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- PDB-6k36: Crystal structure of BioU from Synechocystis sp.PCC6803 conjugate... -

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Basic information

Entry
Database: PDB / ID: 6k36
TitleCrystal structure of BioU from Synechocystis sp.PCC6803 conjugated with DAPA
ComponentsSlr0355 protein
KeywordsOXIDOREDUCTASE / BioU / biotin biosynthesis / dehydrogenase / cyanobacteria
Function / homology
Function and homology information


8-amino-7-oxononanoate carboxylating dehydrogenase / biotin biosynthetic process / amino acid metabolic process / transaminase activity / NAD binding / NADP binding / oxidoreductase activity
Similarity search - Function
(S)-8-amino-7-oxononanoate synthase BioU-like / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(8S)-8-azanylnonanoic acid / (S)-8-amino-7-oxononanoate synthase BioU
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSakaki, K. / Tomita, T. / Nishiyama, M.
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.
Authors: Sakaki, K. / Ohishi, K. / Shimizu, T. / Kobayashi, I. / Mori, N. / Matsuda, K. / Tomita, T. / Watanabe, H. / Tanaka, K. / Kuzuyama, T. / Nishiyama, M.
History
DepositionMay 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Slr0355 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0262
Polymers37,8531
Non-polymers1731
Water41423
1
A: Slr0355 protein
hetero molecules

A: Slr0355 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0524
Polymers75,7062
Non-polymers3472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4310 Å2
ΔGint-29 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.114, 71.114, 98.198
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

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Components

#1: Protein Slr0355 protein / BioU


Mass: 37852.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: slr0355 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55650
#2: Chemical ChemComp-CWF / (8S)-8-azanylnonanoic acid


Mass: 173.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.89 Å3/Da / Density % sol: 35.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% (w/v) PEG 3350, 0.2M potassium formate, 0.21M HEPES-NaOH (pH7.0)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13306 / % possible obs: 99.9 % / Redundancy: 8.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.031 / Net I/σ(I): 29.4
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.604 / Num. unique obs: 642 / CC1/2: 0.88 / Rpim(I) all: 0.211

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ITD

6itd


Resolution: 2.3→30.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.266 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.288 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 695 5.2 %RANDOM
Rwork0.19557 ---
obs0.19998 12589 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.443 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.15 Å20 Å2
2--0.29 Å20 Å2
3----0.95 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 12 23 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132490
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172339
X-RAY DIFFRACTIONr_angle_refined_deg1.51.6393368
X-RAY DIFFRACTIONr_angle_other_deg1.3571.5895415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3775324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04423.109119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33215411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3491513
X-RAY DIFFRACTIONr_chiral_restr0.0650.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022837
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
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_it4.2335.4441299
X-RAY DIFFRACTIONr_mcbond_other4.2285.4431298
X-RAY DIFFRACTIONr_mcangle_it6.1248.1631622
X-RAY DIFFRACTIONr_mcangle_other6.1248.1641623
X-RAY DIFFRACTIONr_scbond_it4.9066.1311190
X-RAY DIFFRACTIONr_scbond_other4.9046.1311191
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3868.9711747
X-RAY DIFFRACTIONr_long_range_B_refined9.39265.9542680
X-RAY DIFFRACTIONr_long_range_B_other9.3965.9632681
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.295→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 50 -
Rwork0.257 898 -
obs--98.75 %

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