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

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Basic information

Entry
Database: PDB / ID: 7yoi
TitleCrystal 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
Components
  • Cysteine synthase
  • peptide from serine acetyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Transferase / single mutant / O-acetyl-L-serine sulfhydrylase / Haemophilus influenzae / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 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
B: peptide from serine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)34,5522
Polymers34,5522
Non-polymers00
Water99155
1
A: Cysteine synthase
B: peptide from serine acetyltransferase

A: Cysteine synthase
B: peptide from serine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)69,1054
Polymers69,1054
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area5900 Å2
ΔGint-34 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.970, 112.970, 44.520
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


Mass: 900.930 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
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: 100 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 10, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.14→41.454 Å / Num. obs: 15711 / % possible obs: 97.64 % / Redundancy: 14.6 % / CC1/2: 0.873 / CC star: 0.965 / Net I/σ(I): 73.27
Reflection shellResolution: 2.14→2.217 Å / Num. unique obs: 1218 / CC1/2: 0.77 / % possible all: 76.8

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Processing

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

1y7l


Resolution: 2.14→41.454 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.74 / SU ML: 0.226 / Cross valid method: FREE R-VALUE / ESU R: 0.324 / ESU R Free: 0.239
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2714 767 4.993 %
Rwork0.2198 14594 -
all0.222 --
obs-15361 97.636 %
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: 30.896 Å2
Baniso -1Baniso -2Baniso -3
1--3.947 Å20 Å20 Å2
2---3.947 Å20 Å2
3---7.894 Å2
Refinement stepCycle: LAST / Resolution: 2.14→41.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 0 55 2349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122327
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.6323154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6565309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4222.63295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27915392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9591513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021705
X-RAY DIFFRACTIONr_nbd_refined0.2280.21031
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21595
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.296
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.215
X-RAY DIFFRACTIONr_mcbond_it1.9042.9931242
X-RAY DIFFRACTIONr_mcangle_it2.9774.4821549
X-RAY DIFFRACTIONr_scbond_it2.3343.2091085
X-RAY DIFFRACTIONr_scangle_it3.5734.6821605
X-RAY DIFFRACTIONr_lrange_it6.87455.8349749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.1960.321310.307751X-RAY DIFFRACTION68
2.196-2.2560.248740.2631064X-RAY DIFFRACTION100
2.256-2.3210.312350.2351052X-RAY DIFFRACTION100
2.321-2.3930.265430.2261013X-RAY DIFFRACTION100
2.393-2.4710.291610.224974X-RAY DIFFRACTION100
2.471-2.5580.376590.231914X-RAY DIFFRACTION100
2.558-2.6540.296550.232918X-RAY DIFFRACTION100
2.654-2.7620.344440.215903X-RAY DIFFRACTION100
2.762-2.8850.213490.196830X-RAY DIFFRACTION100
2.885-3.0260.283530.214780X-RAY DIFFRACTION100
3.026-3.1890.262300.217812X-RAY DIFFRACTION100
3.189-3.3820.295450.22701X-RAY DIFFRACTION100
3.382-3.6150.24350.215698X-RAY DIFFRACTION100
3.615-3.9040.275340.213646X-RAY DIFFRACTION100
3.904-4.2760.278210.207591X-RAY DIFFRACTION100
4.276-4.7790.255320.194537X-RAY DIFFRACTION100
4.779-5.5150.325160.234499X-RAY DIFFRACTION100
5.515-6.7460.233180.254407X-RAY DIFFRACTION100
6.746-9.5070.206220.176318X-RAY DIFFRACTION100
9.507-41.4540.177100.183186X-RAY DIFFRACTION99.4924

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