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- PDB-3er6: Crystal structure of a putative transcriptional regulator protein... -

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Basic information

Entry
Database: PDB / ID: 3er6
TitleCrystal structure of a putative transcriptional regulator protein from Vibrio parahaemolyticus
ComponentsPutative transcriptional regulator proteinTranscriptional regulation
Keywordsstructural genomics / unknown function / DNA-binding / Transcription / Transcription regulation / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like ...HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Homeobox-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative transcriptional regulator protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Chang, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative transcriptional regulator protein from Vibrio parahaemolyticus
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Chang, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transcriptional regulator protein
B: Putative transcriptional regulator protein
C: Putative transcriptional regulator protein
D: Putative transcriptional regulator protein
E: Putative transcriptional regulator protein
F: Putative transcriptional regulator protein


Theoretical massNumber of molelcules
Total (without water)139,9726
Polymers139,9726
Non-polymers00
Water10,034557
1
A: Putative transcriptional regulator protein
B: Putative transcriptional regulator protein


Theoretical massNumber of molelcules
Total (without water)46,6572
Polymers46,6572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-14 kcal/mol
Surface area15910 Å2
MethodPISA
2
C: Putative transcriptional regulator protein
D: Putative transcriptional regulator protein


Theoretical massNumber of molelcules
Total (without water)46,6572
Polymers46,6572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-11 kcal/mol
Surface area16050 Å2
MethodPISA
3
E: Putative transcriptional regulator protein
F: Putative transcriptional regulator protein


Theoretical massNumber of molelcules
Total (without water)46,6572
Polymers46,6572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-13 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.268, 105.268, 101.745
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Putative transcriptional regulator protein / Transcriptional regulation


Mass: 23328.645 Da / Num. of mol.: 6 / Mutation: N92K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VPA0716 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87I90
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 2.1M DL-malic acid pH 7, pH 7.0, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.9→91.287 Å / Num. all: 99393 / Num. obs: 99393 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 8.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.2 / Num. measured all: 87086 / Num. unique all: 14542 / Rsym value: 0.589 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.301 / WRfactor Rwork: 0.247 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.809 / SU B: 3.709 / SU ML: 0.108 / SU R Cruickshank DPI: 0.15 / SU Rfree: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.15 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4958 5 %RANDOM
Rwork0.192 ---
obs0.194 99277 100 %-
all-99277 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 82.68 Å2 / Biso mean: 39.239 Å2 / Biso min: 18.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.43 Å20 Å2
2--0.87 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8805 0 0 557 9362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0229012
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.95512239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85851135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32724.338385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.091151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7851534
X-RAY DIFFRACTIONr_chiral_restr0.1170.21404
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216766
X-RAY DIFFRACTIONr_mcbond_it1.0621.55632
X-RAY DIFFRACTIONr_mcangle_it1.86129079
X-RAY DIFFRACTIONr_scbond_it3.00233380
X-RAY DIFFRACTIONr_scangle_it4.6274.53155
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 355 -
Rwork0.319 6982 -
all-7337 -
obs-6982 99.97 %

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