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- PDB-1xd7: Crystal structure of a putative DNA binding protein -

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Basic information

Entry
Database: PDB / ID: 1xd7
TitleCrystal structure of a putative DNA binding protein
ComponentsywnA
KeywordsDNA BINDING PROTEIN / Structural Genomics / Protein Structure Initiative / winged helix DNA binding / hypothetical protein / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-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
Putative HTH-type transcriptional regulator YwnA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsAgarwal, R. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative DNA binding protein
Authors: Agarwal, R. / Swaminathan, S.
History
DepositionSep 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 16, 2019Group: Data collection / Structure summary / Category: diffrn / struct / Item: _struct.title
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: ywnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1872
Polymers16,0901
Non-polymers961
Water1086
1
A: ywnA
hetero molecules

A: ywnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3734
Polymers32,1812
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2930 Å2
ΔGint-48 kcal/mol
Surface area12790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.892, 49.362, 51.510
Angle α, β, γ (deg.)90.00, 121.61, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the dimer is generated by the symmetry operator -x, y, -z

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Components

#1: Protein ywnA


Mass: 16090.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Species: Bacillus subtilis / Strain: 168 / Gene: ywnA / Production host: Escherichia coli (E. coli) / References: UniProt: P71036
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG 4000, Ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791, 0.9793, 0.9400, 1.100
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.941
41.11
ReflectionResolution: 2.3→50 Å / Num. all: 5553 / Num. obs: 5553 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3 / Num. unique all: 247 / % possible all: 39.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→37.06 Å / Rfactor Rfree error: 0.022 / Data cutoff high absF: 220851.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: the electron density was absent or weak for the missing residues. Data collected with native crystal was used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 162 3.1 %RANDOM
Rwork0.26 ---
obs0.26 5294 83.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6301 Å2 / ksol: 0.347639 e/Å3
Displacement parametersBiso mean: 50.8 Å2
Baniso -1Baniso -2Baniso -3
1--14.42 Å20 Å2-2.98 Å2
2--16.87 Å20 Å2
3----2.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.3→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 5 6 894
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.128 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.463 13 2.9 %
Rwork0.399 428 -
obs--41.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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