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- PDB-3lvm: Crystal Structure of E.coli IscS -

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Basic information

Entry
Database: PDB / ID: 3lvm
TitleCrystal Structure of E.coli IscS
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / cysteine desulfurase / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / [2Fe-2S] cluster assembly / tRNA processing / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / metal ion binding / cytoplasm
Similarity search - Function
Cysteine desulfurase IscS / Cysteine desulfurase / 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) ...Cysteine desulfurase IscS / Cysteine desulfurase / 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
PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase IscS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsShi, R. / Proteau, A. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Plos Biol. / Year: 2010
Title: Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions.
Authors: Shi, R. / Proteau, A. / Villarroya, M. / Moukadiri, I. / Zhang, L. / Trempe, J.F. / Matte, A. / Armengod, M.E. / Cygler, M.
History
DepositionFeb 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Cysteine desulfurase
B: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1484
Polymers94,6542
Non-polymers4942
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-32 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.776, 99.197, 118.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteine desulfurase /


Mass: 47326.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: iscS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6B9, cysteine desulfurase
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG 6000, 0.1M Bicine pH 8.5, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 52419 / % possible obs: 93.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.068 / Χ2: 0.996 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.123.80.41936900.911166.7
2.12-2.214.10.3844880.955181
2.21-2.314.50.32149840.998190.2
2.31-2.435.30.27654301.006198
2.43-2.5860.23455591.007199.8
2.58-2.786.30.1655591.0121100
2.78-3.066.40.1155871.0021100
3.06-3.516.50.06856260.9941100
3.51-4.426.50.04556841.005199.9
4.42-506.70.03858120.993198.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P3W

1p3w


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.266 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2683 5.1 %RANDOM
Rwork0.198 ---
obs0.2 52318 93.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.97 Å2 / Biso mean: 39.009 Å2 / Biso min: 21.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2---1.43 Å20 Å2
3---3.25 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6143 0 30 310 6483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226293
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.978488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66523.426289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29151127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1331557
X-RAY DIFFRACTIONr_chiral_restr0.0970.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024727
X-RAY DIFFRACTIONr_nbd_refined0.1950.22820
X-RAY DIFFRACTIONr_nbtor_refined0.30.24311
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2387
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.26
X-RAY DIFFRACTIONr_mcbond_it0.6941.54012
X-RAY DIFFRACTIONr_mcangle_it1.12826247
X-RAY DIFFRACTIONr_scbond_it2.07832560
X-RAY DIFFRACTIONr_scangle_it3.5734.52240
LS refinement shellResolution: 2.048→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 153 -
Rwork0.277 2500 -
all-2653 -
obs--65.04 %
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)
12.73030.03420.36393.5440.20432.49970.021-0.0125-0.46420.1406-0.06640.23750.2842-0.11410.0455-0.12160.0009-0.0489-0.0798-0.05860.12425.7006-15.5307-16.2213
20.6976-0.0598-0.18770.30380.05690.36270.0012-0.00020.12210.0163-0.0230.0244-0.024-0.01640.0218-0.0540.0219-0.0049-0.0892-0.00890.0323.63896.8303-7.237
32.92320.89580.43643.89930.60372.0054-0.01550.2270.3064-0.1114-0.0202-0.0722-0.2417-0.01190.0357-0.12870.0140.0292-0.10240.04990.10563.105315.0805-18.9205
40.51690.01080.0840.3182-0.03250.3687-0.0327-0.0104-0.1082-0.0031-0.0308-0.09010.03240.00170.0635-0.06070.0168-0.0038-0.0885-0.00180.053845.9795-6.7291-7.6845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 11
2X-RAY DIFFRACTION1A264 - 398
3X-RAY DIFFRACTION2A12 - 263
4X-RAY DIFFRACTION3B-5 - 11
5X-RAY DIFFRACTION3B264 - 393
6X-RAY DIFFRACTION4B12 - 263

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