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- PDB-6p5q: X-ray structure of Fe(II)-soaked UndA bound to lauric acid -

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Basic information

Entry
Database: PDB / ID: 6p5q
TitleX-ray structure of Fe(II)-soaked UndA bound to lauric acid
ComponentsUndA
KeywordsOXIDOREDUCTASE / desaturase / iron / decarboxylase / fatty acid
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
LAURIC ACID / : / TENA/THI-4 family protein
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsRajakovich, L.J. / Mitchell, A.J. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Substrate-Triggered Formation of a Peroxo-Fe2(III/III) Intermediate during Fatty Acid Decarboxylation by UndA.
Authors: Zhang, B. / Rajakovich, L.J. / Van Cura, D. / Blaesi, E.J. / Mitchell, A.J. / Tysoe, C.R. / Zhu, X. / Streit, B.R. / Rui, Z. / Zhang, W. / Boal, A.K. / Krebs, C. / Bollinger Jr., J.M.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UndA
B: UndA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0729
Polymers70,3562
Non-polymers7167
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UndA
hetero molecules

A: UndA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,16410
Polymers70,3562
Non-polymers8088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4900 Å2
ΔGint-57 kcal/mol
Surface area21800 Å2
MethodPISA
3
B: UndA
hetero molecules

B: UndA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9808
Polymers70,3562
Non-polymers6246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4430 Å2
ΔGint-57 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.009, 74.148, 142.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21B-406-

HOH

31B-410-

HOH

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Components

#1: Protein UndA


Mass: 35177.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q4K8M0*PLUS
#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.84→34 Å / Num. obs: 61998 / % possible obs: 98.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 19.19 Å2 / CC1/2: 0.942 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.1
Reflection shellResolution: 1.86→1.89 Å / Rmerge(I) obs: 0.469 / Num. unique obs: 3070

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WWJ

4wwj


Resolution: 1.86→33.08 Å / SU ML: 0.1859 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5952 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2166 3087 5.13 %
Rwork0.1978 57043 -
obs0.1987 60130 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.11 Å2
Refinement stepCycle: LAST / Resolution: 1.86→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 38 250 4282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274156
X-RAY DIFFRACTIONf_angle_d0.5335630
X-RAY DIFFRACTIONf_chiral_restr0.0339591
X-RAY DIFFRACTIONf_plane_restr0.0031719
X-RAY DIFFRACTIONf_dihedral_angle_d15.88732481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.890.30071220.23652568X-RAY DIFFRACTION97.25
1.89-1.920.36561300.33232151X-RAY DIFFRACTION83.71
1.92-1.950.32711150.29362489X-RAY DIFFRACTION94.21
1.95-1.990.25971440.22872608X-RAY DIFFRACTION99.93
1.99-2.030.26211520.21042591X-RAY DIFFRACTION100
2.03-2.070.20291390.20092634X-RAY DIFFRACTION100
2.07-2.110.20521390.19532597X-RAY DIFFRACTION100
2.11-2.160.2251230.19862628X-RAY DIFFRACTION100
2.16-2.220.2271620.20552605X-RAY DIFFRACTION100
2.22-2.280.28941310.23812340X-RAY DIFFRACTION89.5
2.28-2.340.22391550.19912624X-RAY DIFFRACTION99.93
2.34-2.420.22741560.18762620X-RAY DIFFRACTION100
2.42-2.510.22221330.1892628X-RAY DIFFRACTION100
2.51-2.610.20211450.18232624X-RAY DIFFRACTION100
2.61-2.720.19541330.20042686X-RAY DIFFRACTION100
2.72-2.870.24991190.20272657X-RAY DIFFRACTION100
2.87-3.050.22681360.21222653X-RAY DIFFRACTION100
3.05-3.280.22361480.20432663X-RAY DIFFRACTION100
3.28-3.610.20031490.19872644X-RAY DIFFRACTION99.22
3.61-4.130.19711480.16442473X-RAY DIFFRACTION92.48
4.13-5.210.14161600.15232707X-RAY DIFFRACTION99.97
5.21-33.080.21671480.22853X-RAY DIFFRACTION99.21

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