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- PDB-6kg0: NifS from Helicobacter pylori, soaked with L-cysteine for 118 sec -

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Basic information

Entry
Database: PDB / ID: 6kg0
TitleNifS from Helicobacter pylori, soaked with L-cysteine for 118 sec
ComponentsCysteine desulfurase IscS
KeywordsBIOSYNTHETIC PROTEIN / iron / sulfur / cysteine desulfurase / reaction intermediate
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / [2Fe-2S] cluster assembly / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / metal ion binding / cytoplasm
Similarity search - Function
Cysteine desulfurase NifS, proteobacteria / Cysteine desulfurase IscS / Cysteine desulfurase / Aminotransferase class V domain / Aminotransferase class-V / 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 ...Cysteine desulfurase NifS, proteobacteria / Cysteine desulfurase IscS / Cysteine desulfurase / Aminotransferase class V domain / Aminotransferase class-V / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C6P / ISOPROPYL ALCOHOL / Cysteine desulfurase IscS
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsNakamura, R. / Takahashi, Y. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K14510 Japan
CitationJournal: Febs J. / Year: 2020
Title: Snapshots of PLP-substrate and PLP-product external aldimines as intermediates in two types of cysteine desulfurase enzymes.
Authors: Nakamura, R. / Hikita, M. / Ogawa, S. / Takahashi, Y. / Fujishiro, T.
History
DepositionJul 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine desulfurase IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5734
Polymers44,1251
Non-polymers4483
Water19811
1
A: Cysteine desulfurase IscS
hetero molecules

A: Cysteine desulfurase IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1468
Polymers88,2502
Non-polymers8966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6230 Å2
ΔGint-53 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.200, 103.200, 134.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cysteine desulfurase IscS / NifS


Mass: 44125.230 Da / Num. of mol.: 1 / Mutation: L2V, K138R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: iscS, HP_0220 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O25008, cysteine desulfurase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-C6P / N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE / 4-((1-CARBOXY-2-THIOL-ETHYLAMINO)-METHYL)-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM


Mass: 352.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O7PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.05 Å3/Da / Density % sol: 69.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 17% (w/v) PEF 4000, 8.5% (v/v) 2-propanol, 15%(v/v) glycerol, 85mM HEPES-NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019 / Details: Si(111) double crystal monochromator
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→46.2 Å / Num. obs: 18835 / % possible obs: 100 % / Redundancy: 7.086 % / Biso Wilson estimate: 73.219 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.09 / Χ2: 1.019 / Net I/σ(I): 14.18 / Num. measured all: 265780 / Scaling rejects: 7
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
2.7-2.87.3290.7832.2828348386938680.8610.842100
2.8-37.1750.533.3144999627462720.9460.571100
3-3.46.9420.2327.1359560858085800.9850.251100
3.4-47.3040.116.6152983725472540.9960.108100
4-66.9730.06126.0556613811981190.9970.066100
6-106.8340.04731.3118308267926790.9980.051100
10-46.26.770.04634.1749697407340.9970.04999.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WT2

5wt2


Resolution: 2.78→46.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 24.229 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.248 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 942 5 %RANDOM
Rwork0.1836 ---
obs0.1854 17892 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 240.97 Å2 / Biso mean: 91.83 Å2 / Biso min: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---1.75 Å20 Å2
3---3.5 Å2
Refinement stepCycle: final / Resolution: 2.78→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 27 11 2813
Biso mean--82.96 61.72 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122850
X-RAY DIFFRACTIONr_angle_refined_deg2.1861.6323860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3925356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24322.394142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.3915495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1841518
X-RAY DIFFRACTIONr_chiral_restr0.1550.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022134
LS refinement shellResolution: 2.78→2.852 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 68 -
Rwork0.318 1288 -
all-1356 -
obs--100 %
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)
10.55310.6861-0.575211.0144-5.40992.79290.31940.0121-0.28480.1682-0.34940.3397-0.14290.1380.02990.4836-0.02430.00960.0873-0.05380.317-26.2433-35.314918.4401
23.0309-0.19784.15973.9738-2.507710.0087-0.00540.39680.03350.14110.05890.90260.2605-0.7836-0.05350.1019-0.0920.13170.6227-0.11120.3122-37.7211-22.8145-3.7695
34.27130.45450.0463.32540.87243.3703-0.1148-0.38090.76650.8972-0.0837-0.1072-1.02510.43060.19850.8564-0.1412-0.10910.1798-0.03840.2241-19.0198-8.657913.7437
42.7253-0.34350.27643.6746-1.91966.0092-0.1195-0.9066-0.25231.5345-0.1207-0.3059-0.00780.31870.24020.9079-0.0680.02280.39230.01070.2495-24.1686-30.739425.6028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 14
2X-RAY DIFFRACTION2A15 - 54
3X-RAY DIFFRACTION3A55 - 236
4X-RAY DIFFRACTION4A237 - 384

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