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- PDB-3lm4: Crystal Structure of 2,3-Dihydroxy Biphenyl dioxygenase from Rhod... -

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Basic information

Entry
Database: PDB / ID: 3lm4
TitleCrystal Structure of 2,3-Dihydroxy Biphenyl dioxygenase from Rhodococcus sp. (strain RHA1)
ComponentsCatechol 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / NYSGXRC / PSI-II / Protein structure Initiative / 2hydroxyl 6 oxo 6 phenyl hexa 2-4 dienoic acid / Peroxide / structural genomics / New York SGX Research Center for Structural Genomics / Dioxygenase
Function / homology
Function and homology information


catechol 2,3-dioxygenase / catechol 2,3-dioxygenase activity / metal ion binding
Similarity search - Function
: / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / Chem-HPX / HYDROGEN PEROXIDE / Catechol 2,3-dioxygenase
Similarity search - Component
Biological speciesRhodococcus jostii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSyed Ibrahim, B. / Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of 2,3-Dihydroxy Biphenyl dioxygenase from Rhodococcus sp. (strain RHA1)
Authors: Syed Ibrahim, B. / Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catechol 2,3-dioxygenase
B: Catechol 2,3-dioxygenase
C: Catechol 2,3-dioxygenase
D: Catechol 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,53916
Polymers155,3074
Non-polymers1,23212
Water13,475748
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17940 Å2
ΔGint-126 kcal/mol
Surface area42260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.923, 76.189, 251.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Catechol 2,3-dioxygenase / 2 / 3-Dihydroxy Biphenyl dioxygenase


Mass: 38826.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii (bacteria) / Strain: RHA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q0S9X1, catechol 2,3-dioxygenase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O2
#4: Chemical
ChemComp-HPX / (2Z,4E)-2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOIC ACID


Mass: 218.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H10O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE EXTRA ELECTRON DENSITY IN THE ACTIVE SITE WAS MODELED WITH LIGAND (2Z,4E)-2-HYDROXY-6-OXO-6- ...THE EXTRA ELECTRON DENSITY IN THE ACTIVE SITE WAS MODELED WITH LIGAND (2Z,4E)-2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOIC ACID. FE ION HAS BEEN ASSIGNED AS FE III

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bicine, 65% MPD, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2009 / Details: Mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 110846 / Num. obs: 110846 / % possible obs: 83 % / Redundancy: 12.3 % / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 5.3 / Num. unique all: 10740 / % possible all: 81.4

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→37.67 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 52162.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The extra electron density in the active site was modeled with ligand (2Z,4E)-2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOIC ACID. Fe ion has been assigned as Fe III
RfactorNum. reflection% reflectionSelection details
Rfree0.21 5415 5 %RANDOM
Rwork0.184 ---
obs0.184 107506 80.3 %-
all-110846 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.033 Å2 / ksol: 0.344843 e/Å3
Displacement parametersBiso mean: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2--2.1 Å20 Å2
3----1.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10318 0 76 748 11142
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.062.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 832 5.1 %
Rwork0.21 15369 -
obs-16650 73.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2die.pardie.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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