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

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Basic information

Entry
Database: PDB / ID: 6cjb
TitleCrystal structure of Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1 covalently bound to Pyridoxal phosphate
ComponentsCystathionine beta-lyase
KeywordsLYASE / SSGCID / pyridoxal phosphate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


cystathionine beta-lyase / transsulfuration / pyridoxal phosphate binding / lyase activity
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 / Pyridoxal phosphate-dependent transferase ...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
FORMIC ACID / Cystathionine beta-lyase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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 covalently bound to Pyridoxal phosphate
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 1.1Oct 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 1.2Nov 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: Cystathionine beta-lyase
B: Cystathionine beta-lyase
C: Cystathionine beta-lyase
D: Cystathionine beta-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,4229
Polymers173,1454
Non-polymers2765
Water23,6541313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20280 Å2
ΔGint-127 kcal/mol
Surface area43600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.070, 97.060, 176.860
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: 43286.363 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1313 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Molecular Dimensions Morpheus screen G7: 10% PEG 4000, 25% Glycerol, 20mM of each N-formate, trisodium citrate, sodium potassium l-tartrate sodium oxamate: 100M MOPS/HEPES-Na pH 7.5: LepnA. ...Details: Molecular Dimensions Morpheus screen G7: 10% PEG 4000, 25% Glycerol, 20mM of each N-formate, trisodium citrate, sodium potassium l-tartrate sodium oxamate: 100M MOPS/HEPES-Na pH 7.5: LepnA.00906.a.B1.PS38320 at 18.01mg/ml + 3mM PLP, 3mM Homocysteine, 3mM Pyruvate: cryo: direct: tray 295496 G7: puck MWL3-10

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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 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→46.8 Å / Num. obs: 166145 / % possible obs: 99.7 % / Redundancy: 4.867 % / Biso Wilson estimate: 20.53 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.043 / Χ2: 1.037 / Net I/σ(I): 23.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.82.8940.512.1119630.740.6398.3
1.8-1.842.9930.392.73118100.8350.47899.1
1.84-1.93.1090.3093.58115240.8960.37599.7
1.9-1.963.2390.2494.6112530.9390.399.8
1.96-2.023.3730.1866.34108670.9620.22299.8
2.02-2.093.5280.1478.36105450.9780.17499.8
2.09-2.174.2280.11712.07102250.9880.13499.9
2.17-2.264.720.09515.7897900.9920.10799.9
2.26-2.364.9230.08318.4194340.9950.093100
2.36-2.475.1960.07221.2290310.9960.0899.9
2.47-2.615.5410.06125.285920.9980.068100
2.61-2.776.1420.05131.6381880.9980.056100
2.77-2.967.2310.04439.7276560.9990.048100
2.96-3.27.3640.03746.9571630.9990.039100
3.2-3.57.3550.02857.2661410.03100
3.5-3.917.3280.02366600610.025100
3.91-4.527.2980.0272.22531910.022100
4.52-5.537.2640.0272.67453610.021100
5.53-7.837.1770.02266.28356910.023100
7.83-46.86.650.01680.39206010.01899.2

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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: PDB entry 4iy7 teramer as per Morda

4iy7


Resolution: 1.75→46.8 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.23
RfactorNum. reflection% reflection
Rfree0.169 1991 1.2 %
Rwork0.1466 --
obs0.1469 166128 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.85 Å2 / Biso mean: 27.3108 Å2 / Biso min: 8.19 Å2
Refinement stepCycle: final / Resolution: 1.75→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11630 0 18 1328 12976
Biso mean--35.78 36.99 -
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 (%)
1.75-1.79380.29621570.2457113861154398
1.7938-1.84230.26021480.212115161166499
1.8423-1.89650.20491180.1861163511753100
1.8965-1.95770.21521100.17131167211782100
1.9577-2.02770.1851390.1631163611775100
2.0277-2.10890.16811220.15791168211804100
2.1089-2.20480.20291510.15181166411815100
2.2048-2.32110.13251310.14221171411845100
2.3211-2.46650.18381590.14631170111860100
2.4665-2.65690.19161350.14711175311888100
2.6569-2.92420.18931530.14341177611929100
2.9242-3.34730.15561700.13891181211982100
3.3473-4.21680.13951430.12671193412077100
4.2168-46.81680.14151550.13281225612411100
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)
10.7395-0.5134-0.11050.99490.25220.47070.01680.17570.0452-0.1011-0.0202-0.037-0.1049-0.0233-0.00120.1414-0.0213-0.01370.18190.02750.11446.625-13.8101-37.7918
21.05530.2781-0.18691.51080.28191.5275-0.04330.0653-0.23310.179-0.00960.05890.4553-0.06690.03970.2442-0.04070.00640.1204-0.01440.1309-0.2219-41.3313-27.7042
33.4111.14082.89031.20041.36673.46030.08070.0005-0.2669-0.01580.1143-0.12780.1868-0.0915-0.19780.292-0.03430.01310.1793-0.0510.17889.1066-46.8252-34.9106
40.446-0.0518-0.32120.78980.28070.6497-0.01950.2028-0.0884-0.02220.01260.02760.1655-0.0995-0.00650.1322-0.0273-0.01660.1479-0.02250.09266.0833-32.164-33.4671
51.3625-0.34140.13361.50860.16191.0269-0.06390.1152-0.280.14530.1044-0.20640.33840.2028-0.01950.19510.0484-0.00290.1607-0.0520.181724.5705-38.7956-30.6473
61.5691-0.6341-0.00512.26770.22232.2582-0.1118-0.1174-0.3080.53660.1177-0.0170.66710.07460.01830.40620.0861-0.03150.1775-0.0080.240324.6269-41.4406-16.3516
70.9223-0.077-0.09260.35880.08520.6854-0.0265-0.0595-0.01030.16210.029-0.05250.09560.05390.00080.17060.0005-0.02480.10390.01320.08957.5027-19.2384-8.1481
81.75190.0549-0.19141.84330.1581.7231-0.00930.0897-0.01450.1866-0.11710.34570.1102-0.46030.11070.1381-0.06610.02940.2702-0.04230.1799-20.6049-24.4863-17.4373
90.8196-0.049-0.0390.41910.26760.5985-0.0132-0.0319-0.02170.1634-0.01710.12050.128-0.16910.02260.1464-0.02730.02170.12760.01390.0959-9.8955-17.1305-10.356
102.02790.1296-0.09241.17760.05871.0355-0.0360.24780.3315-0.05670.00590.322-0.1868-0.29650.05110.13880.038-0.02010.18320.04220.2033-14.06530.6364-21.5974
110.9423-0.0608-0.24350.42580.10460.9472-0.0311-0.05580.06780.14550.0987-0.20.01320.2782-0.0570.1427-0.0038-0.07440.2148-0.02040.195330.9812-11.4726-14.6108
122.93040.63281.19511.8131-0.33320.74260.17170.48170.2973-0.41680.2068-0.6615-0.35090.77330.14210.2063-0.25220.13560.5571-0.06920.596947.24895.8349-32.8825
130.5572-0.1307-0.1070.93260.18920.8554-0.02220.06420.1084-0.01760.1428-0.3624-0.00230.4661-0.03890.0883-0.046-0.00920.3643-0.04530.277940.0155-11.6972-33.746
142.1342-0.053-0.67742.4437-0.81122.04190.09620.25490.399-0.18810.0171-0.1779-0.34390.2706-0.07770.2232-0.07910.0680.31720.03440.223730.7379-7.9718-50.9006
150.7908-0.4599-0.38611.13890.86951.23160.07750.17320.1884-0.1834-0.0009-0.0993-0.22590.041-0.08920.1943-0.0293-0.01030.1660.06670.166412.14083.1947-32.6679
161.19590.21690.2730.67160.11911.041-0.0142-0.07540.44570.07310.1368-0.3536-0.42850.3298-0.05710.3398-0.1502-0.0410.2492-0.06470.45330.816318.6703-14.9092
171.27210.8129-0.81183.0902-2.391.91090.0553-0.17990.4961-0.01890.1113-0.041-0.70050.22280.0390.5145-0.1048-0.00830.1017-0.04470.394420.592525.0107-8.8094
181.08980.13320.14151.1940.1580.6899-0.02590.06570.4648-0.10560.0309-0.083-0.43860.1706-0.08650.3148-0.0808-0.02080.12760.01860.327517.616419.3949-16.1385
190.99390.0093-0.20650.68410.19721.11-0.00330.04210.2630.03580.0431-0.0993-0.22350.0648-0.03970.1755-0.0336-0.02950.07530.01010.184214.62827.8867-14.9485
201.06950.1006-0.1721.5078-0.39281.96490.062-0.27680.38020.2699-0.019-0.0072-0.4087-0.0296-0.03470.409-0.0387-0.02390.203-0.10280.336412.313119.63393.2464
211.45080.28730.52631.30840.79812.6659-0.0129-0.23380.09390.34340.0594-0.18820.0190.2668-0.02440.2629-0.0182-0.08020.229-0.06490.190518.60832.96186.9307
222.78480.8030.6111.77640.51421.82580.003-0.15250.12510.27030.0291-0.3109-0.20940.2835-0.05210.2869-0.0396-0.07330.2067-0.06960.228319.50346.63535.1171
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 'B' and (resid 3 through 87 )B3 - 87
8X-RAY DIFFRACTION8chain 'B' and (resid 88 through 145 )B88 - 145
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 236 )B146 - 236
10X-RAY DIFFRACTION10chain 'B' and (resid 237 through 383 )B237 - 383
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 87 )C3 - 87
12X-RAY DIFFRACTION12chain 'C' and (resid 88 through 145 )C88 - 145
13X-RAY DIFFRACTION13chain 'C' and (resid 146 through 300 )C146 - 300
14X-RAY DIFFRACTION14chain 'C' and (resid 301 through 383 )C301 - 383
15X-RAY DIFFRACTION15chain 'D' and (resid 3 through 65 )D3 - 65
16X-RAY DIFFRACTION16chain 'D' and (resid 66 through 145 )D66 - 145
17X-RAY DIFFRACTION17chain 'D' and (resid 146 through 166 )D146 - 166
18X-RAY DIFFRACTION18chain 'D' and (resid 167 through 196 )D167 - 196
19X-RAY DIFFRACTION19chain 'D' and (resid 197 through 270 )D197 - 270
20X-RAY DIFFRACTION20chain 'D' and (resid 271 through 300 )D271 - 300
21X-RAY DIFFRACTION21chain 'D' and (resid 301 through 334 )D301 - 334
22X-RAY DIFFRACTION22chain 'D' and (resid 335 through 383 )D335 - 383

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