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- PDB-3jzl: CRYSTAL STRUCTURE OF A PUTATIVE CYSTATHIONINE BETA-LYASE INVOLVED... -

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Entry
Database: PDB / ID: 3jzl
TitleCRYSTAL STRUCTURE OF A PUTATIVE CYSTATHIONINE BETA-LYASE INVOLVED IN ALUMINUM RESISTANCE (LMOF2365_1314) FROM LISTERIA MONOCYTOGENES STR. 4B F2365 AT 1.91 A RESOLUTION
ComponentsPutative cystathionine beta-lyase involved in aluminum resistance
KeywordsLYASE / PUTATIVE CYSTATHIONINE BETA-LYASE INVOLVED IN ALUMINUM RESISTANCE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyMethioning gamme-lyase, C-terminal domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesListeria monocytogenes str. 4b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (YP_013912.1) from Listeria monocytogenes 4b F2365 at 1.91 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cystathionine beta-lyase involved in aluminum resistance
B: Putative cystathionine beta-lyase involved in aluminum resistance
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6496
Polymers91,2662
Non-polymers3824
Water4,936274
1
A: Putative cystathionine beta-lyase involved in aluminum resistance
B: Putative cystathionine beta-lyase involved in aluminum resistance
hetero molecules

A: Putative cystathionine beta-lyase involved in aluminum resistance
B: Putative cystathionine beta-lyase involved in aluminum resistance
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,29812
Polymers182,5334
Non-polymers7658
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area18820 Å2
ΔGint-110 kcal/mol
Surface area50330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.407, 153.173, 183.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A4 - 119
2114B4 - 119
1216A120 - 125
2216B120 - 125
1314A126 - 325
2314B126 - 325
1416A327 - 357
2416B327 - 357
1514A384 - 407
2514B384 - 407
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT A TETRAMER IS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative cystathionine beta-lyase involved in aluminum resistance


Mass: 45633.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes str. 4b (bacteria)
Strain: F2365 / Gene: LMOf2365_1314, YP_013912.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q720C5, cystathionine beta-lyase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.1 Å3/Da / Density % sol: 41.43 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30.0000% polyethylene glycol 600, 5.0000% polyethylene glycol 1000, 10.0000% Glycerol, 0.1M MES pH 6.0, ADDITIVE: 0.001 M PYRIDOXAL-5'-PHOSPHATE, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9792
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.91→39.436 Å / Num. obs: 58916 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.376 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.62
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.91-1.980.3981.5139048441171.2
1.98-2.060.371.91946510726192.8
2.06-2.150.2952.52019410866198
2.15-2.260.2313.22121311161198.9
2.26-2.410.1794.12307412040199.3
2.41-2.590.1365.32136311100199.2
2.59-2.850.0987.22199111394198.9
2.85-3.260.06510.42177711285198
3.26-4.10.03816.52117111007195.3
4.1-39.4360.02822.42116910951193.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→39.436 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 12.928 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.159
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GLYCEROL,USED AS A CRYO- PROTECTANT,WAS MODELED INTO THE STRUCRURE. 5.ELECTRON DENSITY MAPS SUPPORT THE MODELING OF PYRIDOXAL-5'-PHOSPHATE AS N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE (LLP), IN WHICH THE THE PYRIDOXAL-5'-PHOSPHATE IS COVALENTLY BOUND TO THE SIDECHAIN OF LYS 226. 6. ELECTRON DENSITIES CORRESPONDING TO RESIDUES 323-324, 357-358, AND 378-383 ON THE B SUBUNIT WERE DISORDERED; THEREFORE THESE RESIDUES WERE NOT MODELED. 7. TLS PARAMETERS WERE DETERMINED USING THE TLS MOTION DETERMINATION SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2966 5 %RANDOM
Rwork0.21 ---
obs0.211 58875 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 69.74 Å2 / Biso mean: 24.093 Å2 / Biso min: 6.15 Å2
Baniso -1Baniso -2Baniso -3
1-6.46 Å20 Å20 Å2
2---3.05 Å20 Å2
3----3.41 Å2
Refinement stepCycle: LAST / Resolution: 1.91→39.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6018 0 24 274 6316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226260
X-RAY DIFFRACTIONr_bond_other_d0.0020.024098
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9728534
X-RAY DIFFRACTIONr_angle_other_deg1.173310053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8885826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35424.525263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.99915970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7351529
X-RAY DIFFRACTIONr_chiral_restr0.0850.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217092
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021239
X-RAY DIFFRACTIONr_mcbond_it1.11624006
X-RAY DIFFRACTIONr_mcbond_other0.26621644
X-RAY DIFFRACTIONr_mcangle_it1.9246425
X-RAY DIFFRACTIONr_scbond_it3.38662254
X-RAY DIFFRACTIONr_scangle_it4.67582093
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
4192MEDIUM POSITIONAL0.250.5
335LOOSE POSITIONAL1.375
4192MEDIUM THERMAL0.742
335LOOSE THERMAL1.4910
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 178 -
Rwork0.4 3549 -
all-3727 -
obs--84 %
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)
10.20890.10550.02120.47770.10610.2755-0.0103-0.03370.0561-0.0006-0.00620.0804-0.045-0.08560.01650.09460.00360.00840.10440.00480.09496.798697.801675.3789
20.15260.06760.01370.5894-0.06060.2712-0.0084-0.0168-0.0589-0.014-0.0102-0.10530.03840.09650.01850.08750.0042-0.00690.1069-0.00270.094311.462961.658469.82
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 408
2X-RAY DIFFRACTION2B4 - 407

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