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- PDB-7yoh: Crystal structure of I88L single mutant of O-acetylserine sulfhyd... -

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Basic information

Entry
Database: PDB / ID: 7yoh
TitleCrystal structure of I88L single mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Haemophilus influenzae at 2.5 A
Components
  • Cysteine synthase
  • Peptide from Serine acetyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / I88L / single mutant / O-acetylserine sulfhydrylase / Haemophilus influenzae / high-affinity inhibitory peptide from serine acetyltransferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm / cytosol
Similarity search - Function
Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site ...Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
Serine acetyltransferase / Cysteine synthase
Similarity search - Component
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKumar, N. / Rahisuddin, R. / Saini, N. / Singh, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5236/MED/29/504/2012 India
CitationJournal: To Be Published
Title: Crystal structure of I88L single mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella ...Title: Crystal structure of I88L single mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella typhimurium at 2.14 A
Authors: Kumar, N. / Rahisuddin, R. / Saini, N. / Singh, A.K.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine synthase
P: Peptide from Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4633
Polymers34,4272
Non-polymers351
Water30617
1
A: Cysteine synthase
P: Peptide from Serine acetyltransferase
hetero molecules

A: Cysteine synthase
P: Peptide from Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9266
Polymers68,8554
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area6180 Å2
ΔGint-43 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.750, 112.750, 44.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Cysteine synthase / CSase / O-acetylserine (thiol)-lyase / OAS-TL / O-acetylserine sulfhydrylase / O-acetyl-L-serine sulfhydrylase


Mass: 33651.465 Da / Num. of mol.: 1 / Mutation: I88L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Gene: cysK, HI_1103 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P45040, cysteine synthase
#2: Protein/peptide Peptide from Serine acetyltransferase / SAT


Mass: 775.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus influenzae Rd KW20 (bacteria) / References: UniProt: P43886
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 1.3M Sodium citrate / PH range: 7.3-7.9

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 11, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.5→41.36 Å / Num. obs: 9865 / % possible obs: 99.54 % / Redundancy: 15.5 % / Biso Wilson estimate: 35.63 Å2 / CC1/2: 0.886 / CC star: 0.969 / Net I/σ(I): 126.45
Reflection shellResolution: 2.5→2.581 Å / Rmerge(I) obs: 0.7904 / Num. unique obs: 970 / CC1/2: 0.835 / % possible all: 99.69

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y7L

1y7l


Resolution: 2.5→41.36 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.863 / SU B: 16.799 / SU ML: 0.368 / Cross valid method: FREE R-VALUE / ESU R Free: 0.374
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2949 515 5.24 %
Rwork0.2435 9313 -
all0.246 --
obs-9828 99.585 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.395 Å2
Baniso -1Baniso -2Baniso -3
1--4.548 Å20 Å20 Å2
2---4.548 Å20 Å2
3---9.096 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 1 17 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122318
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6313149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6825313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80722.6694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36315371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.741513
X-RAY DIFFRACTIONr_chiral_restr0.1160.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021722
X-RAY DIFFRACTIONr_nbd_refined0.2360.21074
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.285
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2940.25
X-RAY DIFFRACTIONr_mcbond_it3.1774.021258
X-RAY DIFFRACTIONr_mcangle_it5.0436.0141569
X-RAY DIFFRACTIONr_scbond_it3.1753.8451060
X-RAY DIFFRACTIONr_scangle_it4.7995.7311580
X-RAY DIFFRACTIONr_lrange_it8.98273.4049816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.329490.318662X-RAY DIFFRACTION99.7195
2.565-2.6350.365330.285661X-RAY DIFFRACTION97.4719
2.635-2.7110.384490.266605X-RAY DIFFRACTION100
2.711-2.7950.328460.25634X-RAY DIFFRACTION98.2659
2.795-2.8860.33310.21619X-RAY DIFFRACTION100
2.886-2.9870.225250.206583X-RAY DIFFRACTION100
2.987-3.10.276250.209585X-RAY DIFFRACTION100
3.1-3.2260.232290.216550X-RAY DIFFRACTION100
3.226-3.370.357210.236540X-RAY DIFFRACTION100
3.37-3.5340.321270.266498X-RAY DIFFRACTION99.6205
3.534-3.7250.305340.295481X-RAY DIFFRACTION99.8062
3.725-3.950.345290.275455X-RAY DIFFRACTION99.384
3.95-4.2220.256110.245436X-RAY DIFFRACTION99.7768
4.222-4.5590.255290.209395X-RAY DIFFRACTION100
4.559-4.9930.253170.197385X-RAY DIFFRACTION100
4.993-5.5790.346300.222328X-RAY DIFFRACTION100
5.579-6.4370.364100.244302X-RAY DIFFRACTION100
6.437-7.8710.43140.241265X-RAY DIFFRACTION100
7.871-11.0770.115120.158206X-RAY DIFFRACTION100
11.077-41.360.13940.173123X-RAY DIFFRACTION99.2188

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