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- PDB-3oxn: The crystal structure of a putative transcriptional regulator fro... -

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Basic information

Entry
Database: PDB / ID: 3oxn
TitleThe crystal structure of a putative transcriptional regulator from Vibrio parahaemolyticus
ComponentsPutative transcriptional regulator, LysR family
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / putative transcriptional regulator / PSI / SGX
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
HTH-type transcriptional regulator YidZ, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...HTH-type transcriptional regulator YidZ, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative transcriptional regulator, LysR family
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of a putative transcriptional regulator from Vibrio parahaemolyticus
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator, LysR family
B: Putative transcriptional regulator, LysR family
C: Putative transcriptional regulator, LysR family
D: Putative transcriptional regulator, LysR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3365
Polymers111,2404
Non-polymers961
Water1,47782
1
A: Putative transcriptional regulator, LysR family
D: Putative transcriptional regulator, LysR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7163
Polymers55,6202
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-35 kcal/mol
Surface area18480 Å2
MethodPISA
2
B: Putative transcriptional regulator, LysR family
C: Putative transcriptional regulator, LysR family


Theoretical massNumber of molelcules
Total (without water)55,6202
Polymers55,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-14 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.316, 50.488, 108.116
Angle α, β, γ (deg.)86.19, 82.89, 86.74
Int Tables number1
Space group name H-MP1
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
Putative transcriptional regulator, LysR family


Mass: 27809.906 Da / Num. of mol.: 4 / Fragment: sequence database residues 99-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP0027 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) Codon+ril Stratagene / References: UniProt: Q87TP2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.8 M Ammonia Sulfate, 1 M MES pH6.5, 10 mM Cobalt Chloride hexahydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 11, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 38304 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2923 / % possible all: 71.3

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→38.906 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 33.32 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 1364 5.05 %RANDOM
Rwork0.2455 ---
obs0.2479 27017 93.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.08 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 42.33 Å2
Baniso -1Baniso -2Baniso -3
1--8.7166 Å2-7.6067 Å2-6.6116 Å2
2--0.8117 Å23.5827 Å2
3---7.9049 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6790 0 5 82 6877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096975
X-RAY DIFFRACTIONf_angle_d1.39513
X-RAY DIFFRACTIONf_dihedral_angle_d20.6862577
X-RAY DIFFRACTIONf_chiral_restr0.0851094
X-RAY DIFFRACTIONf_plane_restr0.0051225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.79660.3891150.30652275X-RAY DIFFRACTION82
2.7966-2.90850.35711270.31432355X-RAY DIFFRACTION87
2.9085-3.04080.38851310.29332459X-RAY DIFFRACTION90
3.0408-3.20110.3341450.272547X-RAY DIFFRACTION93
3.2011-3.40150.31811340.23852602X-RAY DIFFRACTION94
3.4015-3.6640.23521390.23462661X-RAY DIFFRACTION97
3.664-4.03230.36121310.22662645X-RAY DIFFRACTION97
4.0323-4.6150.22921390.20072737X-RAY DIFFRACTION98
4.615-5.81130.2461410.22112673X-RAY DIFFRACTION98
5.8113-38.91010.26121620.25062699X-RAY DIFFRACTION99

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