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- PDB-2nwb: Crystal Structure of a Putative 2,3-dioxygenase (SO4414) from She... -

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Basic information

Entry
Database: PDB / ID: 2nwb
TitleCrystal Structure of a Putative 2,3-dioxygenase (SO4414) from Shewanella oneidensis in complex with ferric heme. Northeast Structural Genomics Target SoR52.
ComponentsConserved domain protein
KeywordsOXIDOREDUCTASE / Dioxygenase / Heme-binding protein / Hemoprotein / all alpha-helical protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / heme binding / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #600 / Monodechloroaminopyrrolnitrin synthase PrnB / Monodechloroaminopyrrolnitrin synthase PrnB / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #480 / Tryptophan/Indoleamine 2,3-dioxygenase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Tryptophan 2,3-dioxygenase KynA
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsForouhar, F. / Anderson, J.L.R. / Mowat, C.G. / Hussain, A. / Seetharaman, J. / Bruckmann, C. / Thackray, S.J. / Khan, N. / Cunningham, K. / Janjua, H. ...Forouhar, F. / Anderson, J.L.R. / Mowat, C.G. / Hussain, A. / Seetharaman, J. / Bruckmann, C. / Thackray, S.J. / Khan, N. / Cunningham, K. / Janjua, H. / Zhao, L. / Xiao, R. / Ma, L.C. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Champman, S.K. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase.
Authors: Forouhar, F. / Anderson, J.L. / Mowat, C.G. / Vorobiev, S.M. / Hussain, A. / Abashidze, M. / Bruckmann, C. / Thackray, S.J. / Seetharaman, J. / Tucker, T. / Xiao, R. / Ma, L.C. / Zhao, L. / ...Authors: Forouhar, F. / Anderson, J.L. / Mowat, C.G. / Vorobiev, S.M. / Hussain, A. / Abashidze, M. / Bruckmann, C. / Thackray, S.J. / Seetharaman, J. / Tucker, T. / Xiao, R. / Ma, L.C. / Zhao, L. / Acton, T.B. / Montelione, G.T. / Chapman, S.K. / Tong, L.
History
DepositionNov 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE. AUTHOR STATES THAT THE BIOLOGICAL UNIT COULD BE EITHER TETRAMER (SEE REMARK 350) OR MONOMER, SINCE THE CLOSE PROTEIN HOMOLOG IN HUMAN (IDO) IS A MONOMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved domain protein
B: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8373
Polymers92,2202
Non-polymers6161
Water5,531307
1
A: Conserved domain protein
B: Conserved domain protein
hetero molecules

A: Conserved domain protein
B: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,6746
Polymers184,4414
Non-polymers1,2332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area12440 Å2
ΔGint-77 kcal/mol
Surface area59400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)138.851, 68.698, 87.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Conserved domain protein / Putative 2 / 3-dioxygenase


Mass: 46110.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_4414 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8E972
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / pH: 7
Details: 100mM Tris-HCl, 20% PEG3350, 50 mM Magnesium formate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97911
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.4→29.26 Å / Num. obs: 33304 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.07 / Net I/σ(I): 16.98
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.81 / Rsym value: 0.63 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZEE

1zee


Resolution: 2.4→19.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 223710.04 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: XTALVIEW WAS ALSO THE PROGRAM USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1366 4.9 %RANDOM
Rwork0.217 ---
obs0.217 27775 83.2 %-
all-33304 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.4477 Å2 / ksol: 0.308835 e/Å3
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.72 Å20 Å20 Å2
2--3.32 Å20 Å2
3---3.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 43 307 6398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.241 156 4.7 %
Rwork0.235 3155 -
obs--59.9 %

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