19591410.14912684X-RAY DIFFRACTION100
4.1691-5.25080.16141420.12622698X-RAY DIFFRACTION100
5.25-40.20.18331440.14222730X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -22.2021 Å / Origin y: 3.1265 Å / Origin z: 71.6361 Å
111213212223313233
T0.1683 Å2-0.0098 Å20.0007 Å2-0.2118 Å2-0.0161 Å2--0.1776 Å2
L0.3925 °2-0.0864 °20.0142 °2-0.8124 °2-0.1603 °2--0.5027 °2
S0.0116 Å °-0.0045 Å °0.0305 Å °-0.0285 Å °-0.0673 Å °-0.0004 Å °0.0158 Å °-0.0467 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 406
2X-RAY DIFFRACTION1allA425
3X-RAY DIFFRACTION1allB2 - 406
4X-RAY DIFFRACTION1allB425
5X-RAY DIFFRACTION1allS1 - 163
6X-RAY DIFFRACTION1allD1 - 2
7X-RAY DIFFRACTION1allC1
8X-RAY DIFFRACTION1allE1

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