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- PDB-8kg1: Crystal structure of the cargo cysteine desulfurase from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 8kg1
TitleCrystal structure of the cargo cysteine desulfurase from Mycobacterium smegmatis
Componentscysteine desulfurase
KeywordsTRANSFERASE / cargo protein / cysteine desulfurase
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding
Similarity search - Function
Cysteine desulfurase, SufS / 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
cysteine desulfurase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, X. / Tang, Y. / Liu, Y. / Ma, M. / Gao, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171259 China
National Natural Science Foundation of China (NSFC)32201033 China
CitationJournal: To be published
Title: Crystal structure of the cargo cysteine desulfurase from Mycobacterium smegmatis
Authors: Liu, X. / Tang, Y.
History
DepositionAug 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cysteine desulfurase
B: cysteine desulfurase


Theoretical massNumber of molelcules
Total (without water)93,0492
Polymers93,0492
Non-polymers00
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-29 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.092, 112.092, 120.813
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-702-

HOH

21B-808-

HOH

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Components

#1: Protein cysteine desulfurase


Mass: 46524.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: MSMEI_4425
Production host: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: I7GDP6, cysteine desulfurase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: The reservoir solution consisted of 0.1mM Bis-Tris pH6.5 and 9-24%w/v PEG10000. Protein crystals grew by vapor diffusion at 16℃ in sitting drops. Yellow crystals with a hexagonal ...Details: The reservoir solution consisted of 0.1mM Bis-Tris pH6.5 and 9-24%w/v PEG10000. Protein crystals grew by vapor diffusion at 16℃ in sitting drops. Yellow crystals with a hexagonal morphology appeared within 24 h and reached their full size after 5-7 days.
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.03845 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2023
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03845 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 51350 / % possible obs: 100 % / Redundancy: 18.6 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.032 / Rrim(I) all: 0.141 / Χ2: 0.943 / Net I/σ(I): 7.8 / Num. measured all: 957416
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.1-2.1417.41.7425500.890.9710.4291.7930.841
2.14-2.1818.41.49325300.9160.9780.3591.5360.856
2.18-2.2217.91.18325320.9320.9820.2871.2180.856
2.22-2.2617.70.98225040.9540.9880.241.0110.898
2.26-2.31190.79125710.9620.990.1870.8130.888
2.31-2.3718.90.7425180.9730.9930.1710.760.937
2.37-2.4218.70.54125480.9740.9930.1290.5570.894
2.42-2.4918.40.43825730.9830.9960.1050.4510.907
2.49-2.5617.60.3525200.9860.9960.0860.3610.914
2.56-2.65190.29525560.9840.9960.070.3040.933
2.65-2.7418.20.23725580.9910.9980.0570.2440.919
2.74-2.8519.20.19425520.9930.9980.0450.1990.941
2.85-2.9819.50.16525440.9930.9980.0380.1690.941
2.98-3.1419.40.14325620.9950.9990.0330.1471.002
3.14-3.3318.60.12825780.9940.9980.030.1321.044
3.33-3.5919.20.11725880.9960.9990.0270.121.088
3.59-3.9519.70.10425770.9950.9990.0240.1071.047
3.95-4.5219.40.09725960.9960.9990.0220.0990.983
4.52-5.718.60.08726450.9960.9990.0210.090.856
5.7-5018.10.07527480.9960.9990.0180.0771.078

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.04 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 2605 5.08 %
Rwork0.1492 --
obs0.1511 51305 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6225 0 0 529 6754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076412
X-RAY DIFFRACTIONf_angle_d0.8438737
X-RAY DIFFRACTIONf_dihedral_angle_d7.826906
X-RAY DIFFRACTIONf_chiral_restr0.053977
X-RAY DIFFRACTIONf_plane_restr0.0091153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.2164950.17692467X-RAY DIFFRACTION95
2.14-2.180.20521640.17632495X-RAY DIFFRACTION100
2.18-2.230.22191600.16612527X-RAY DIFFRACTION100
2.23-2.280.21631500.15942524X-RAY DIFFRACTION100
2.28-2.330.19771270.15682557X-RAY DIFFRACTION100
2.33-2.390.2041610.15592511X-RAY DIFFRACTION100
2.39-2.450.20591360.15612549X-RAY DIFFRACTION100
2.45-2.520.21011400.15712528X-RAY DIFFRACTION100
2.52-2.60.17141250.152596X-RAY DIFFRACTION100
2.6-2.70.19881230.14762539X-RAY DIFFRACTION100
2.7-2.810.18641510.14822550X-RAY DIFFRACTION100
2.81-2.930.19161140.15352575X-RAY DIFFRACTION100
2.93-3.090.18811350.14582566X-RAY DIFFRACTION100
3.09-3.280.21641500.15022553X-RAY DIFFRACTION100
3.28-3.530.17551120.14492589X-RAY DIFFRACTION100
3.53-3.890.16911560.13532583X-RAY DIFFRACTION100
3.89-4.450.14581360.12932615X-RAY DIFFRACTION100
4.45-5.60.14911140.14212651X-RAY DIFFRACTION100
5.61-45.040.19561560.16192725X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -45.7343 Å / Origin y: 60.2486 Å / Origin z: -18.4209 Å
111213212223313233
T0.0912 Å20.0477 Å20.0229 Å2-0.166 Å20.0062 Å2--0.1118 Å2
L1.0103 °20.3908 °20.0264 °2-0.5468 °20.0124 °2--0.7538 °2
S0.0539 Å °-0.0636 Å °-0.0785 Å °0.0381 Å °-0.0284 Å °-0.0087 Å °-0.1692 Å °-0.0882 Å °-0.0154 Å °
Refinement TLS groupSelection details: all

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