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- PDB-2ckf: Crystal Structure of the Terminal Component of the PAH-hydroxylat... -

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Basic information

Entry
Database: PDB / ID: 2ckf
TitleCrystal Structure of the Terminal Component of the PAH-hydroxylating Dioxygenase from Sphingomonas sp CHY-1
Components
  • RING-HYDROXYLATING DIOXYGENASE ALPHA SUBUNIT
  • RING-HYDROXYLATING DIOXYGENASE BETA SUBUNIT
KeywordsOXIDOREDUCTASE / RIESKE NON HEME IRON DIOXYGENASE / PYRENE DIOXYGENASE / RING-HYDROXYLATING DIOXYGENASE / HIGH-MOLECULAR-WEIGHT POLYCYCLIC AROMATIC HYDROCARBONS
Function / homology
Function and homology information


3-phenylpropionate catabolic process / dioxygenase activity / catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 ...Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Nuclear Transport Factor 2; Chain: A, - #50 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / Ring-hydroxylating dioxygenase beta subunit / Ring-hydroxylating dioxygenase alpha subunit
Similarity search - Component
Biological speciesSPHINGOMONAS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJakoncic, J. / Meyer, C. / Jouanneau, Y. / Stojanoff, V.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: The Catalytic Pocket of the Ring-Hydroxylating Dioxygenase from Sphingomonas Chy-1.
Authors: Jakoncic, J. / Jouanneau, Y. / Meyer, C. / Stojanoff, V.
History
DepositionApr 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_label_atom_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_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_conn.ptnr2_label_seq_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: RING-HYDROXYLATING DIOXYGENASE ALPHA SUBUNIT
B: RING-HYDROXYLATING DIOXYGENASE BETA SUBUNIT
C: RING-HYDROXYLATING DIOXYGENASE ALPHA SUBUNIT
D: RING-HYDROXYLATING DIOXYGENASE BETA SUBUNIT
E: RING-HYDROXYLATING DIOXYGENASE ALPHA SUBUNIT
F: RING-HYDROXYLATING DIOXYGENASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,73812
Polymers215,0436
Non-polymers6956
Water19,7441096
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27630 Å2
ΔGint-164.8 kcal/mol
Surface area60340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.644, 112.730, 190.626
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 RING-HYDROXYLATING DIOXYGENASE ALPHA SUBUNIT / PYRENE DIOXYGENASE


Mass: 50847.559 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPHINGOMONAS SP. (bacteria) / Strain: CHY-1 / Plasmid: PSD9 / Production host: PSEUDOMONAS PUTIDA (bacteria) / Strain (production host): KT2442 / References: UniProt: Q65AT1
#2: Protein RING-HYDROXYLATING DIOXYGENASE BETA SUBUNIT / PYRENE DIOXYGENASE


Mass: 20833.363 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPHINGOMONAS SP. (bacteria) / Strain: CHY-1 / Plasmid: PSD9 / Production host: PSEUDOMONAS PUTIDA (bacteria) / Strain (production host): KT2442 / References: UniProt: Q65AT0
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1096 / 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: 2.43 Å3/Da / Density % sol: 49 %
Description: 1NDO ALPHA SUBUNIT WITH 1WQL TRUNCATED BETA SUBUNIT WERE USED FOR THE MOLECULAR REPLACEMENT
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2005 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→35 Å / Num. obs: 168606 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.1 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEE REMARK BELOW

Resolution: 1.85→35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.119 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL REFINEMENT WAS CARRIED OUT WITH NCS RESTRAINTS. THE LAST STEPS OF THE REFINEMENT WAS CARRIED OUT WITHOUT NCS RESTRAINTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 8495 5 %RANDOM
Rwork0.197 ---
obs0.199 161018 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.63 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14677 0 15 1096 15788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02115154
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.92320564
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91351821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47423.264815
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84152385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.10315127
X-RAY DIFFRACTIONr_chiral_restr0.1220.22094
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.27299
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.210212
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.21222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0051.59253
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.534214494
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.30936862
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3324.56058
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 588
Rwork0.246 11675

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