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- PDB-1zee: X-Ray Crystal Structure of Protein SO4414 from Shewanella oneiden... -

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Basic information

Entry
Database: PDB / ID: 1zee
TitleX-Ray Crystal Structure of Protein SO4414 from Shewanella oneidensis. Northeast Structural Genomics Consortium Target SoR52.
Componentshypothetical protein SO4414
KeywordsUNKNOWN FUNCTION / all alpha-protein. / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


tryptophan 2,3-dioxygenase / L-tryptophan 2,3-dioxygenase activity / L-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
Tryptophan 2,3-dioxygenase KynA
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsForouhar, F. / Abashidze, M. / Vorobiev, S.M. / Conover, K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Hypothetical Protein SO4414 from Shewanella oneidensis, NESG Target SoR52
Authors: Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Conover, K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein SO4414
B: hypothetical protein SO4414


Theoretical massNumber of molelcules
Total (without water)93,4912
Polymers93,4912
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-7 kcal/mol
Surface area31060 Å2
MethodPISA
2
A: hypothetical protein SO4414
B: hypothetical protein SO4414

A: hypothetical protein SO4414
B: hypothetical protein SO4414


Theoretical massNumber of molelcules
Total (without water)186,9824
Polymers186,9824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9930 Å2
ΔGint-32 kcal/mol
Surface area57570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.082, 68.024, 90.954
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 hypothetical protein SO4414


Mass: 46745.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: GeneID:1172013 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
Keywords: Substitution of Met residues by Seleno-Met residues and addition of C-tag (LEHHHHHH). SO4414
References: UniProt: Q8E972
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG3350, 150 mM lithium sulfate, and 5 mM DTT., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 72798 / Num. obs: 70105 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.053 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 4.46 / Num. unique all: 7238 / Rsym value: 0.268 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→27.5 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 296623.33 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: SnB was used prior to SOLVE/RESOLVE. XtalView was used for structure refinement in addition to CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 6315 9.9 %RANDOM
Rwork0.234 ---
all0.237 70105 --
obs0.234 63574 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.9119 Å2 / ksol: 0.300486 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.69 Å20 Å20 Å2
2--2.36 Å20 Å2
3---1.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.31→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5906 0 0 309 6215
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 874 10 %
Rwork0.267 7895 -
obs-7895 71.4 %

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