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- PDB-5ijg: Crystal structure of O-acetylhomoserine sulfhydrolase from Brucel... -

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Basic information

Entry
Database: PDB / ID: 5ijg
TitleCrystal structure of O-acetylhomoserine sulfhydrolase from Brucella melitensis at 2.0 A resolution
ComponentsCys/Met metabolism pyridoxal-phosphate-dependent enzyme
KeywordsHYDROLASE / O-acetylhomoserine / sulfhydrolase / Brucella melitensis / PLP / pyridoxal / Transferase
Function / homology
Function and homology information


cystathionine gamma-synthase / cystathionine gamma-synthase activity (acts on O-phosphohomoserine) / cystathionine gamma-synthase activity / transsulfuration / pyridoxal phosphate binding
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
PYRIDOXAL-5'-PHOSPHATE / Cystathionine gamma-synthase
Similarity search - Component
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Koolikova, V.V. / Kotlov, M.I. / Demidkina, T.V. / Popov, V.O.
CitationJournal: To Be Published
Title: Crystal structure of O-acetylhomoserine sulfhydrolase from Brucella melitensis at 2.0 A resolution
Authors: Boyko, K.M. / Nikolaeva, A.Y. / Koolikova, V. / Demidkina, T.V. / Popov, V.O.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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: Cys/Met metabolism pyridoxal-phosphate-dependent enzyme
B: Cys/Met metabolism pyridoxal-phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1905
Polymers91,6042
Non-polymers5863
Water8,773487
1
A: Cys/Met metabolism pyridoxal-phosphate-dependent enzyme
B: Cys/Met metabolism pyridoxal-phosphate-dependent enzyme
hetero molecules

A: Cys/Met metabolism pyridoxal-phosphate-dependent enzyme
B: Cys/Met metabolism pyridoxal-phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,38110
Polymers183,2084
Non-polymers1,1736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area16440 Å2
ΔGint-97 kcal/mol
Surface area50620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.710, 109.710, 110.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cys/Met metabolism pyridoxal-phosphate-dependent enzyme / Cystathionine gamma-synthase


Mass: 45802.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria)
Gene: BMEI0103, BAWG_0092 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YJI0, cystathionine gamma-synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#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.: 487 / 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: 2.1 Å3/Da / Density % sol: 41.45 % / Description: rod-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM di-ammonium tartrate pH 7.0, 12% PEG3350, 4 mM n-decyl-b-D-maltopyranoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→95.01 Å / Num. obs: 52389 / % possible obs: 99.9 % / Redundancy: 18.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.025 / Rrim(I) all: 0.107 / Net I/σ(I): 19.6 / Num. measured all: 960069 / Scaling rejects: 236
Reflection shellResolution: 2→2.05 Å / Redundancy: 16 % / Rmerge(I) obs: 1.164 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
Aimless0.5.17data scaling
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NMY

3nmy
PDB Unreleased entry


Resolution: 2→95.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.614 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22346 2599 5 %RANDOM
Rwork0.16965 ---
obs0.17246 49750 99.85 %-
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 mean: 41.576 Å2
Baniso -1Baniso -2Baniso -3
1-12.67 Å20 Å20 Å2
2--12.67 Å20 Å2
3----25.33 Å2
Refinement stepCycle: LAST / Resolution: 2→95.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5617 0 6 487 6110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195746
X-RAY DIFFRACTIONr_bond_other_d0.0020.025450
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9657802
X-RAY DIFFRACTIONr_angle_other_deg1.503312491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8255750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15623.787235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27815874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8271536
X-RAY DIFFRACTIONr_chiral_restr0.1450.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026548
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021282
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8754.0243018
X-RAY DIFFRACTIONr_mcbond_other3.8754.0233017
X-RAY DIFFRACTIONr_mcangle_it4.846.0153762
X-RAY DIFFRACTIONr_mcangle_other4.8396.0163763
X-RAY DIFFRACTIONr_scbond_it4.5874.3812728
X-RAY DIFFRACTIONr_scbond_other4.5844.3812728
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3346.4324041
X-RAY DIFFRACTIONr_long_range_B_refined7.67733.2226641
X-RAY DIFFRACTIONr_long_range_B_other7.67833.2256642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 170 -
Rwork0.219 3636 -
obs--99.22 %

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