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- PDB-9iqh: Crystal structure of sulfhydrylase -

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Basic information

Entry
Database: PDB / ID: 9iqh
TitleCrystal structure of sulfhydrylase
ComponentsO-succinylhomoserine sulfhydrylase
KeywordsLYASE / Biosynthesis / CdS quantum dots / SQR enzyme / Extracellular polyphosphate / Cadmium waste recycle
Function / homology
Function and homology information


homocysteine biosynthetic process / carbon-sulfur lyase activity / 'de novo' L-methionine biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
O-succinylhomoserine sulfhydrylase / : / 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
PYRIDOXAL-5'-PHOSPHATE / O-succinylhomoserine sulfhydrylase
Similarity search - Component
Biological speciesAcidithiobacillus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLi, X.J. / Chen, L.X. / Lin, J.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271525 China
CitationJournal: Rsc Chem Biol / Year: 2025
Title: A one-step route for the conversion of Cd waste into CdS quantum dots by Acidithiobacillus sp. via unique biosynthesis pathways.
Authors: Li, X.J. / Wang, T.Q. / Qi, L. / Li, F.W. / Xia, Y.Z. / Zhang, C.J. / Chen, L.X. / Lin, J.Q.
History
DepositionJul 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-succinylhomoserine sulfhydrylase
B: O-succinylhomoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8214
Polymers87,3272
Non-polymers4942
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-39 kcal/mol
Surface area29140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.732, 82.799, 77.496
Angle α, β, γ (deg.)90.000, 110.320, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

21B-663-

HOH

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Components

#1: Protein O-succinylhomoserine sulfhydrylase / OSH sulfhydrylase / OSHS sulfhydrylase


Mass: 43663.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus (bacteria) / Gene: metZ, DN052_15485 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A2W1K030, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) polyethylene glycol 3350 and 200 mM magnesium sulfate heptahydrate at pH 5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5405 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5405 Å / Relative weight: 1
ReflectionResolution: 2.27→23.14 Å / Num. obs: 34171 / % possible obs: 95.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 23.74 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.8
Reflection shellResolution: 2.27→2.351 Å / Num. unique obs: 2285 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→23.14 Å / SU ML: 0.2492 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2148 1734 5.09 %
Rwork0.1623 32360 -
obs0.165 34094 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.44 Å2
Refinement stepCycle: LAST / Resolution: 2.27→23.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5989 0 30 489 6508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00396216
X-RAY DIFFRACTIONf_angle_d0.67318469
X-RAY DIFFRACTIONf_chiral_restr0.0439951
X-RAY DIFFRACTIONf_plane_restr0.00691120
X-RAY DIFFRACTIONf_dihedral_angle_d13.99182243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.340.2749920.19641942X-RAY DIFFRACTION68.3
2.34-2.410.27631400.19022278X-RAY DIFFRACTION81.28
2.41-2.50.3461390.20052642X-RAY DIFFRACTION93.23
2.5-2.60.26851220.18342813X-RAY DIFFRACTION99.22
2.6-2.720.22821510.18392804X-RAY DIFFRACTION99.56
2.72-2.860.28421720.19622829X-RAY DIFFRACTION99.54
2.86-3.040.22541430.18152801X-RAY DIFFRACTION99.83
3.04-3.270.24931570.18052835X-RAY DIFFRACTION99.8
3.27-3.60.21981420.16192826X-RAY DIFFRACTION99.46
3.6-4.120.1891610.1442839X-RAY DIFFRACTION99.73
4.12-5.180.15651520.12442872X-RAY DIFFRACTION99.7
5.18-23.140.15121630.142879X-RAY DIFFRACTION99.77

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