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- PDB-4qma: Crystal Structure of a Putative Cysteine Dioxygnase From Ralstoni... -

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Basic information

Entry
Database: PDB / ID: 4qma
TitleCrystal Structure of a Putative Cysteine Dioxygnase From Ralstonia eutropha: An Alternative Modeling of 2GM6 from JCSG Target 361076
ComponentsCysteine dioxygenase type I
KeywordsOXIDOREDUCTASE / PUTATIVE "Gln-type" CYSTEINE DIOXYGENASE / JOINT CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / iron ion binding
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Jelly Rolls / Up-down Bundle / Sandwich ...ATP synthase delta/epsilon subunit, C-terminal domain / Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / OXYGEN MOLECULE / Cysteine dioxygenase type I
Similarity search - Component
Biological speciesRalstonia eutropha JMP134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsHartman, S.H. / Driggers, C.M. / Karplus, P.A. / Joint Center for Structural Genomics (JCSG)
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
SupersessionNov 26, 2014ID: 2GM6
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Apr 29, 2015Group: Structure summary
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_ref_seq_dif / 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.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine dioxygenase type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,84614
Polymers23,0071
Non-polymers83913
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.007, 57.007, 216.683
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-525-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cysteine dioxygenase type I


Mass: 23007.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha JMP134 (bacteria) / Strain: JMP 134 / LMG 1197 / Gene: Reut_B5045, YP_299237.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46R41

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Non-polymers , 5 types, 222 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.4M (NH4)2SO4, 0.1M TRIS, PH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211
SYNCHROTRONSSRL BL9-220.97925, 0.91837, 0.97882
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 13, 2006
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979251
30.918371
40.978821
ReflectionResolution: 1.65→45 Å / Num. all: 44377 / Num. obs: 44377 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21 % / Rmerge(I) obs: 0.113 / Rsym value: 0.025 / Net I/σ(I): 14.1
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 16.5 % / Rmerge(I) obs: 0.5335 / Mean I/σ(I) obs: 0.6 / Num. unique all: 2185 / Rsym value: 1.302 / % 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
RefinementStarting model: Fourier Synthesis based on 2GM6

2gm6
PDB Unreleased entry


Resolution: 1.65→44.748 Å / SU ML: 0.21 / σ(F): 0.1 / Phase error: 26.22 / Stereochemistry target values: ML
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. FE MODELED BASED ON ANOMALOUS DIFFERENCE MAP, GEOMETRY, PROTEIN ENVIRONMENT, AND EXCITATION SCAN. 4. SO4 AND EDO MODELED BASED ON CYRSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2217 5 %Same as ReCDO, random 5% to 1.65 Ang
Rwork0.1741 ---
obs0.1754 42041 99.87 %-
all-82002 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→44.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 49 209 1757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141637
X-RAY DIFFRACTIONf_angle_d1.2132213
X-RAY DIFFRACTIONf_dihedral_angle_d13.641602
X-RAY DIFFRACTIONf_chiral_restr0.052227
X-RAY DIFFRACTIONf_plane_restr0.006293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66940.42011270.36272697X-RAY DIFFRACTION100
1.6694-1.68980.35631210.36022727X-RAY DIFFRACTION100
1.6898-1.71120.34651270.36282683X-RAY DIFFRACTION100
1.7112-1.73370.40531510.33962690X-RAY DIFFRACTION100
1.7337-1.75740.33041480.32852676X-RAY DIFFRACTION100
1.7574-1.78250.32381310.32492714X-RAY DIFFRACTION100
1.7825-1.80910.29091370.31382648X-RAY DIFFRACTION100
1.8091-1.83740.2871310.31442757X-RAY DIFFRACTION100
1.8374-1.86750.3041270.28872632X-RAY DIFFRACTION100
1.8675-1.89970.32921660.27552694X-RAY DIFFRACTION100
1.8997-1.93430.24251560.2452622X-RAY DIFFRACTION100
1.9343-1.97150.27541390.2382716X-RAY DIFFRACTION100
1.9715-2.01170.26121430.22862669X-RAY DIFFRACTION100
2.0117-2.05550.23611370.21592698X-RAY DIFFRACTION100
2.0555-2.10330.26211170.21982720X-RAY DIFFRACTION100
2.1033-2.15590.21931570.19792646X-RAY DIFFRACTION100
2.1559-2.21420.22151650.1792669X-RAY DIFFRACTION100
2.2142-2.27930.17481580.17062709X-RAY DIFFRACTION100
2.2793-2.35290.22551610.16452648X-RAY DIFFRACTION100
2.3529-2.4370.19111400.16582684X-RAY DIFFRACTION100
2.437-2.53450.18191290.1582687X-RAY DIFFRACTION100
2.5345-2.64990.19661360.15392689X-RAY DIFFRACTION100
2.6499-2.78960.20391460.1622701X-RAY DIFFRACTION100
2.7896-2.96430.22961630.17612693X-RAY DIFFRACTION100
2.9643-3.19310.1791450.17252662X-RAY DIFFRACTION100
3.1931-3.51440.21291410.15962689X-RAY DIFFRACTION100
3.5144-4.02260.15571340.14862692X-RAY DIFFRACTION100
4.0226-5.0670.1351340.12242699X-RAY DIFFRACTION100
5.067-44.76460.19621360.16582688X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 36.5971 Å / Origin y: 21.0005 Å / Origin z: 37.2235 Å
111213212223313233
T0.3632 Å20.0757 Å2-0.0615 Å2-0.2898 Å2-0.0215 Å2--0.269 Å2
L0.9058 °20.4243 °2-0.4857 °2-1.4719 °2-0.638 °2--3.055 °2
S-0.1417 Å °0.0201 Å °0.1114 Å °-0.196 Å °0.0637 Å °0.1759 Å °-0.203 Å °-0.3025 Å °0.0594 Å °
Refinement TLS groupSelection details: chain 'A' and resid 11 through 202

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