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- PDB-4qm9: Crystal Structure of a Putative Cysteine Dioxygenase From Bacillu... -

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Basic information

Entry
Database: PDB / ID: 4qm9
TitleCrystal Structure of a Putative Cysteine Dioxygenase From Bacillus subtilis with Cys-bound
ComponentsCysteine dioxygenase
KeywordsOXIDOREDUCTASE / Cupin fold / catalyzes oxidation of cysteine to cysteine sulfinate
Function / homology
Function and homology information


cysteine dioxygenase / cysteine dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferrous iron binding
Similarity search - Function
Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CYSTEINE / : / Cysteine dioxygenase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHartman, S.H. / Driggers, C.M. / Karplus, P.A.
CitationJournal: Protein Sci. / Year: 2015
Title: Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs.
Authors: Driggers, C.M. / Hartman, S.J. / Karplus, P.A.
History
DepositionJun 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Mar 4, 2020Group: Database references / Structure summary / Category: struct / struct_ref_seq_dif / Item: _struct.title / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Cysteine dioxygenase
B: Cysteine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5826
Polymers39,2282
Non-polymers3544
Water1,20767
1
A: Cysteine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7913
Polymers19,6141
Non-polymers1772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cysteine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7913
Polymers19,6141
Non-polymers1772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.530, 65.530, 199.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Cysteine dioxygenase / CDO


Mass: 19614.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU31140, cdoA, Cysteine Dioxygenase, yubC / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21-DE3 / References: UniProt: O32085, cysteine dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Purified enzyme was concentrated to 10 mg/mL and 4 uL was mixed with 4 uL of a reservoir containing 18% (w/v) PEG 4000, 0.1 M potassium acetate, 0.05 M MES, pH 6.0, VAPOR DIFFUSION, HANGING ...Details: Purified enzyme was concentrated to 10 mg/mL and 4 uL was mixed with 4 uL of a reservoir containing 18% (w/v) PEG 4000, 0.1 M potassium acetate, 0.05 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2013
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 20271 / Num. obs: 20271 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.4 % / Rmerge(I) obs: 0.186 / Rsym value: 0.038 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.7 % / Rmerge(I) obs: 2.892 / Mean I/σ(I) obs: 1 / Num. unique all: 1939 / Rsym value: 0.767 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eqe

3eqe


Resolution: 2.3→46.66 Å / SU ML: 0.41 / σ(F): 1.33 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 849 4.2 %same as 3eqe, random 5 % beyond 2.82 Ang
Rwork0.1902 ---
obs0.193 20197 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 16 67 2432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122427
X-RAY DIFFRACTIONf_angle_d1.063285
X-RAY DIFFRACTIONf_dihedral_angle_d14.272893
X-RAY DIFFRACTIONf_chiral_restr0.039373
X-RAY DIFFRACTIONf_plane_restr0.005428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44410.39721450.32683147X-RAY DIFFRACTION100
2.4441-2.63280.34731320.2733144X-RAY DIFFRACTION100
2.6328-2.89770.28021360.24653170X-RAY DIFFRACTION100
2.8977-3.3170.29381390.21293196X-RAY DIFFRACTION100
3.317-4.17860.27281460.18283242X-RAY DIFFRACTION100
4.1786-46.66930.21371510.14943449X-RAY DIFFRACTION100
Refinement TLS params.

S33: -0.0256 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4491.9202-0.69136.3275-0.72283.10950.0524-0.0162-0.07250.04-0.011-0.36030.15520.21830.53330.01650.01490.2695-0.02860.315-39.7783-19.1826143.0918
25.84040.7922-0.22344.9847-1.28924.07790.08060.2746-0.3025-0.3123-0.0497-0.05440.52610.13380.5465-0.020.04460.3242-0.04780.3337-39.10831.5766123.0224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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