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

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Basic information

Entry
Database: PDB / ID: 3hvy
TitleCrystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_348457.1) from Clostridium acetobutylicum at 2.00 A resolution
ComponentsCystathionine beta-lyase family protein, YNBB B.subtilis ortholog
KeywordsLYASE / NP_348457.1 / PUTATIVE CYSTATHIONINE BETA-LYASE INVOLVED IN ALUMINUM RESISTANCE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Aluminium resistance protein
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
Cystathionine beta-lyase family protein, YNBB B.subtilis ortholog
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_348457.1) from Clostridium acetobutylicum at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: Cystathionine beta-lyase family protein, YNBB B.subtilis ortholog
B: Cystathionine beta-lyase family protein, YNBB B.subtilis ortholog
C: Cystathionine beta-lyase family protein, YNBB B.subtilis ortholog
D: Cystathionine beta-lyase family protein, YNBB B.subtilis ortholog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,69826
Polymers194,4894
Non-polymers1,20922
Water15,583865
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23720 Å2
ΔGint-71 kcal/mol
Surface area50580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.830, 186.620, 93.710
Angle α, β, γ (deg.)90.000, 103.060, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 426
2113B1 - 426
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Cystathionine beta-lyase family protein, YNBB B.subtilis ortholog


Mass: 48622.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CA_C1833, NP_348457.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97I22
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.43
Details: 0.9500M sodium citrate, 0.1M sodium cacodylate pH 6.43, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97968
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2008 / 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: 0.97968 Å / Relative weight: 1
ReflectionResolution: 2→30.029 Å / Num. obs: 131295 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.52 % / Biso Wilson estimate: 26.888 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.52
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.3461.62910023106190
2.07-2.150.2352.22956823497192.3
2.15-2.250.2522.93696325746195
2.25-2.370.2223.84134325714196.9
2.37-2.520.194.94654126137198.6
2.52-2.710.156.85283025521199.3
2.71-2.990.1029.55685926778199.4
2.99-3.420.0614.55580425980199.6
3.42-4.30.03521.65625225967199.4
4.3-30.0290.02925.45682526210199

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→30.029 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 6.687 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.128
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. SODIUM (NA) CATIONS AND ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYSTALLIZATION AND CRYOPROTECTION SOLUTIONS WERE MODELED INTO THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.187 6601 5 %RANDOM
Rwork0.145 ---
obs0.147 131250 99.26 %-
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: 116.2 Å2 / Biso mean: 36.557 Å2 / Biso min: 17.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å21.51 Å2
2---0.54 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→30.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12909 0 76 865 13850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02213300
X-RAY DIFFRACTIONr_bond_other_d0.0020.028939
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.96917949
X-RAY DIFFRACTIONr_angle_other_deg0.995321824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.77251703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83324.359562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.549152295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7961570
X-RAY DIFFRACTIONr_chiral_restr0.10.22019
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214919
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022675
X-RAY DIFFRACTIONr_nbd_refined0.2290.32949
X-RAY DIFFRACTIONr_nbd_other0.1960.39885
X-RAY DIFFRACTIONr_nbtor_refined0.1870.56889
X-RAY DIFFRACTIONr_nbtor_other0.0930.56664
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.51441
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0430.53
X-RAY DIFFRACTIONr_metal_ion_refined0.1350.515
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.34
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.517
X-RAY DIFFRACTIONr_mcbond_it1.85538372
X-RAY DIFFRACTIONr_mcbond_other0.54133495
X-RAY DIFFRACTIONr_mcangle_it3.078513448
X-RAY DIFFRACTIONr_scbond_it5.84785029
X-RAY DIFFRACTIONr_scangle_it7.692114501
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
2443TIGHT POSITIONAL0.040.05
2881LOOSE POSITIONAL0.25
2443TIGHT THERMAL0.230.5
2881LOOSE THERMAL1.6210
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 460 -
Rwork0.208 8985 -
all-9445 -
obs--96.86 %
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)
10.59750.06020.02910.89880.30320.4614-0.05260.11530.1853-0.19590.0326-0.1425-0.08360.07860.02-0.0263-0.0145-0.001-0.03580.05220.026132.147786.830915.9568
20.5769-0.0174-0.04540.5638-0.10230.4407-0.04520.1189-0.0734-0.09920.00770.05090.0023-0.09190.0375-0.0639-0.01360.0057-0.0165-0.0317-0.112.66449.860613.1745
30.27060.0432-0.21141.0577-0.0290.2730.0282-0.10980.10260.186-0.0105-0.0639-0.0250.0135-0.0177-0.04-0.0163-0.0566-0.0155-0.0605-0.015825.207886.345551.088
40.4348-0.05380.02110.68910.05280.5105-0.028-0.0905-0.04330.1157-0.0182-0.04060.0320.04140.0462-0.0656-0.00290.0095-0.03780.0236-0.087319.07845.333748.0633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 426
2X-RAY DIFFRACTION2B0 - 426
3X-RAY DIFFRACTION3C1 - 426
4X-RAY DIFFRACTION4D0 - 426

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