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- PDB-6d9f: Protein 60 with aldehyde deformylating oxidase activity from Kita... -

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Basic information

Entry
Database: PDB / ID: 6d9f
TitleProtein 60 with aldehyde deformylating oxidase activity from Kitasatospora setae
ComponentsPutative VlmB homolog
KeywordsLYASE / Ferritin-like
Function / homologyRibonucleotide reductase-like / Ferritin-like superfamily / oxidoreductase activity / metal ion binding / : / Putative VlmB homolog
Function and homology information
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å
AuthorsArenas, R. / Wilson, D.K. / Mak, W.S. / Siegel, J.B.
CitationJournal: Biochemistry / Year: 2020
Title: Discovery, Design, and Structural Characterization of Alkane-Producing Enzymes across the Ferritin-like Superfamily.
Authors: Mak, W.S. / Wang, X. / Arenas, R. / Cui, Y. / Bertolani, S. / Deng, W.Q. / Tagkopoulos, I. / Wilson, D.K. / Siegel, J.B.
History
DepositionApr 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative VlmB homolog
B: Putative VlmB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,50412
Polymers73,8402
Non-polymers66410
Water1,928107
1
A: Putative VlmB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4729
Polymers36,9201
Non-polymers5528
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative VlmB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0323
Polymers36,9201
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.630, 79.030, 124.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative VlmB homolog


Mass: 36919.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054) (bacteria)
Strain: ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054
Gene: vlmB, KSE_09070 / Production host: Escherichia coli (E. coli) / References: UniProt: E4N6B3
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.66 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.075 M TRIS hydrochloride pH 8.5, 1.5 M Ammonium sulfate, 25% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.03→66.76 Å / Num. obs: 50138 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.8
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3667 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.03→66.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.3 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23395 2501 5 %RANDOM
Rwork0.19773 ---
obs0.19957 47581 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.396 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.03→66.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 30 107 5146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195132
X-RAY DIFFRACTIONr_bond_other_d0.0010.024873
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9676971
X-RAY DIFFRACTIONr_angle_other_deg0.884311189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2345641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19122.314242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4741564
X-RAY DIFFRACTIONr_chiral_restr0.0980.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021089
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_it2.8454.0992570
X-RAY DIFFRACTIONr_mcbond_other2.844.0982569
X-RAY DIFFRACTIONr_mcangle_it3.8936.1373209
X-RAY DIFFRACTIONr_mcangle_other3.8936.1383210
X-RAY DIFFRACTIONr_scbond_it3.6544.612562
X-RAY DIFFRACTIONr_scbond_other3.6494.612562
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4486.7493763
X-RAY DIFFRACTIONr_long_range_B_refined6.74850.1645959
X-RAY DIFFRACTIONr_long_range_B_other6.74950.1645954
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.031→2.084 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 204 -
Rwork0.343 3458 -
obs--99.86 %

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