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- PDB-6wci: Crystal structure of a cysteine desulfurase SufS from Stenotropho... -

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Basic information

Entry
Database: PDB / ID: 6wci
TitleCrystal structure of a cysteine desulfurase SufS from Stenotrophomonas maltophilia K279a
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / National Institute of Allergy and Infectious Diseases / NIAID / structural genomics / biosynthesis / multi-drug resistant gram-negative bacterium / opportunistic pathogen / PLP / L-cysteine / L-alanine / sulfurtransferase / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / transaminase activity / 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
Cysteine desulfurase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a cysteine desulfurase SufS from Stenotrophomonas maltophilia K279a
Authors: Edwards, T.E. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D.
History
DepositionMar 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)94,0475
Polymers93,8272
Non-polymers2203
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-41 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.260, 219.650, 166.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-801-

HOH

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Components

#1: Protein Cysteine desulfurase / SufS


Mass: 46913.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: Smlt1153 / Production host: Escherichia coli (E. coli) / References: UniProt: B2FS04, cysteine desulfurase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24 mg/mL StmaA.01104.a.B1.PW38747 + 4 mM L-cysteine against MCSG-1 screen condition F11 (0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG3350), supplemented with 15% ethylene glycol as ...Details: 24 mg/mL StmaA.01104.a.B1.PW38747 + 4 mM L-cysteine against MCSG-1 screen condition F11 (0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG3350), supplemented with 15% ethylene glycol as cryoprotectant, unique puck ID njo9-6, crystal tracking ID 313926f11

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 13, 2020
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→45.35 Å / Num. obs: 55564 / % possible obs: 99 % / Redundancy: 7.903 % / Biso Wilson estimate: 38.794 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.089 / Χ2: 1.034 / Net I/σ(I): 14.34 / Num. measured all: 439141 / Scaling rejects: 599
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
2.05-2.18.1120.6153.6333372412041140.9610.65999.9
2.1-2.168.0210.4744.5131964399039850.970.50999.9
2.16-2.228.0910.395.331094385438430.9790.41999.7
2.22-2.298.1120.3136.4630843382338020.9860.33699.5
2.29-2.378.0570.2737.1629020361436020.9870.29399.7
2.37-2.458.0450.2288.4228528357035460.9890.24599.3
2.45-2.548.0930.199.8927709344834240.9920.20499.3
2.54-2.657.9790.16411.4426060328632660.9930.17699.4
2.65-2.767.990.1413.225096317131410.9930.1599.1
2.76-2.97.9090.11915.3623829304330130.9940.12899
2.9-3.067.8320.0991822516290728750.9960.10798.9
3.06-3.247.820.08720.0921271275427200.9950.09498.8
3.24-3.477.6210.07323.0619511258925600.9960.07898.9
3.47-3.747.5470.06525.8617895241123710.9970.0798.3
3.74-4.17.4860.0628.1716401223521910.9960.06598
4.1-4.587.5330.05829.5914878202119750.9970.06297.7
4.58-5.297.660.05730.4113651182317820.9970.06197.8
5.29-6.487.7250.05130.311588154415000.9970.05597.2
6.48-9.177.7160.04531.479051121711730.9980.04996.4
9.17-45.357.1420.04130.9848647286810.9980.04493.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXphenix1.17.1-3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6C9E

6c9e


Resolution: 2.05→45.35 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 1981 3.57 %
Rwork0.1718 53543 -
obs0.1736 55524 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.76 Å2 / Biso mean: 42.8277 Å2 / Biso min: 17.29 Å2
Refinement stepCycle: final / Resolution: 2.05→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6166 0 13 443 6622
Biso mean--56.21 44.42 -
Num. residues----805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10.31191560.237538163972100
2.1-2.160.25971280.219437993927100
2.16-2.220.25411370.213237813918100
2.22-2.290.29041650.19913808397399
2.29-2.380.25511240.200937943918100
2.38-2.470.23951380.2023799393799
2.47-2.580.26751460.18413807395399
2.58-2.720.23171330.18973819395299
2.72-2.890.24811540.18963796395099
2.89-3.110.24051370.18233828396599
3.11-3.430.21271460.18093833397999
3.43-3.920.20751160.15753843395998
3.92-4.940.19351470.13263864401198
4.94-45.350.19121540.15553956411097
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)
10.83980.2280.16372.5217-0.58393.829-0.03950.0114-0.05580.3849-0.02930.151-0.1655-0.22020.0540.20440.01660.03730.1901-0.04360.2297-4.5647-9.7114-4.8066
20.7809-0.1452-0.64912.4432-0.64662.66570.00790.0671-0.074-0.22810.02050.27720.4029-0.2909-0.01610.2095-0.0759-0.00820.2464-0.00680.2768-9.8781-30.9086-23.0377
31.141-0.50360.23253.1759-0.64581.7761-0.0807-0.0378-0.21450.42190.15430.40940.1763-0.3061-0.09160.2502-0.04350.09840.2746-0.01490.2909-10.3833-28.4207-4.2951
46.89431.6923-2.82335.5596-0.18366.6593-0.01940.48930.3171-0.21140.16970.2567-0.4955-0.5458-0.15390.23740.0328-0.07670.2501-0.00040.2109-7.1474-4.2013-28.054
55.42142.4132.31114.30210.78874.2837-0.02440.4928-0.1182-0.31090.0499-0.4055-0.11110.5482-0.03530.1823-0.01350.0610.29350.03310.25556.7695-10.6118-32.3049
60.99260.2680.62493.83741.07321.3859-0.02240.08980.0362-0.29450.0308-0.4619-0.15590.3810.00790.2052-0.02310.03660.28620.03830.23146.3355-9.9585-28.1078
70.95420.2690.05622.7395-0.14254.8942-0.0971-0.1393-0.01820.77660.0221-0.12470.33430.25030.06940.43190.0505-0.0330.2002-0.02310.2844.7379-13.64988.7154
80.68480.1760.2483.1198-0.31821.1755-0.0363-0.0776-0.12670.49350.0246-0.16850.26380.07670.01350.33130.06550.00450.24370.00270.23547.3083-36.2956-0.8166
91.50770.15810.34151.3204-0.69682.2472-0.0015-0.1859-0.16690.98170.0307-0.10250.13970.1141-0.02920.7650.0847-0.04490.28850.02790.354410.5424-44.195811.5507
101.3903-0.64130.39443.18941.16233.0939-0.02630.0098-0.06250.28820.139-0.2910.30570.4303-0.10540.24380.0325-0.00260.23670.01970.265910.212-29.4972-5.8992
110.0976-0.2894-0.14991.2960.47461.0923-0.2356-0.2474-0.2411.8525-0.03130.19550.4368-0.1280.13031.58840.08980.14760.4350.03040.3328-1.6486-28.844226.615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 93 )A14 - 93
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 235 )A94 - 235
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 309 )A236 - 309
4X-RAY DIFFRACTION4chain 'A' and (resid 310 through 330 )A310 - 330
5X-RAY DIFFRACTION5chain 'A' and (resid 331 through 366 )A331 - 366
6X-RAY DIFFRACTION6chain 'A' and (resid 367 through 418 )A367 - 418
7X-RAY DIFFRACTION7chain 'B' and (resid 15 through 72 )B15 - 72
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 149 )B73 - 149
9X-RAY DIFFRACTION9chain 'B' and (resid 150 through 235 )B150 - 235
10X-RAY DIFFRACTION10chain 'B' and (resid 236 through 309 )B236 - 309
11X-RAY DIFFRACTION11chain 'B' and (resid 310 through 417 )B310 - 417

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