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- PDB-6w72: BlsA photo-activated state -

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Basic information

Entry
Database: PDB / ID: 6w72
TitleBlsA photo-activated state
ComponentsBLUF domain-containing protein
KeywordsFLAVOPROTEIN / BLUF / photoreceptor
Function / homologySensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Acylphosphatase-like domain superfamily / blue light photoreceptor activity / FAD binding / FLAVIN MONONUCLEOTIDE / BLUF domain-containing protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.76 Å
AuthorsChitrakar, I. / French, J.B.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124898 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM092714 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R25GM103962 United States
National Science Foundation (NSF, United States)MCB1750637 United States
National Science Foundation (NSF, United States)CHE1223819 United States
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Structural Basis for the Regulation of Biofilm Formation and Iron Uptake in A. baumannii by the Blue-Light-Using Photoreceptor, BlsA.
Authors: Chitrakar, I. / Iuliano, J.N. / He, Y. / Woroniecka, H.A. / Tolentino Collado, J. / Wint, J.M. / Walker, S.G. / Tonge, P.J. / French, J.B.
History
DepositionMar 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Mar 6, 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: BLUF domain-containing protein
B: BLUF domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1974
Polymers37,2842
Non-polymers9132
Water4,792266
1
A: BLUF domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0982
Polymers18,6421
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BLUF domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0982
Polymers18,6421
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.404, 39.286, 92.823
Angle α, β, γ (deg.)90.000, 103.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BLUF domain-containing protein / Blue light sensor protein / Sensors of blue-light using FAD family protein / BlsA


Mass: 18642.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ycgF, A7M79_14390, B9X91_17880, BGC29_03740, CHQ89_03035, DLI75_12900, E2533_15865, E2536_08065, EKS29_07115, FD887_10435, FD913_14645, FJU79_06305, SAMEA104305351_02412
Production host: Escherichia coli (E. coli) / References: UniProt: V5VB82
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium Chloride 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.91979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91979 Å / Relative weight: 1
ReflectionResolution: 1.76→29.63 Å / Num. obs: 32248 / % possible obs: 94.6 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.038 / Rrim(I) all: 0.079 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.76-1.83.20.551451714130.8540.3240.6441.557.3
7.86-29.624.40.03417674010.9990.0170.03824.997.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.5.31data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.76→29.63 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.186 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 1542 4.8 %RANDOM
Rwork0.1925 ---
obs0.1945 30701 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.77 Å2 / Biso mean: 23.295 Å2 / Biso min: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å2-0.16 Å2
2---0.57 Å20 Å2
3----0.76 Å2
Refinement stepCycle: final / Resolution: 1.76→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 62 266 2655
Biso mean--27.1 35.89 -
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132462
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172125
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.6783343
X-RAY DIFFRACTIONr_angle_other_deg1.4871.5974934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7124.037161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11915424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5341514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022770
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02536
LS refinement shellResolution: 1.76→1.804 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.326 75 -
Rwork0.332 1336 -
obs--55.9 %

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