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- PDB-5vpr: Crystal Structure of Cysteine desulfurase from Elizabethkingia an... -

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Basic information

Entry
Database: PDB / ID: 5vpr
TitleCrystal Structure of Cysteine desulfurase from Elizabethkingia anophelis with covalently bound pyridoxal phosphate
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / SSGCID / Cysteine desulfurase / Elizabethkingia anophelis / pyridoxal phosphate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...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 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cysteine desulfurase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (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 Cysteine desulfurase from Elizabethkingia anophelis with covalently bound pyridoxal phosphate
Authors: Dranow, D.M. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 4, 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 1.3Nov 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


Theoretical massNumber of molelcules
Total (without water)46,4681
Polymers46,4681
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.180, 82.040, 70.120
Angle α, β, γ (deg.)90.000, 99.440, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cysteine desulfurase /


Mass: 46467.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: BD94_3973 / Plasmid: ElanA.01104.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A077EMQ8, cysteine desulfurase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ElanA.01104.a.B1.PW37984 at 18.07 mg/ml mixed 1:1 with Morpheus(a7): 10% (w/v) PEG-4000, 20% (v/v) glycerol, 0.1 M MOPS/HEPES-Na, pH = 7.5, 0.03 M each magnesium chloride and calcium ...Details: ElanA.01104.a.B1.PW37984 at 18.07 mg/ml mixed 1:1 with Morpheus(a7): 10% (w/v) PEG-4000, 20% (v/v) glycerol, 0.1 M MOPS/HEPES-Na, pH = 7.5, 0.03 M each magnesium chloride and calcium chloride, harvested directly.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→35.282 Å / Num. obs: 29282 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.62 % / Biso Wilson estimate: 40.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.048 / Χ2: 1.009 / Net I/σ(I): 18.22 / Num. measured all: 106003 / Scaling rejects: 31
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
2.05-2.13.7480.5233.218234220421970.8350.61199.7
2.1-2.163.7580.3684.637921210421080.9020.43100
2.16-2.223.7570.3175.577634204020320.9370.3799.6
2.22-2.293.7290.2217.447487201420080.960.25899.7
2.29-2.373.7270.188.877246195119440.9710.21199.6
2.37-2.453.7210.14410.797033188818900.9810.168100
2.45-2.543.6870.10313.436604180017910.9890.1299.5
2.54-2.653.6610.08116.766403176317490.9920.09599.2
2.65-2.763.6210.06719.045986166716530.9940.07999.2
2.76-2.93.6020.05522.195716160115870.9960.06599.1
2.9-3.063.5380.04426.065374153715190.9970.05298.8
3.06-3.243.5160.03928.165070145814420.9970.04698.9
3.24-3.473.4550.03730.574654136013470.9970.04499
3.47-3.743.460.03332.714290125712400.9980.0498.6
3.74-4.13.3390.0333.93840116711500.9980.03598.5
4.1-4.583.4570.02935.93619107110470.9980.03497.8
4.58-5.293.5340.02836.7332449359180.9980.03398.2
5.29-6.483.5120.02736.8527647987870.9980.03198.6
6.48-9.173.4730.02337.2520566165920.9990.02796.1
9.17-35.2822.9470.02433.618283582810.9970.02978.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J8Q

5j8q


Resolution: 2.05→35.282 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9
RfactorNum. reflection% reflection
Rfree0.2039 1935 6.61 %
Rwork0.1701 --
obs0.1724 29272 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.69 Å2 / Biso mean: 54.4928 Å2 / Biso min: 26.27 Å2
Refinement stepCycle: final / Resolution: 2.05→35.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 0 126 2884
Biso mean---52.29 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062810
X-RAY DIFFRACTIONf_angle_d0.8133816
X-RAY DIFFRACTIONf_chiral_restr0.051447
X-RAY DIFFRACTIONf_plane_restr0.004492
X-RAY DIFFRACTIONf_dihedral_angle_d12.9841670
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 (%)
2.0501-2.10130.2581220.234520052127100
2.1013-2.15810.27361310.205719412072100
2.1581-2.22160.23911360.200819412077100
2.2216-2.29330.27861460.198519492095100
2.2933-2.37530.25421390.200819592098100
2.3753-2.47030.24031470.188119522099100
2.4703-2.58270.24441560.1841946210299
2.5827-2.71890.22691450.18771947209299
2.7189-2.88910.25531500.19231938208899
2.8891-3.11210.24111330.18611962209599
3.1121-3.4250.21521350.18041963209899
3.425-3.92010.18221160.15851982209899
3.9201-4.93670.16771340.13641947208198
4.9367-35.28760.15981450.15851905205095
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)
12.81810.27120.78571.76110.2273.7636-0.089-0.3502-0.50190.13360.2524-0.02390.6348-0.1133-0.14130.39620.06560.08450.20870.07180.43370.4978-60.18068.6015
21.5620.58070.00034.10792.5123.3033-0.163-0.16620.1393-0.57470.2371-0.1109-0.7179-0.39-0.05790.42290.14550.0480.32180.04950.3514-6.7953-35.54558.5309
31.5738-0.6956-0.09334.41722.30692.6115-0.2103-0.50490.25720.05930.2156-0.145-0.2599-0.1565-0.0550.37980.2060.02290.4845-0.00610.3348-4.2763-35.144920.1925
43.4167-0.67630.91741.35110.31572.9234-0.4252-0.81850.01010.45180.4096-0.23790.1280.06650.01190.49220.2086-0.00790.44480.01230.37748.6368-51.941921.9817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 58 )A1 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 142 )A59 - 142
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 244 )A143 - 244
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 406 )A245 - 406

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