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- PDB-2f2e: Crystal Structure of PA1607, a Putative Transcription Factor -

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Basic information

Entry
Database: PDB / ID: 2f2e
TitleCrystal Structure of PA1607, a Putative Transcription Factor
ComponentsPA1607
KeywordsDNA BINDING PROTEIN/STRUCTURAL GENOMICS / Transcription factor / helix-trun-helix / APC5613 / structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA BINDING PROTEIN-STRUCTURAL GENOMICS COMPLEX
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Helix-turn-helix, HxlR type / HxlR-like helix-turn-helix / HxlR-type HTH domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-D-glucopyranose / HTH hxlR-type domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsSieminska, E.A. / Xu, X. / Zheng, H. / Lunin, V. / Cuff, M. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Sanders, D.A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2007
Title: The X-ray crystal structure of PA1607 from Pseudomonas aureginosa at 1.9 A resolution--a putative transcription factor.
Authors: Sieminska, E.A. / Xu, X. / Savchenko, A. / Sanders, D.A.
History
DepositionNov 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: PA1607
B: PA1607
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3117
Polymers32,7462
Non-polymers5645
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-88 kcal/mol
Surface area14390 Å2
MethodPISA
2
A: PA1607
B: PA1607
hetero molecules

A: PA1607
B: PA1607
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,62214
Polymers65,4934
Non-polymers1,12910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area15320 Å2
ΔGint-191 kcal/mol
Surface area27340 Å2
MethodPISA
3
A: PA1607
B: PA1607
hetero molecules

A: PA1607
B: PA1607
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,62214
Polymers65,4934
Non-polymers1,12910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area15810 Å2
ΔGint-206 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.884, 78.865, 78.941
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-524-

HOH

21B-531-

HOH

DetailsThis protein is a dimer in solution

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Components

#1: Protein PA1607


Mass: 16373.173 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1607 / Plasmid: pET15-modified / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I3B4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 10mg/ml protein, 0.1 M Tris, 0.2 M LiSO4, 28 % PEG 3350, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932, 0.97948
DetectorDate: Apr 1, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.979481
ReflectionResolution: 1.85→78 Å / Num. obs: 24599

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→35.27 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.596 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25099 1130 5.1 %RANDOM
Rwork0.17697 ---
obs0.18081 21007 90.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.558 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å20 Å2-2.14 Å2
2---1.83 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 32 329 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222262
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9763070
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62322.264106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91615362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3851527
X-RAY DIFFRACTIONr_chiral_restr0.1190.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021739
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21150
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21546
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3470.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2541.51442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74422243
X-RAY DIFFRACTIONr_scbond_it2.9653909
X-RAY DIFFRACTIONr_scangle_it4.0134.5824
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 38 -
Rwork0.224 890 -
obs--51.5 %

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