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- PDB-7mcq: Crystal structure of Staphylococcus aureus Cystathionine gamma ly... -

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Basic information

Entry
Database: PDB / ID: 7mcq
TitleCrystal structure of Staphylococcus aureus Cystathionine gamma lyase, AOAA-bound enzyme in dimeric form
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 / methionine biosynthetic process / 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 / 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 ...: / 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
4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE / Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 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 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,66812
Polymers82,5632
Non-polymers1,10510
Water1,56787
1
A: Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase
H: Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)167,33624
Polymers165,1264
Non-polymers2,21020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area25660 Å2
ΔGint-172 kcal/mol
Surface area43520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.354, 104.354, 287.362
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERHISHIS(chain 'A' and (resid 1 through 284 or resid 286...AA1 - 2841 - 284
12VALVALLEULEU(chain 'A' and (resid 1 through 284 or resid 286...AA286 - 380286 - 380
13IK2IK2IK2IK2(chain 'A' and (resid 1 through 284 or resid 286...AC401
21SERSERHISHIS(chain 'H' and (resid 1 through 66 or (resid 67...HB1 - 2841 - 284
22VALVALLEULEU(chain 'H' and (resid 1 through 66 or (resid 67...HB286 - 380286 - 380
23IK2IK2IK2IK2(chain 'H' and (resid 1 through 66 or (resid 67...HH401

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Components

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


Mass: 41281.598 Da / Num. of mol.: 2
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-IK2 / 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.74 Å3/Da / Density % sol: 74.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris-HCl, pH 7.6, 1.4 M Tri sodium Citrate, 10 mM AOAA

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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 EIGER2 X 16M / Detector: PIXEL / Date: Nov 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91956 Å / Relative weight: 1
ReflectionResolution: 2.845→30 Å / Num. obs: 38274 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 45.56 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.061 / Net I/σ(I): 2.6
Reflection shellResolution: 2.845→2.9 Å / Rmerge(I) obs: 1.056 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1874 / CC1/2: 0.845 / Rpim(I) all: 0.316 / % possible all: 100

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Processing

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

4ixz


Resolution: 2.84→29.76 Å / SU ML: 0.3168 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6094 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.209 3689 5.2 %
Rwork0.1771 67224 -
obs0.1788 38274 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.27 Å2
Refinement stepCycle: LAST / Resolution: 2.84→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 66 87 5937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785955
X-RAY DIFFRACTIONf_angle_d1.05658096
X-RAY DIFFRACTIONf_chiral_restr0.059972
X-RAY DIFFRACTIONf_plane_restr0.00671034
X-RAY DIFFRACTIONf_dihedral_angle_d18.41932144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.880.35631370.30922536X-RAY DIFFRACTION98.16
2.88-2.920.30141380.28282606X-RAY DIFFRACTION99.93
2.92-2.960.29541440.27642614X-RAY DIFFRACTION99.78
2.96-3.010.3131380.25832560X-RAY DIFFRACTION99.93
3.01-3.050.29981470.24892610X-RAY DIFFRACTION99.93
3.05-3.10.26441420.2372537X-RAY DIFFRACTION99.89
3.1-3.160.28211450.22552624X-RAY DIFFRACTION100
3.16-3.220.24611350.22082581X-RAY DIFFRACTION99.85
3.22-3.280.26131480.21422589X-RAY DIFFRACTION99.71
3.28-3.340.23321450.20432579X-RAY DIFFRACTION100
3.34-3.420.2321380.22580X-RAY DIFFRACTION99.89
3.42-3.50.19841460.16932608X-RAY DIFFRACTION99.89
3.5-3.580.20471480.1692603X-RAY DIFFRACTION99.96
3.58-3.680.20231340.16112561X-RAY DIFFRACTION99.93
3.68-3.790.21561450.14992598X-RAY DIFFRACTION99.71
3.79-3.910.20371380.14122587X-RAY DIFFRACTION99.82
3.91-4.050.15871420.13292581X-RAY DIFFRACTION99.74
4.05-4.210.16291430.13732602X-RAY DIFFRACTION99.78
4.21-4.40.14051440.12942576X-RAY DIFFRACTION99.82
4.4-4.630.1531460.12022597X-RAY DIFFRACTION99.93
4.63-4.920.13611390.1272604X-RAY DIFFRACTION99.82
4.92-5.30.16661450.14132588X-RAY DIFFRACTION99.82
5.3-5.830.20911380.15692573X-RAY DIFFRACTION99.56
5.83-6.670.21611470.19682581X-RAY DIFFRACTION99.82
6.67-8.370.191420.16962594X-RAY DIFFRACTION99.93
8.37-29.760.24151350.20922555X-RAY DIFFRACTION97.89

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