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- PDB-3fd0: Crystal structure of putative cystathionine beta-lyase involved i... -

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Basic information

Entry
Database: PDB / ID: 3fd0
TitleCrystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_470671.1) from LISTERIA INNOCUA at 2.12 A resolution
Componentsputative cystathionine beta-lyase involved in aluminum resistance
KeywordsLYASE / NP_470671.1 / putative cystathionine beta-lyase involved in aluminum resistance / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Unknown function
Function / homology
Function and homology information


Putative methionine gamma-lyase / Methionine gamma-lyase / Methioning gamme-lyase, C-terminal domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lin1335 protein
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_470671.1) from LISTERIA INNOCUA at 2.12 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)93,02836
Polymers90,6322
Non-polymers2,39734
Water8,953497
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)186,05672
Polymers181,2634
Non-polymers4,79368
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area31030 Å2
ΔGint97 kcal/mol
Surface area50960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.890, 131.890, 116.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 408
2115B1 - 408
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUGGESTS THAT A TETRAMER IS THE STABLE OLIGOMERIC FORM IN SOLUTION.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein putative cystathionine beta-lyase involved in aluminum resistance / Lin1335 protein


Mass: 45315.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin1335, NP_470671.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q92C56

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Non-polymers , 5 types, 531 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2000M Ca(OAc)2, 10.0000% PEG-8000, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97967
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979671
ReflectionResolution: 2.12→29.185 Å / Num. obs: 66693 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.13 % / Biso Wilson estimate: 32.23 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.14
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.12-2.20.8751.695673313565199.8
2.2-2.280.6572.34864311625199.8
2.28-2.390.5152.85734213653199.9
2.39-2.510.3793.85171612299199.9
2.51-2.670.2715.25514613089199.9
2.67-2.880.2016.95543113116199.8
2.88-3.160.12710.45273812465199.8
3.16-3.620.07716.25514013022199.9
3.62-4.550.05245434312829199.8
4.55-29.1850.0427.95529812989199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.12→29.185 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.55 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.135
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.RESIDUE LYS226 IN BOTH CHAINS HAS BEEN MODELED AS LLP - A LYSINE WITH A SCHIFF BASE LINKAGE TO PYRIDOXAL-5'PHOSPHATE (PLP). THERE IS CLEAR AND UNAMBIGUOUS ELECTRON DENSITY IN THE EXPERIMENTALLY PHASED MAPS FOR THIS COVALENT MODIFICATION. THIS IS AT THE PUTATIVE ACTIVE SITE OF BOTH PROTOMERS. 5.CALCIUM (CA) AND POLYETHYLENE GLYCOL FRAGMENTS (PEG AND PGE) FROM THE CRYSTALLIZATION AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3382 5.1 %RANDOM
Rwork0.152 ---
obs0.154 66656 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.1 Å2 / Biso mean: 34.7 Å2 / Biso min: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0.31 Å20 Å2
2---0.61 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.12→29.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6279 0 154 497 6930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226581
X-RAY DIFFRACTIONr_bond_other_d0.0010.024474
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9828878
X-RAY DIFFRACTIONr_angle_other_deg1.489310923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5595832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19824.685286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.377151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6791533
X-RAY DIFFRACTIONr_chiral_restr0.0910.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217292
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021275
X-RAY DIFFRACTIONr_mcbond_it1.54534071
X-RAY DIFFRACTIONr_mcbond_other0.43331675
X-RAY DIFFRACTIONr_mcangle_it2.55556571
X-RAY DIFFRACTIONr_scbond_it4.72582510
X-RAY DIFFRACTIONr_scangle_it6.816112298
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 248 -
Rwork0.217 4612 -
all-4860 -
obs--99.73 %
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)
10.6520.0281-0.31440.39140.00470.4929-0.01180.0422-0.0340.03910.00610.10240.0346-0.14670.0057-0.0843-0.01260.0201-0.0549-0.0052-0.069577.623960.072226.6484
20.77150.0848-0.03940.7427-0.13290.55690.0372-0.1394-0.23320.1701-0.0207-0.010.1360.0247-0.01650.03530.0027-0.0213-0.08490.0243-0.0282100.738827.242332.3095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 408
2X-RAY DIFFRACTION2B1 - 408

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