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- PDB-7xel: SufS soaked with D-penicillamine -

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Basic information

Entry
Database: PDB / ID: 7xel
TitleSufS soaked with D-penicillamine
ComponentsCysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase / Inhibitor
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding
Similarity search - Function
Cysteine desulfurase, SufS / Cysteine desulfurase / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakamura, R. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K19340 Japan
CitationJournal: to be published
Title: X-ray crystallographic snapshots of the thioazolidine formation upon the PLP during inhibition of SufS by D-cysteine
Authors: Nakamura, R. / Takahashi, Y. / Fujishiro, T.
History
DepositionMar 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2395
Polymers46,8151
Non-polymers4244
Water6,377354
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,47810
Polymers93,6292
Non-polymers8498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area9440 Å2
ΔGint4 kcal/mol
Surface area26510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.000, 93.000, 129.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cysteine desulfurase SufS


Mass: 46814.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: sufS, csd, yurW, BSU32690 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O32164, cysteine desulfurase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris-HCl, 50 mM Lithium sulfate, 50% (v/v) PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→46.5 Å / Num. obs: 60337 / % possible obs: 100 % / Redundancy: 7.373 % / Biso Wilson estimate: 46.951 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.036 / Χ2: 0.922 / Net I/σ(I): 25.54 / Num. measured all: 444887 / Scaling rejects: 58
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
1.8-1.97.6480.8052.3168472895689530.80.864100
1.9-2.17.440.3085.929763613130131240.9670.331100
2.1-2.57.4210.09817.5411409615378153740.9960.106100
2.5-37.320.04635.769672952295180.9990.05100
3-47.2140.02758.0354797760275960.9990.02999.9
4-67.0210.02367.5327986398639860.9990.025100
6-106.9690.02269.099583137513750.9990.024100
10-46.56.4360.02268.7126454184110.9990.02498.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZS9

5zs9


Resolution: 1.8→46.5 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.835 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3017 5 %RANDOM
Rwork0.1587 ---
obs0.1602 57316 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.64 Å2 / Biso mean: 46.637 Å2 / Biso min: 27.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.1 Å2-0 Å2
2---0.19 Å2-0 Å2
3---0.62 Å2
Refinement stepCycle: final / Resolution: 1.8→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 28 354 3549
Biso mean--62.97 58.8 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0123257
X-RAY DIFFRACTIONr_angle_refined_deg2.4641.6334413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53223.54161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65515538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4191514
X-RAY DIFFRACTIONr_chiral_restr0.1920.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022439
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 220 -
Rwork0.311 4189 -
all-4409 -
obs--99.98 %
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)
10.0318-0.08570.0261.05840.48920.65680.05820.03850.0029-0.049-0.0245-0.00490.01650.196-0.03380.14830.03720.00330.1089-0.02290.104964.216-6.495537.3949
20.12450.0722-0.08340.48270.07130.48670.10040.0235-0.0103-0.1282-0.11920.1157-0.0384-0.05870.01880.17530.0727-0.0780.0871-0.05880.106940.6507-4.249529.748
30.2984-0.0898-0.01750.79270.59150.72870.03010.1047-0.04690.081-0.05720.06760.26650.03910.0270.24920.0669-0.03430.0649-0.05380.094654.533-29.867634.5874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 56
2X-RAY DIFFRACTION2A57 - 300
3X-RAY DIFFRACTION3A301 - 405

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