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- PDB-6cja: Crystal structure of Cystathionine beta-lyase from Legionella pne... -

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Basic information

Entry
Database: PDB / ID: 6cja
TitleCrystal structure of Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1 in complex with Alanyl-PLP and Serine
ComponentsCystathionine beta-lyase
KeywordsLYASE / SSGCID / pyridoxal phosphate / Alanyl-pyridoxal phosphate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


cystathionine beta-lyase / cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / L-cysteine biosynthetic process via L-cystathionine / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
: / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / 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 ...: / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-F0G / SERINE / Cystathionine beta-lyase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1 in complex with Alanyl-PLP and Serine
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionFeb 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine beta-lyase
B: Cystathionine beta-lyase
C: Cystathionine beta-lyase
D: Cystathionine beta-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,20315
Polymers172,2334
Non-polymers1,97011
Water30,3911687
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20440 Å2
ΔGint-116 kcal/mol
Surface area43310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.170, 97.110, 175.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cystathionine beta-lyase


Mass: 43058.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: metC, lpg0890 / Plasmid: LepnA.00906.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q5ZX43, cystathionine beta-lyase
#2: Chemical
ChemComp-F0G / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine / PLP-Ala


Type: L-peptide linking / Mass: 318.220 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N2O7P
#3: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1687 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Molecular Dimensions Morpheus screen H11: 10% w/v PEG 4000, 20% v/v glycerol: 20mM of each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM bicine/Trizma base pH 8.5: ...Details: Molecular Dimensions Morpheus screen H11: 10% w/v PEG 4000, 20% v/v glycerol: 20mM of each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM bicine/Trizma base pH 8.5: LepnA.00906.a.B1.PS38320 at 18.01mg/ml: cryo: direct: tray 295502 H11: puck MWL3-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→46.803 Å / Num. obs: 180706 / % possible obs: 99.9 % / Redundancy: 9.086 % / Biso Wilson estimate: 16.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.077 / Χ2: 1.106 / Net I/σ(I): 18.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.744.2720.4972.31131410.7890.56999.2
1.74-1.795.6260.4223.24129210.8810.468100
1.79-1.845.8770.3524.05125870.9210.388100
1.84-1.96.1450.2845.29122070.9550.312100
1.9-1.966.390.2346.74118480.9710.255100
1.96-2.036.680.1928.74114560.9790.20999.9
2.03-2.117.0390.15911110590.9880.17399.9
2.11-2.198.5020.14314.6106620.9910.152100
2.19-2.299.4460.12717.69102570.9940.135100
2.29-2.49.8820.11519.6197960.9960.122100
2.4-2.5310.4630.10621.6593660.9960.112100
2.53-2.6911.4230.09325.388250.9970.097100
2.69-2.8713.4310.08329.9683210.9980.086100
2.87-3.114.2170.07234.3477900.9980.075100
3.1-3.414.0710.06238.9671530.9990.065100
3.4-3.814.0430.05342.8565170.9990.055100
3.8-4.3914.0460.04745.6957930.9990.049100
4.39-5.3814.1290.04446.1249120.9990.046100
5.38-7.614.3220.04642.4438650.9990.048100
7.6-46.80313.4950.03748.1922300.9990.03899.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3026)refinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LLP bound structure

Resolution: 1.7→46.803 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.04
RfactorNum. reflection% reflection
Rfree0.168 2008 1.11 %
Rwork0.1407 --
obs0.141 180685 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.36 Å2 / Biso mean: 20.2527 Å2 / Biso min: 5.96 Å2
Refinement stepCycle: final / Resolution: 1.7→46.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11646 0 130 1705 13481
Biso mean--22.64 33.03 -
Num. residues----1524
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 (%)
1.7-1.74250.2891700.2418125011267199
1.7425-1.78960.22241390.19881264812787100
1.7896-1.84230.23131350.17141267112806100
1.8423-1.90180.18131590.14731267412833100
1.9018-1.96970.15021280.13771265912787100
1.9697-2.04860.191280.14071269112819100
2.0486-2.14180.17331010.14341274612847100
2.1418-2.25480.15691420.14191272012862100
2.2548-2.3960.17051550.14151272312878100
2.396-2.5810.17271550.1441275912914100
2.581-2.84070.1751450.14011277612921100
2.8407-3.25170.16451490.13541286013009100
3.2517-4.09640.16151550.12291292613081100
4.0964-46.82080.12731470.12681332313470100
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)
10.8909-0.3633-0.28840.70350.25410.45130.0270.14510.0531-0.0507-0.0032-0.0153-0.0604-0.0192-0.02560.0912-0.0078-0.00960.12130.01820.0876.5066-13.6942-37.5069
20.92360.31-0.1731.1122-0.00830.868-0.03120.085-0.18590.06360.00090.01060.2164-0.06120.020.1455-0.0235-0.00380.0876-0.02150.1077-0.8199-41.426-27.5224
34.50041.56893.93911.3311.85425.11720.0870.1764-0.27360.01290.0824-0.08990.32470.0543-0.14170.1819-0.0150.00880.0813-0.03750.12818.5129-47.017-34.8422
40.3254-0.1319-0.32040.79950.28670.4473-0.00790.1672-0.0962-0.01690.00320.04140.0953-0.07720.00420.0987-0.0178-0.01070.1187-0.01840.08615.5741-32.2436-33.7181
51.1686-0.15020.19151.0671-0.0050.72240.01060.1136-0.23050.1030.0571-0.19570.26390.1471-0.03190.16560.0375-0.02490.1253-0.04810.15323.8633-39.2537-30.4779
61.28160.0151-0.31411.2765-0.21081.24560.0373-0.063-0.17130.24710.0188-0.17020.31040.107-0.02180.260.0486-0.07360.1093-0.01490.168623.8152-41.791-15.6988
72.07312.07611.77912.09841.86361.8742-2.6648-2.2212.20513.02482.96552.3254-2.0716-0.7095-0.29680.42780.2494-0.03690.3336-0.01380.46139.0967-34.746-13.2908
80.5058-0.01220.01510.42090.14560.49440.00830.0159-0.00510.1009-0.00630.00740.0777-0.0312-0.00640.1137-0.0081-0.00180.06750.00830.0705-0.5459-21.1633-12.0885
90.91080.5155-0.33232.1098-0.64211.13870.0094-0.0227-0.02190.0831-0.02770.20990.0599-0.21080.01920.0991-0.01440.03430.1231-0.01290.1087-19.2175-17.0415-9.1984
101.00340.04830.04170.80290.10580.649-0.02880.11130.18640.02930.00440.1385-0.1063-0.14890.0210.09440.01290.00710.1120.02130.1108-11.6885-3.48-20.0104
112.15022.18551.98192.26762.08621.93812.77162.3998-1.6822-2.9486-2.5737-2.31881.52652.9005-0.21260.45930.18720.10310.4965-0.04430.4842-9.3042-14.5737-30.5188
120.3895-0.0046-0.05010.32260.09470.5522-0.01390.04110.03430.03850.0477-0.1032-0.03860.1928-0.02950.0993-0.0158-0.03510.1682-0.01210.146334.6999-6.1391-19.634
132.8010.9751.09091.5926-0.38830.92610.02180.3366-0.0417-0.26410.0005-0.3344-0.08340.6955-0.08860.1598-0.08790.02950.5129-0.03330.312653.95330.572-33.0728
140.88950.43310.56310.38880.26310.53290.01010.02280.03390.00380.0556-0.23150.03830.4473-0.05220.1014-0.0098-0.02060.3324-0.03040.236647.6285-9.2663-30.9743
150.3789-0.0304-0.0190.51790.18950.9326-0.01320.12130.0493-0.0680.0403-0.1317-0.03550.2366-0.00940.0723-0.01860.00610.194-0.00060.141334.1713-11.3306-41.1477
162-5.4757-3.25812-4.7932-0.1278-1.1176-2.44641.0141-0.54820.043-5.4064-6.32430.68840.42330.04510.19650.5820.00380.52729.13993.1663-38.4157
170.5429-0.1937-0.1460.36960.25190.86930.04090.11550.1155-0.0524-0.0073-0.0279-0.11130.0213-0.02650.1273-0.0097-0.0040.11870.03770.142812.12192.9762-32.3113
181.43710.11350.27550.66710.00120.7950.0205-0.03120.27490.07290.023-0.1164-0.29850.2589-0.0550.2345-0.1008-0.01460.172-0.0180.228730.980618.3454-14.6942
190.80170.5779-0.79333.5909-2.39991.87510.0374-0.03020.2928-0.05140.07020.0387-0.4380.1215-0.0720.3624-0.0614-0.03410.112-0.02910.274421.479825.4093-9.276
201.0010.3324-0.19871.4926-0.39680.83480.02190.01870.2725-0.0608-0.05120.0015-0.29890.111-0.01510.2245-0.0459-0.01970.09030.0150.204717.819119.125-15.9996
211.0085-0.1076-0.3920.34440.15291.23750.02570.04140.1760.0390.0301-0.0407-0.17990.0493-0.04660.1293-0.0179-0.01410.05420.00390.138214.60197.916-15.252
220.80.20340.06091.6875-0.92062.43290.0181-0.20.27120.1737-0.05060.028-0.4356-0.08880.06160.2554-0.0062-0.0110.1362-0.06840.231412.420219.51873.3401
231.32690.06650.07650.62740.191.2690.0093-0.16490.07090.1585-0.0046-0.0828-0.08450.1433-0.0050.1822-0.0199-0.03290.1315-0.03760.128219.05694.95675.9143
246.90496.25282.08045.6631.91421.96150.16361.14871.05930.10260.66811.49633.92364.6056-0.82960.3345-0.0238-0.01340.4765-0.16460.321330.11632.1782-5.9512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 65 )A3 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 145 )A66 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 166 )A146 - 166
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 236 )A167 - 236
5X-RAY DIFFRACTION5chain 'A' and (resid 237 through 300 )A237 - 300
6X-RAY DIFFRACTION6chain 'A' and (resid 301 through 383 )A301 - 383
7X-RAY DIFFRACTION7chain 'A' and (resid 401 through 401 )A401
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 123 )B3 - 123
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 196 )B124 - 196
10X-RAY DIFFRACTION10chain 'B' and (resid 197 through 383 )B197 - 383
11X-RAY DIFFRACTION11chain 'B' and (resid 401 through 401 )B401
12X-RAY DIFFRACTION12chain 'C' and (resid 3 through 123 )C3 - 123
13X-RAY DIFFRACTION13chain 'C' and (resid 124 through 145 )C124 - 145
14X-RAY DIFFRACTION14chain 'C' and (resid 146 through 196 )C146 - 196
15X-RAY DIFFRACTION15chain 'C' and (resid 197 through 383 )C197 - 383
16X-RAY DIFFRACTION16chain 'C' and (resid 401 through 401 )C401
17X-RAY DIFFRACTION17chain 'D' and (resid 3 through 65 )D3 - 65
18X-RAY DIFFRACTION18chain 'D' and (resid 66 through 145 )D66 - 145
19X-RAY DIFFRACTION19chain 'D' and (resid 146 through 167 )D146 - 167
20X-RAY DIFFRACTION20chain 'D' and (resid 168 through 196 )D168 - 196
21X-RAY DIFFRACTION21chain 'D' and (resid 197 through 270 )D197 - 270
22X-RAY DIFFRACTION22chain 'D' and (resid 271 through 300 )D271 - 300
23X-RAY DIFFRACTION23chain 'D' and (resid 301 through 383 )D301 - 383
24X-RAY DIFFRACTION24chain 'D' and (resid 401 through 401 )D401

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