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- PDB-4qm8: Crystal Structure of a Putative Cysteine Dioxygnase From Bacillus... -

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Basic information

Entry
Database: PDB / ID: 4qm8
TitleCrystal Structure of a Putative Cysteine Dioxygnase From Bacillus subtilis: A Alternative Modeling of 3EQE
ComponentsCysteine dioxygenase
KeywordsOXIDOREDUCTASE / Cupin Fold / Cysteine dioxygnease
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 / Resolution: 2.82 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 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Remark 0THIS ENTRY 4QM8 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3EQESF DETERMINED ...THIS ENTRY 4QM8 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3EQESF DETERMINED BY AUTHORS OF THE PDB ENTRY 3EQE:S.M.VOROBIEV,M.SU,J.SEETHARAMAN,J.BENACH,F.FOROUHAR, G.CLAYTON,B.COOPER,H.WANG,E.L.FOOTE,C.CICCOSANTI,L.MAO, R.XIAO,T.B.ACTON,G.T.MONTELIONE,J.F.HUNT,L.TONG,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)

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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)40,1456
Polymers39,7912
Non-polymers3544
Water1,13563
1
A: Cysteine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0723
Polymers19,8951
Non-polymers1772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cysteine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0723
Polymers19,8951
Non-polymers1772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.830, 65.830, 197.190
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: 19895.480 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: pET21 / 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.: 63 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAUTHORS HAVE DECLARED THAT THE ACTIVE SITE DENSITY AT THIS RESOLUTION IS NOT DEFINITIVE, SO TO BE ...AUTHORS HAVE DECLARED THAT THE ACTIVE SITE DENSITY AT THIS RESOLUTION IS NOT DEFINITIVE, SO TO BE CONSERVATIVE OUR FINAL REFINEMENT AND DEPOSITION USED THE MINIMAL INTERPRETATION OF THREE WATERS IN THE ACTIVE SITE. TO ENSURE THAT USERS OF THE COORDINATES ARE AWARE THAT CYS MAY BE BOUND, WE ALSO INCLUDE IN THE FILE, WITH OCCUPANCY SET TO ZERO, THE COORDINATES AND B-FACTORS WE OBTAINED BY REFINING A BOUND CYS AT 100% OCCUPANCY

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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: 2.68 Å3/Da / Density % sol: 54.18 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3EQE.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
SHELXDEphasing
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementResolution: 2.82→46.51 Å / SU ML: 0.39 / σ(F): 1.98 / Phase error: 26.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 465 4.19 %
Rwork0.177 --
obs0.18 11097 99.6 %
all-19930 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 16 63 2431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112416
X-RAY DIFFRACTIONf_angle_d1.1743273
X-RAY DIFFRACTIONf_dihedral_angle_d14.395891
X-RAY DIFFRACTIONf_chiral_restr0.042371
X-RAY DIFFRACTIONf_plane_restr0.005427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8203-3.22830.3031470.22053408X-RAY DIFFRACTION99
3.2283-4.06690.2771520.19823498X-RAY DIFFRACTION100
4.0669-46.51970.23181660.15623726X-RAY DIFFRACTION100
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.21443.0178-0.40067.1499-0.1943.75450.0274-0.01360.1388-0.09070.0361-0.46680.00370.168-0.02670.58860.01520.04160.3245-0.00650.3469-39.7633-19.2955141.5321
27.03650.9998-0.33363.9853-1.83593.9340.23180.1474-0.4566-0.0828-0.12070.04590.58310.005-0.12910.688-0.0340.05150.372-0.07350.4085-39.10921.9788121.6725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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