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- PDB-3gkq: Terminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingo... -

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Basic information

Entry
Database: PDB / ID: 3gkq
TitleTerminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1
ComponentsTerminal oxygenase component of carbazole 1,9a-dioxygenase
KeywordsOXIDOREDUCTASE / Rieske nonheme iron oxygenase / electron transfer / putidaredoxin-type ferredoxin / Dioxygenase
Function / homology
Function and homology information


dioxygenase activity / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
N-terminal domain of TfIIb - #680 / Homotrimeric ring hydroxylase, catalytic domain / Homotrimeric ring hydroxylase / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. ...N-terminal domain of TfIIb - #680 / Homotrimeric ring hydroxylase, catalytic domain / Homotrimeric ring hydroxylase / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single Sheet / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / Terminal oxygenase component of carbazole 1,9a-dioxygenase
Similarity search - Component
Biological speciesSphingomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsUmeda, T. / Nojiri, H.
CitationJournal: To be Published
Title: Specific interaction via putidaredoxin-type ferredoxin in carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1
Authors: Umeda, T. / Katsuki, J. / Ashikawa, Y. / Inoue, K. / Usami, Y. / Noguchi, H. / Terada, T. / Abo, M. / Fujimoto, Z. / Yamane, H. / Nojiri, H.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 8, 2015Group: Refinement description
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ref_seq_dif.details / _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: Terminal oxygenase component of carbazole 1,9a-dioxygenase
B: Terminal oxygenase component of carbazole 1,9a-dioxygenase
C: Terminal oxygenase component of carbazole 1,9a-dioxygenase
D: Terminal oxygenase component of carbazole 1,9a-dioxygenase
E: Terminal oxygenase component of carbazole 1,9a-dioxygenase
F: Terminal oxygenase component of carbazole 1,9a-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,71024
Polymers263,9856
Non-polymers1,72518
Water39,7772208
1
A: Terminal oxygenase component of carbazole 1,9a-dioxygenase
B: Terminal oxygenase component of carbazole 1,9a-dioxygenase
C: Terminal oxygenase component of carbazole 1,9a-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,85512
Polymers131,9933
Non-polymers8639
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-35 kcal/mol
Surface area43110 Å2
MethodPISA
2
D: Terminal oxygenase component of carbazole 1,9a-dioxygenase
E: Terminal oxygenase component of carbazole 1,9a-dioxygenase
F: Terminal oxygenase component of carbazole 1,9a-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,85512
Polymers131,9933
Non-polymers8639
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-35 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.147, 159.019, 167.774
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Terminal oxygenase component of carbazole 1,9a-dioxygenase


Mass: 43997.535 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas (bacteria) / Strain: KA1 / Gene: carAaII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2PFA6
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2208 / 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

Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2M ammonium sulfate, 0.75M Tris hydrochloride, 0.25M calcium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.088 Å / Num. all: 355392 / Num. obs: 355392 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 3.5

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.07 Å
RfactorNum. reflection% reflection
Rfree0.436 --
Rwork0.2012 --
all0.436 354902 -
obs0.2144 354902 99.8 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.14 Å2
2---0.25 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17862 0 36 2208 20106

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