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- PDB-5x5h: Crystal structure of metB from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 5x5h
TitleCrystal structure of metB from Corynebacterium glutamicum
ComponentsCystathionine beta-lyases/cystathionine gamma-synthases
KeywordsTRANSFERASE / PLP-binding domain
Function / homology
Function and homology information


cystathionine gamma-synthase / cystathionine gamma-synthase activity (acts on O-phosphohomoserine) / cystathionine gamma-synthase activity / methionine biosynthetic process / transsulfuration / pyridoxal phosphate binding / lyase activity
Similarity search - Function
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 ...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
PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-lyases/cystathionine gamma-synthases
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
CitationJournal: J. Agric. Food Chem. / Year: 2017
Title: Structural Insights into Substrate Specificity of Cystathionine gamma-Synthase from Corynebacterium glutamicum
Authors: Sagong, H.-Y. / Kim, K.-J.
History
DepositionFeb 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 16, 2020Group: Derived calculations / Structure summary / Category: struct / struct_conn / struct_conn_type
Item: _struct.title / _struct_conn.conn_type_id ..._struct.title / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn_type.id
Revision 1.3Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystathionine beta-lyases/cystathionine gamma-synthases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1007
Polymers42,5281
Non-polymers5726
Water4,576254
1
A: Cystathionine beta-lyases/cystathionine gamma-synthases
hetero molecules

A: Cystathionine beta-lyases/cystathionine gamma-synthases
hetero molecules

A: Cystathionine beta-lyases/cystathionine gamma-synthases
hetero molecules

A: Cystathionine beta-lyases/cystathionine gamma-synthases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,39928
Polymers170,1114
Non-polymers2,28824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area26700 Å2
ΔGint-169 kcal/mol
Surface area43800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.574, 149.851, 161.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Cystathionine beta-lyases/cystathionine gamma-synthases


Mass: 42527.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl2446 / Plasmid: pET30a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q79VD9, cystathionine gamma-synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 17, 2016
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.51→80.93 Å / Num. obs: 55876 / % possible obs: 99.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 42.7
Reflection shellHighest resolution: 1.51 Å / Redundancy: 5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 16 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-2000data processing
MOLREPphasing
HKL-2000data scaling
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QHX

3qhx


Resolution: 1.51→80.93 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.978 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.066
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1723 2742 5 %RANDOM
Rwork0.1477 ---
obs0.149 52555 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.44 Å2 / Biso mean: 17.951 Å2 / Biso min: 8.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å20 Å2
2--0.09 Å2-0 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 1.51→80.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 35 254 3211
Biso mean--23 28.45 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193010
X-RAY DIFFRACTIONr_bond_other_d0.0020.022782
X-RAY DIFFRACTIONr_angle_refined_deg2.4651.974087
X-RAY DIFFRACTIONr_angle_other_deg1.19136457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3424.882127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90715484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2671513
X-RAY DIFFRACTIONr_chiral_restr0.1560.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213355
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02574
LS refinement shellResolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 171 -
Rwork0.158 3659 -
all-3830 -
obs--93.6 %

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