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- PDB-3teo: APO Form of carbon disulfide hydrolase (selenomethionine form) -

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Basic information

Entry
Database: PDB / ID: 3teo
TitleAPO Form of carbon disulfide hydrolase (selenomethionine form)
ComponentsCarbon disulfide hydrolase
KeywordsHYDROLASE / BETA CARBONIC ANHYDRASE FOLD / CARBON DISULFIDE HYDROLYSIS
Function / homology
Function and homology information


carbon disulfide hydrolase / hydrogen sulfide biosynthetic process / carbonate dehydratase activity / hydrolase activity / zinc ion binding / identical protein binding
Similarity search - Function
Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PE3 / Carbon disulfide hydrolase
Similarity search - Component
Biological speciesAcidianus sp. A1-3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsSmeulders, M.J. / Barends, T.R.M.B. / Pol, A. / Scherer, A. / Zandvoort, M.H. / Udvarhelyi, A. / Khadem, A. / Menzel, A. / Hermans, J. / Shoeman, R.L. ...Smeulders, M.J. / Barends, T.R.M.B. / Pol, A. / Scherer, A. / Zandvoort, M.H. / Udvarhelyi, A. / Khadem, A. / Menzel, A. / Hermans, J. / Shoeman, R.L. / Wessels, H.J.C.T. / van den Heuvel, L.P. / Russ, L. / Schlichting, I. / Jetten, M.S.M. / Op den Camp, H.J.M.
CitationJournal: Nature / Year: 2011
Title: Evolution of a new enzyme for carbon disulphide conversion by an acidothermophilic archaeon.
Authors: Smeulders, M.J. / Barends, T.R. / Pol, A. / Scherer, A. / Zandvoort, M.H. / Udvarhelyi, A. / Khadem, A.F. / Menzel, A. / Hermans, J. / Shoeman, R.L. / Wessels, H.J. / van den Heuvel, L.P. / ...Authors: Smeulders, M.J. / Barends, T.R. / Pol, A. / Scherer, A. / Zandvoort, M.H. / Udvarhelyi, A. / Khadem, A.F. / Menzel, A. / Hermans, J. / Shoeman, R.L. / Wessels, H.J. / van den Heuvel, L.P. / Russ, L. / Schlichting, I. / Jetten, M.S. / Op den Camp, H.J.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon disulfide hydrolase
B: Carbon disulfide hydrolase
C: Carbon disulfide hydrolase
D: Carbon disulfide hydrolase
E: Carbon disulfide hydrolase
F: Carbon disulfide hydrolase
G: Carbon disulfide hydrolase
H: Carbon disulfide hydrolase
I: Carbon disulfide hydrolase
J: Carbon disulfide hydrolase
K: Carbon disulfide hydrolase
L: Carbon disulfide hydrolase
M: Carbon disulfide hydrolase
N: Carbon disulfide hydrolase
O: Carbon disulfide hydrolase
P: Carbon disulfide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,81140
Polymers380,76216
Non-polymers2,04924
Water15,133840
1
A: Carbon disulfide hydrolase
B: Carbon disulfide hydrolase
C: Carbon disulfide hydrolase
D: Carbon disulfide hydrolase
E: Carbon disulfide hydrolase
F: Carbon disulfide hydrolase
G: Carbon disulfide hydrolase
H: Carbon disulfide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,40620
Polymers190,3818
Non-polymers1,02512
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51230 Å2
ΔGint-444 kcal/mol
Surface area57760 Å2
MethodPISA
2
I: Carbon disulfide hydrolase
J: Carbon disulfide hydrolase
K: Carbon disulfide hydrolase
L: Carbon disulfide hydrolase
M: Carbon disulfide hydrolase
N: Carbon disulfide hydrolase
O: Carbon disulfide hydrolase
P: Carbon disulfide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,40620
Polymers190,3818
Non-polymers1,02512
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50120 Å2
ΔGint-442 kcal/mol
Surface area56940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.180, 165.510, 115.940
Angle α, β, γ (deg.)90.00, 91.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Carbon disulfide hydrolase


Mass: 23797.604 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: A synthetic insert was used, codon-optimized for E. coli
Source: (gene. exp.) Acidianus sp. A1-3 (archaea) / Strain: A1-3 / Gene: cs2 hydrolase / Plasmid: pET24bcs2hydsynth / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0WXL9*PLUS
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O15
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 25% PEG 1000, 200 mM LiCl 50 mM phosphate/citrate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98089 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2008
Details: LN2 cooled fixed-exit Si(111) monochromator, Dynamically bendable mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98089 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 154688 / Num. obs: 154688 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.2 / Num. unique all: 19000 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.873 / SU B: 8.979 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL MODEL OBTAINED WITH SELENIUM-SAD ON THE SAME CRYSTAL FORM
RfactorNum. reflection% reflectionSelection details
Rfree0.27091 9136 5.6 %THIN RESOLUTION SHELLS DUE TO CRYSTALLOGRAPHIC SYMMETRY
Rwork0.22386 ---
all0.22648 154688 --
obs0.22648 154688 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.246 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.17 Å2
2--1.04 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26297 0 84 840 27221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02226917
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218863
X-RAY DIFFRACTIONr_angle_refined_deg0.8411.96636368
X-RAY DIFFRACTIONr_angle_other_deg0.7673.00145706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.97753215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47823.4571296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.652154895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.02715224
X-RAY DIFFRACTIONr_chiral_restr0.050.24046
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02129385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025551
X-RAY DIFFRACTIONr_mcbond_it0.2321.516091
X-RAY DIFFRACTIONr_mcbond_other0.0251.56494
X-RAY DIFFRACTIONr_mcangle_it0.448226279
X-RAY DIFFRACTIONr_scbond_it0.581310826
X-RAY DIFFRACTIONr_scangle_it0.9734.510089
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.289 12249 -
Rfree-0 -
obs--99.16 %

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