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- PDB-4wx0: UndA complexed with beta-hydroxydodecanoic acid -

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Basic information

Entry
Database: PDB / ID: 4wx0
TitleUndA complexed with beta-hydroxydodecanoic acid
ComponentsTENA/THI-4 family protein
KeywordsOXIDOREDUCTASE / Non-heme iron dependent desaturase/decarboxylase / 1-Undecene biosynthesis / aliphatic medium-chain 1-alkene biosynthesis / metalloenzyme
Function / homology
Function and homology information


Iron-containing redox enzyme / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / (3R)-3-HYDROXYDODECANOIC ACID / PEROXIDE ION / TENA/THI-4 family protein
Similarity search - Component
Biological speciesPseudomonas protegens Pf-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsLi, X. / Cate, J.D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Energy Biosciences Institute and National Cancer Institute United States
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 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)62,08016
Polymers60,7032
Non-polymers1,37714
Water10,142563
1
A: TENA/THI-4 family protein
hetero molecules

A: TENA/THI-4 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,08016
Polymers60,7032
Non-polymers1,37714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5680 Å2
ΔGint-118 kcal/mol
Surface area22410 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)62,08016
Polymers60,7032
Non-polymers1,37714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5670 Å2
ΔGint-117 kcal/mol
Surface area22430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.410, 73.990, 142.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-443-

HOH

31B-402-

HOH

41B-405-

HOH

51B-421-

HOH

61B-437-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 256 / Label seq-ID: 5 - 258

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 577 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HXD / (3R)-3-HYDROXYDODECANOIC ACID / 3-OH-DODECANOATE


Mass: 216.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O3
#4: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2013
RadiationMonochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.7→65.75 Å / Num. obs: 75678 / % possible obs: 95.8 % / Redundancy: 8.4 % / Net I/σ(I): 14.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.1 / % possible all: 70.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SCALAdata scaling
PHASERphasing
PHENIXrefinement
RefinementResolution: 1.7→65.75 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18454 3839 5.1 %RANDOM
Rwork0.13671 ---
obs0.13907 71841 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.927 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0.44 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.7→65.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 76 563 4801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194356
X-RAY DIFFRACTIONr_bond_other_d00.024057
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9375911
X-RAY DIFFRACTIONr_angle_other_deg3.57839287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66123.056216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07815726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5731538
X-RAY DIFFRACTIONr_chiral_restr0.0890.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024891
X-RAY DIFFRACTIONr_gen_planes_other0.010.021079
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_it4.5932.6642052
X-RAY DIFFRACTIONr_mcbond_other4.5812.662051
X-RAY DIFFRACTIONr_mcangle_it5.8823.9892565
X-RAY DIFFRACTIONr_mcangle_other5.8893.9942566
X-RAY DIFFRACTIONr_scbond_it5.7543.1792303
X-RAY DIFFRACTIONr_scbond_other5.6283.1432285
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5944.5463323
X-RAY DIFFRACTIONr_long_range_B_refined7.53223.7685897
X-RAY DIFFRACTIONr_long_range_B_other7.13422.585521
X-RAY DIFFRACTIONr_rigid_bond_restr16.55438410
X-RAY DIFFRACTIONr_sphericity_free40.0395139
X-RAY DIFFRACTIONr_sphericity_bonded16.33758739
Refine LS restraints NCS

Ens-ID: 1 / Number: 15675 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 214 -
Rwork0.351 3898 -
obs--70.9 %

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