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- PDB-7xen: SufS with L-penicillamine -

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Basic information

Entry
Database: PDB / ID: 7xen
TitleSufS with L-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
Chem-9ZN / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsNakamura, R. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K14510 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)46,9652
Polymers46,5871
Non-polymers3781
Water4,216234
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9304
Polymers93,1732
Non-polymers7572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area4340 Å2
ΔGint-19 kcal/mol
Surface area29110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.200, 94.200, 133.200
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: 46586.582 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-9ZN / (2~{R})-3-methyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-sulfanyl-butanoic acid


Mass: 378.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 3.66 Å3/Da / Density % sol: 66.41 %
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: 2.47→47.1 Å / Num. obs: 24689 / % possible obs: 98.3 % / Redundancy: 7.298 % / Biso Wilson estimate: 86.018 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.059 / Χ2: 0.943 / Net I/σ(I): 16.33 / Num. measured all: 180175 / Scaling rejects: 69
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
2.47-2.577.7160.7292.1221380278427710.7820.78299.5
2.57-2.87.6390.4014.0337731496949390.9270.42999.4
2.8-3.17.2070.1838.9331922447844290.9840.19698.9
3.1-47.260.07321.8948285676366510.9970.07998.3
4-66.9010.0531.7828289421940990.9980.05497.2
6-106.9450.03934.029668145213920.9990.04295.9
10-47.17.1080.03335.6929004424080.9990.03592.3

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Processing

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

5zs9


Resolution: 2.47→47.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 13.812 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 1235 5 %RANDOM
Rwork0.1614 ---
obs0.1639 23455 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 183.6 Å2 / Biso mean: 85.8 Å2 / Biso min: 47.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 2.47→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 24 234 3310
Biso mean--75.27 84.99 -
Num. residues----392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123138
X-RAY DIFFRACTIONr_angle_refined_deg2.3091.6424264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7185390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74523.896154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.57815526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7691512
X-RAY DIFFRACTIONr_chiral_restr0.1720.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022365
LS refinement shellResolution: 2.47→2.534 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 92 -
Rwork0.327 1749 -
all-1841 -
obs--99.68 %
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)
10.71460.82420.79223.2206-0.21451.45140.0231-0.07610.2154-0.1935-0.13380.52380.1413-0.10920.11070.1913-0.1059-0.06170.2389-0.00760.185827.4398-6.7696-14.3989
20.26650.2988-0.25441.1073-0.31130.71780.0981-0.02850.00610.1734-0.2728-0.15820.1113-0.02080.17480.3176-0.1407-0.07960.12550.09260.195348.3493-12.4944-9.9429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 65
2X-RAY DIFFRACTION2A66 - 405

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