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- PDB-6m10: Crystal structure of PA4853 (Fis) from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6m10
TitleCrystal structure of PA4853 (Fis) from Pseudomonas aeruginosa
ComponentsPutative Fis-like DNA-binding protein
KeywordsDNA BINDING PROTEIN / nucleoid-associated protein / Fis / DNA-binding protein
Function / homology
Function and homology information


sequence-specific DNA binding / regulation of DNA-templated transcription
Similarity search - Function
DNA-binding protein Fis / : / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative Fis-like DNA-binding protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.985 Å
AuthorsZhang, H. / Gao, Z. / Zhou, J. / Dong, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1732113 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of the nucleoid-associated protein Fis (PA4853) from Pseudomonas aeruginosa.
Authors: Zhou, J. / Gao, Z. / Zhang, H. / Dong, Y.
History
DepositionFeb 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Putative Fis-like DNA-binding protein
C: Putative Fis-like DNA-binding protein
B: Putative Fis-like DNA-binding protein
D: Putative Fis-like DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)46,3694
Polymers46,3694
Non-polymers00
Water00
1
A: Putative Fis-like DNA-binding protein
B: Putative Fis-like DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)23,1842
Polymers23,1842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-28 kcal/mol
Surface area10890 Å2
MethodPISA
2
C: Putative Fis-like DNA-binding protein

C: Putative Fis-like DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)23,1842
Polymers23,1842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3150 Å2
ΔGint-27 kcal/mol
Surface area10590 Å2
MethodPISA
3
D: Putative Fis-like DNA-binding protein

D: Putative Fis-like DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)23,1842
Polymers23,1842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3210 Å2
ΔGint-26 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.490, 194.006, 92.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Putative Fis-like DNA-binding protein


Mass: 11592.145 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA4853 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HUW0

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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: 2.07 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Na-HEPES (pH7.5), 20% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.985→60 Å / Num. obs: 8292 / % possible obs: 97.6 % / Redundancy: 11.1 % / Biso Wilson estimate: 68.5 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.06 / Rrim(I) all: 0.202 / Net I/σ(I): 13.23
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 346 / CC1/2: 0.903 / Rpim(I) all: 0.279 / Rrim(I) all: 0.89 / % possible all: 84.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F36

1f36


Resolution: 2.985→48.502 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.15
RfactorNum. reflection% reflection
Rfree0.2986 826 10.01 %
Rwork0.2612 --
obs0.2649 8253 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.73 Å2 / Biso mean: 64.1176 Å2 / Biso min: 31.5 Å2
Refinement stepCycle: final / Resolution: 2.985→48.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 0 0 2562
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062599
X-RAY DIFFRACTIONf_angle_d0.9983516
X-RAY DIFFRACTIONf_chiral_restr0.045415
X-RAY DIFFRACTIONf_plane_restr0.006453
X-RAY DIFFRACTIONf_dihedral_angle_d20.1091596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9853-3.17230.37371210.3363110887
3.1723-3.41720.38271350.3167120197
3.4172-3.76090.32661390.28031245100
3.7609-4.30490.26751380.2569124599
4.3049-5.42250.28311420.24791279100
5.4225-48.50.27541510.23521349100

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