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- PDB-7md9: Crystal structure of Staphylococcus aureus cystathionine gamma ly... -

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Basic information

Entry
Database: PDB / ID: 7md9
TitleCrystal structure of Staphylococcus aureus cystathionine gamma lyase holoenzyme Y103A mutant
ComponentsBifunctional cystathionine gamma-lyase/homocysteine desulfhydrase
KeywordsLYASE / Amino-acid biosynthesis / Cysteine biosynthesis / Hydrogen sulfide production / PLP dependent enzyme
Function / homology
Function and homology information


cystathionine beta-lyase / cystathionine gamma-synthase / cystathionine gamma-lyase / cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / pyridoxal phosphate binding / identical protein binding / cytoplasm
Similarity search - Function
: / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNuthanakanti, A. / Serganov, A. / Kaushik, A.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)PR171734 United States
Department of Defense (DOD, United States)PR171734P1 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2021
Title: Inhibitors of bacterial H 2 S biogenesis targeting antibiotic resistance and tolerance.
Authors: Shatalin, K. / Nuthanakanti, A. / Kaushik, A. / Shishov, D. / Peselis, A. / Shamovsky, I. / Pani, B. / Lechpammer, M. / Vasilyev, N. / Shatalina, E. / Rebatchouk, D. / Mironov, A. / ...Authors: Shatalin, K. / Nuthanakanti, A. / Kaushik, A. / Shishov, D. / Peselis, A. / Shamovsky, I. / Pani, B. / Lechpammer, M. / Vasilyev, N. / Shatalina, E. / Rebatchouk, D. / Mironov, A. / Fedichev, P. / Serganov, A. / Nudler, E.
History
DepositionApr 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4643
Polymers41,4181
Non-polymers462
Water7,548419
1
H: Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase
hetero molecules

H: Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase
hetero molecules

H: Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase
hetero molecules

H: Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,85412
Polymers165,6704
Non-polymers1848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area21520 Å2
ΔGint-170 kcal/mol
Surface area45370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.892, 104.892, 286.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11H-509-

HOH

21H-766-

HOH

31H-847-

HOH

41H-917-

HOH

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Components

#1: Protein Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase / Cystathionine beta-lyase / Cystathionine gamma-lyase / Cystathionine gamma-synthase


Mass: 41417.617 Da / Num. of mol.: 1 / Mutation: Y103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mccB / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: X5E0F1, cystathionine gamma-lyase, cystathionine beta-lyase, cystathionine gamma-synthase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.76 Å3/Da / Density % sol: 74.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium, pH 7.5, 1.3 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.91956 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91956 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 73637 / % possible obs: 99.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 23.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.035 / Net I/σ(I): 219.2
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 12.4 / Num. unique obs: 4871 / CC1/2: 0.851 / Rpim(I) all: 0.035 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
autoPROC1.14_3260data processing
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IXZ

4ixz


Resolution: 1.8→29.86 Å / SU ML: 0.1761 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.6575 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2051 3805 2.72 %
Rwork0.1845 135986 -
obs0.1851 73637 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 2 419 3320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662978
X-RAY DIFFRACTIONf_angle_d0.86824058
X-RAY DIFFRACTIONf_chiral_restr0.0561489
X-RAY DIFFRACTIONf_plane_restr0.0057520
X-RAY DIFFRACTIONf_dihedral_angle_d3.78752423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.36041310.30654817X-RAY DIFFRACTION94.73
1.82-1.850.32951460.2935076X-RAY DIFFRACTION99.66
1.85-1.870.31691430.27435145X-RAY DIFFRACTION99.6
1.87-1.90.27021430.26375042X-RAY DIFFRACTION99.39
1.9-1.930.22991400.2565051X-RAY DIFFRACTION99.35
1.93-1.960.26621400.2385100X-RAY DIFFRACTION99.68
1.96-1.990.2091430.22395060X-RAY DIFFRACTION99.71
1.99-2.020.2681420.22795080X-RAY DIFFRACTION99.71
2.02-2.060.25921400.21855093X-RAY DIFFRACTION99.89
2.06-2.10.22181400.21195093X-RAY DIFFRACTION99.89
2.1-2.140.231430.20595059X-RAY DIFFRACTION99.87
2.14-2.190.19861450.19935121X-RAY DIFFRACTION99.75
2.19-2.240.20251430.1915066X-RAY DIFFRACTION99.66
2.24-2.30.21531390.19495069X-RAY DIFFRACTION99.69
2.3-2.360.22041430.25069X-RAY DIFFRACTION99.89
2.36-2.430.22321420.21215110X-RAY DIFFRACTION99.7
2.43-2.510.2631410.20765057X-RAY DIFFRACTION99.65
2.51-2.60.22741480.20725114X-RAY DIFFRACTION99.73
2.6-2.70.25691420.19975101X-RAY DIFFRACTION99.87
2.7-2.820.22671450.19645053X-RAY DIFFRACTION99.73
2.82-2.970.20821420.19555084X-RAY DIFFRACTION99.81
2.97-3.160.22471390.18675101X-RAY DIFFRACTION99.6
3.16-3.40.20161400.16885027X-RAY DIFFRACTION99.37
3.4-3.740.14881420.1584973X-RAY DIFFRACTION97.1
3.74-4.280.1231230.13454752X-RAY DIFFRACTION93.27
4.28-5.390.16331340.13634625X-RAY DIFFRACTION90.63
5.39-29.860.20081460.15875048X-RAY DIFFRACTION98.88

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