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- PDB-4wwj: UndA, an oxygen-activating, non-heme iron dependent desaturase/de... -

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Basic information

Entry
Database: PDB / ID: 4wwj
TitleUndA, an oxygen-activating, non-heme iron dependent desaturase/decarboxylase
ComponentsTENA/THI-4 family protein
KeywordsOXIDOREDUCTASE / Non-heme iron dependent desaturase/decarboxylase / 1-Undecene biosynthesis / aliphatic medium-chain 1-alkenes biosynthesis / metalloenzyme
Function / homologyIron-containing redox enzyme / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha / metal ion binding / : / TENA/THI-4 family protein
Function and homology information
Biological speciesPseudomonas protegens Pf-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, X. / Cate, J.D.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Microbial biosynthesis of medium-chain 1-alkenes by a nonheme iron oxidase.
Authors: Rui, Z. / Li, X. / Zhu, X. / Liu, J. / Domigan, B. / Barr, I. / Cate, J.H. / Zhang, W.
History
DepositionNov 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _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_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TENA/THI-4 family protein
B: TENA/THI-4 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,41621
Polymers60,7032
Non-polymers1,71319
Water9,818545
1
A: TENA/THI-4 family protein
hetero molecules

A: TENA/THI-4 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,32020
Polymers60,7032
Non-polymers1,61718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area6480 Å2
ΔGint-163 kcal/mol
Surface area22160 Å2
MethodPISA
2
B: TENA/THI-4 family protein
hetero molecules

B: TENA/THI-4 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,51222
Polymers60,7032
Non-polymers1,80920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area6920 Å2
ΔGint-190 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.380, 218.440, 67.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-434-

HOH

31B-407-

HOH

41B-429-

HOH

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Components

#1: Protein TENA/THI-4 family protein / UndA / oxygen-activating non-heme iron dependent desaturase/decarboxylase


Mass: 30351.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens Pf-5 (bacteria) / Gene: PFL_4321 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4K8M0, Oxidoreductases
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.28 Å3/Da / Density % sol: 71.27 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 0.1 M MES, 1.8 M ammonium sulfate, 0.2 mM iron(II) ammonium sulfate, pH 6.5-7.0
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: ALS BL831
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2013
RadiationMonochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.9→118.69 Å / Num. all: 82394 / Num. obs: 82274 / % possible obs: 99.9 % / Redundancy: 4.4 % / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.3 % / % possible all: 99.99

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OQL

3oql


Resolution: 1.9→118.69 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19577 4120 5 %RANDOM
Rwork0.14469 ---
obs0.14724 78154 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0 Å2
2---0.06 Å2-0 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.9→118.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4170 0 95 545 4810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194389
X-RAY DIFFRACTIONr_bond_other_d0.0520.024093
X-RAY DIFFRACTIONr_angle_refined_deg1.9981.9425954
X-RAY DIFFRACTIONr_angle_other_deg1.03439368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6515518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08123.148216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51615736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5571538
X-RAY DIFFRACTIONr_chiral_restr0.1330.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024911
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021079
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7723.0292063
X-RAY DIFFRACTIONr_mcbond_other5.7613.0252062
X-RAY DIFFRACTIONr_mcangle_it6.5464.5072581
X-RAY DIFFRACTIONr_mcangle_other6.5514.5132582
X-RAY DIFFRACTIONr_scbond_it7.2333.6982326
X-RAY DIFFRACTIONr_scbond_other7.143.6652306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7035.2123343
X-RAY DIFFRACTIONr_long_range_B_refined7.86526.7595938
X-RAY DIFFRACTIONr_long_range_B_other7.66525.865650
X-RAY DIFFRACTIONr_rigid_bond_restr6.33638481
X-RAY DIFFRACTIONr_sphericity_free28.6215145
X-RAY DIFFRACTIONr_sphericity_bonded15.08158789
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 285 -
Rwork0.316 5753 -
obs--99.79 %

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