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- PDB-7rw3: E. coli cysteine desulfurase SufS N99D -

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Basic information

Entry
Database: PDB / ID: 7rw3
TitleE. coli cysteine desulfurase SufS N99D
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / cysteine desulfurase / SufS / PLP
Function / homology
Function and homology information


selenocysteine lyase / selenocysteine lyase activity / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsDunkle, J.A. / Gogar, R. / Frantom, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: The beta-latch structural element of the SufS cysteine desulfurase mediates active site accessibility and SufE transpersulfurase positioning.
Authors: Gogar, R.K. / Carroll, F. / Conte, J.V. / Nasef, M. / Dunkle, J.A. / Frantom, P.A.
History
DepositionAug 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7612
Polymers44,5141
Non-polymers2471
Water1,27971
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5224
Polymers89,0272
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5560 Å2
ΔGint-15 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.760, 124.760, 137.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 44513.645 Da / Num. of mol.: 1 / Mutation: N99D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: sufS, AM464_26295, AUQ13_12030, BANRA_00144, BANRA_00498, BUE81_02100, BvCms2454_03222, BvCmsHHP056_00376, BvCmsKKP036_02154, BvCmsKSP026_00913, BW690_21095, C2U48_26455, C3F40_02340, C5F72_ ...Gene: sufS, AM464_26295, AUQ13_12030, BANRA_00144, BANRA_00498, BUE81_02100, BvCms2454_03222, BvCmsHHP056_00376, BvCmsKKP036_02154, BvCmsKSP026_00913, BW690_21095, C2U48_26455, C3F40_02340, C5F72_12470, C5F73_16550, CA593_19565, CI694_12360, D0X26_02680, D3821_13970, D9D44_08095, D9I97_06950, D9J52_00990, DJ503_04985, DT034_04565, E2119_03595, E4K51_04160, E4K53_02750, E4K55_02210, EA213_01125, EAI52_07715, EC3234A_33c01830, ECTO6_02268, EEP23_12650, EI021_02920, EI041_09080, EIZ93_02005, EL75_1975, EL79_2015, ETECE1441_02263, ETECE925_02258, EYD11_10615, EYV18_16700, F1E19_09770, F9X20_017695, F9X20_17865, FKC84_00740, FRV13_11320, FV293_04975, G5688_08175, G5696_08550, GHD50_00995, GKF86_07510, GKF89_05190, GQE33_02870, GQE34_20940, GQE67_02970, GRW02_06095, GRW05_00495, GRW57_07250, GRW81_10520, H4P50_11345, H4P51_11710, HH707_000397, HLT96_01805, HLU13_01505, HMQ05_01935, HNN86_11820, HNO08_06140, HNV44_03825, HV065_07405, HVV53_04920, HVX22_10640, HVX24_10540, HVY79_11755, HVY93_10710, HVZ24_10295, HX136_13565, NCTC10429_03516, NCTC13148_01082, NCTC8500_02620, NCTC9045_02773, NCTC9062_00321, NCTC9073_05651, RK56_009090, SAMEA3472047_04360, SAMEA3472080_01352, SAMEA3484427_00841, SAMEA3484429_00952, SAMEA3752559_02324, SAMEA3753300_02697, SK85_01902, WP2S18E08_22360, WP7S17E04_19980
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A090LEQ9, cysteine desulfurase, selenocysteine lyase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 6 Å3/Da / Density % sol: 80 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 4-4.5M NaCl, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→39.45 Å / Num. obs: 48187 / % possible obs: 98.8 % / Redundancy: 9.911 % / Biso Wilson estimate: 40.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.086 / Χ2: 0.904 / Net I/σ(I): 22.99 / Num. measured all: 477586 / Scaling rejects: 1290
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.363.7510.8911.3212027355532060.5621.03290.2
2.36-2.424.8840.8811.6316386343633550.6830.98697.6
2.42-2.496.4850.7422.3321959339833860.8020.80799.6
2.49-2.578.230.5753.5626831326232600.8940.61499.9
2.57-2.658.7580.5444.0527771317831710.9240.57899.8
2.65-2.759.1990.4235.828120306630570.9410.44999.7
2.75-2.8510.30.3177.2930756298729860.9710.334100
2.85-2.9711.30.23710.3632273285628560.9860.249100
2.97-3.112.5860.1715.2134751276127610.9940.178100
3.1-3.2513.3990.13818.8335092261926190.9960.143100
3.25-3.4312.9790.10425.7332641252525150.9970.10999.6
3.43-3.6412.5040.0833.1329522237923610.9990.08499.2
3.64-3.8911.860.06442.6826354225022220.9990.06798.8
3.89-4.212.3230.04552.9125804211420940.9990.04799.1
4.2-4.612.740.03364.74246771937193710.035100
4.6-5.1412.5120.03168.12220711765176410.03299.9
5.14-5.9412.1320.03560.59193501595159510.036100
5.94-7.2711.5950.03461.57155951345134510.036100
7.27-10.2810.4240.0281.88112481079107910.021100
10.28-39.457.0520.02170.543586436180.9990.02396.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdbid 6mr2

6mr2


Resolution: 2.3→39.45 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 1999 4.15 %
Rwork0.2064 46155 -
obs0.2071 48154 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.12 Å2 / Biso mean: 42.1316 Å2 / Biso min: 25.99 Å2
Refinement stepCycle: final / Resolution: 2.3→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 0 15 71 3069
Biso mean--34.16 40.16 -
Num. residues----386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.360.33541280.30292976310490
2.36-2.420.29221380.28033166330497
2.42-2.490.29241410.264732863427100
2.49-2.570.2411420.248132843426100
2.57-2.660.30541420.258632833425100
2.66-2.770.29291430.25532973440100
2.77-2.90.24021430.239332863429100
2.9-3.050.28811440.234933313475100
3.05-3.240.2321430.225233123455100
3.24-3.490.23141440.219533163460100
3.49-3.840.21211430.20723302344599
3.84-4.40.19891460.17063360350699
4.4-5.540.18271480.162234093557100
5.54-39.450.18361540.17213547370199

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