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- PDB-6k37: Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 i... -

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Basic information

Entry
Database: PDB / ID: 6k37
TitleCrystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with NAD+ and the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid
ComponentsSlr0355 protein
KeywordsOXIDOREDUCTASE / BioU / biotin biosynthesis / dehydrogenase / Synechocystis
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
(3R)-3-[(1R)-1-azanylethyl]nonanedioic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (S)-8-amino-7-oxononanoate synthase BioU
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Slr0355 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6903
Polymers37,7951
Non-polymers8952
Water32418
1
A: Slr0355 protein
hetero molecules

A: Slr0355 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3796
Polymers75,5902
Non-polymers1,7894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6760 Å2
ΔGint-44 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.414, 70.414, 98.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Slr0355 protein / BioU


Mass: 37794.789 Da / Num. of mol.: 1 / Mutation: K124A
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-CWL / (3R)-3-[(1R)-1-azanylethyl]nonanedioic acid


Mass: 231.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H21NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.87 Å3/Da / Density % sol: 34.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% PEG 3350, 0.2M Ammonium formate, 0.1M HEPES-NaOH (pH7.0), 5mM 3-(1-aminoethyl)-nonanedioic acid, 5mM NAD+

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 10264 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.034 / Net I/σ(I): 28.5
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.646 / Num. unique obs: 541 / CC1/2: 0.901 / Rpim(I) all: 0.212

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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: 2.5→38.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.505 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R Free: 0.347 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26874 486 4.7 %RANDOM
Rwork0.17368 ---
obs0.17797 9754 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.314 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å20 Å2
2--1.04 Å20 Å2
3----3.38 Å2
Refinement stepCycle: 1 / Resolution: 2.5→38.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 60 18 2525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132551
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172368
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.6443462
X-RAY DIFFRACTIONr_angle_other_deg1.3111.5915485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3975326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49623.109119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.74615410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7551513
X-RAY DIFFRACTIONr_chiral_restr0.0570.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02506
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_it3.7085.5961307
X-RAY DIFFRACTIONr_mcbond_other3.6995.5961306
X-RAY DIFFRACTIONr_mcangle_it5.2968.3911632
X-RAY DIFFRACTIONr_mcangle_other5.2948.3911633
X-RAY DIFFRACTIONr_scbond_it4.1816.161244
X-RAY DIFFRACTIONr_scbond_other4.1836.1631242
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3839.041830
X-RAY DIFFRACTIONr_long_range_B_refined8.37767.9132723
X-RAY DIFFRACTIONr_long_range_B_other8.37867.9092722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 39 -
Rwork0.205 698 -
obs--99.73 %

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