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- PDB-6fjh: Crystal structure of the seleniated LkcE from Streptomyces rochei -

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Basic information

Entry
Database: PDB / ID: 6fjh
TitleCrystal structure of the seleniated LkcE from Streptomyces rochei
ComponentsLkcE
KeywordsFLAVOPROTEIN / Amine oxydase / cyclase / Post-PKS enzyme / tayloring enzyme
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / OXYGEN MOLECULE / LkcE
Similarity search - Component
Biological speciesStreptomyces rochei subsp. volubilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / SAD / Resolution: 3.15 Å
AuthorsDorival, J. / Risser, F. / Jacob, C. / Collin, S. / Drager, G. / Kirschning, A. / Paris, C. / Chagot, B. / Gruez, A. / Weissman, K.J.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyPKS-PPIs / AAP JCJC SVS3 8 2011 France
CitationJournal: Nat Commun / Year: 2018
Title: Insights into a dual function amide oxidase/macrocyclase from lankacidin biosynthesis.
Authors: Dorival, J. / Risser, F. / Jacob, C. / Collin, S. / Drager, G. / Paris, C. / Chagot, B. / Kirschning, A. / Gruez, A. / Weissman, K.J.
History
DepositionJan 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LkcE
B: LkcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4078
Polymers99,7262
Non-polymers1,6816
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-47 kcal/mol
Surface area32380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.300, 125.300, 154.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein LkcE


Mass: 49863.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rochei subsp. volubilis (bacteria)
Gene: lkcE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G4V2H3
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 3350, 200 mM ammonium acetate, 100 mM Bis Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.15→48.66 Å / Num. obs: 40627 / % possible obs: 99.9 % / Redundancy: 7.585 % / Biso Wilson estimate: 90.38 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.141 / Χ2: 1.112 / Net I/σ(I): 13.62 / Num. measured all: 308163 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.15-3.27.0070.8022.5818710.7790.86599.3
3.2-47.7610.3247.17189100.9720.347100
4-67.5110.10117.68139700.9950.109100
6-107.3840.05825.5946160.9980.06299.9
10-207.4450.03938.1811170.9990.04299.9
20-48.666.720.03137.411430.9990.03391.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
PHASER2.5.2phasing
SHELXDEphasing
PDB_EXTRACT3.24data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.15→48.66 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.874 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.431
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1095 5 %RANDOM
Rwork0.198 ---
obs0.2 21897 99.9 %-
Displacement parametersBiso max: 172.62 Å2 / Biso mean: 70.16 Å2 / Biso min: 15.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.8342 Å20 Å20 Å2
2---1.8342 Å20 Å2
3---3.6683 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 3.15→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6807 0 112 196 7115
Biso mean--54.26 56.01 -
Num. residues----861
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2412SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes174HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1120HARMONIC5
X-RAY DIFFRACTIONt_it7118HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion861SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8018SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7118HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9673HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion20.32
LS refinement shellResolution: 3.15→3.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.29 143 5.01 %
Rwork0.222 2714 -
all0.225 2857 -
obs--99.69 %

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