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- PDB-8ztp: Crystal structure of cysteine desulfurase Sufs from Mycoplasma Pn... -

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Basic information

Entry
Database: PDB / ID: 8ztp
TitleCrystal structure of cysteine desulfurase Sufs from Mycoplasma Pneumonia
Componentscysteine desulfurase
KeywordsBIOSYNTHETIC PROTEIN / Sufs / Mycoplasma Pneumonia / PLP-binding / L-Cys
Function / homology
Function and homology information


cysteine desulfurase / transaminase activity
Similarity search - Function
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 speciesMycoplasmoides pneumoniae 19294 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWang, W.M. / Ma, D.Y. / Gong, W.J. / Yao, H. / Liu, Y.H. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: The reduced interaction between SufS and SufU in Mycoplasma penetrans results in diminished sulfotransferase activity.
Authors: Ma, D. / Yao, H. / Liu, Y. / Gong, W. / Zhao, Y. / Wang, R. / Wu, C. / Wang, W. / Wang, H.
History
DepositionJun 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cysteine desulfurase
B: cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5774
Polymers95,0822
Non-polymers4942
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-45 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.516, 91.380, 161.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cysteine desulfurase


Mass: 47541.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Mycoplasmoides pneumoniae 19294 is not available, replaced by Q8EV24 temporarily.
Source: (gene. exp.) Mycoplasmoides pneumoniae 19294 (bacteria)
Gene: MYPE7430 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EV24, cysteine desulfurase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, Jeffamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 14190 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.061 / Rrim(I) all: 0.219 / Χ2: 0.957 / Net I/σ(I): 4 / Num. measured all: 181486
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.2-3.2612.51.0157080.7770.9350.2981.0590.803100
3.26-3.3112.50.8866690.8150.9480.260.9240.842100
3.31-3.3813.60.7616970.8930.9710.2130.790.85100
3.38-3.4513.50.77060.8870.970.1970.7280.848100
3.45-3.5213.50.6136850.9220.9790.1720.6370.856100
3.52-3.613.40.536840.9440.9850.150.5510.897100
3.6-3.6913.20.467280.9330.9820.1310.4780.917100
3.69-3.7913.20.46790.9640.9910.1150.4171.018100
3.79-3.9112.30.3566910.9660.9910.1050.3711.047100
3.91-4.0313.10.2986950.970.9920.0850.311.078100
4.03-4.1813.30.2667050.9780.9940.0750.2761.14100
4.18-4.3412.60.2167060.9810.9950.0630.2251.128100
4.34-4.5412.90.2036970.9880.9970.0590.2111.155100
4.54-4.7813.40.1897160.9880.9970.0540.1971.092100
4.78-5.0813.20.1727130.990.9970.0490.1791.04100
5.08-5.4712.50.1647140.9880.9970.0480.1711.003100
5.47-6.0212.40.1567140.9870.9970.0460.1630.926100
6.02-6.8912.20.1417360.990.9980.0420.1480.897100
6.89-8.6712.50.1097360.9950.9990.0320.1140.858100
8.67-5010.50.0958110.9950.9990.030.0990.73399.9

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XT6

5xt6


Resolution: 3.2→38.599 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 1401 10 %
Rwork0.2359 --
obs0.2391 14003 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→38.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6284 0 30 0 6314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036441
X-RAY DIFFRACTIONf_angle_d0.5418693
X-RAY DIFFRACTIONf_dihedral_angle_d2.9723847
X-RAY DIFFRACTIONf_chiral_restr0.045956
X-RAY DIFFRACTIONf_plane_restr0.0031103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.31430.33431280.2891143X-RAY DIFFRACTION92
3.3143-3.44690.30361370.27161241X-RAY DIFFRACTION100
3.4469-3.60370.33641380.2651243X-RAY DIFFRACTION100
3.6037-3.79350.33141400.25651259X-RAY DIFFRACTION100
3.7935-4.0310.28491390.23651248X-RAY DIFFRACTION100
4.031-4.34180.2391410.22541260X-RAY DIFFRACTION100
4.3418-4.77810.23211400.21881266X-RAY DIFFRACTION100
4.7781-5.46780.24671410.22311278X-RAY DIFFRACTION100
5.4678-6.88250.26681450.2631300X-RAY DIFFRACTION100
6.8825-38.5990.24041520.2051364X-RAY DIFFRACTION99

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