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- PDB-1sf9: Crystal Structure of Bacillus subtilis YfhH Protein : Putative Tr... -

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Basic information

Entry
Database: PDB / ID: 1sf9
TitleCrystal Structure of Bacillus subtilis YfhH Protein : Putative Transcriptional Regulator
ComponentsyfhH hypothetical protein
KeywordsStructural Genomics / unknown function / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Hypothetical protein YfhH domain / Hypothetical protein YfhH like domains / YfhH-like / Hypothetical protein YfhH / Protein of unknown function (DUF1811) / SH3 type barrels. / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Uncharacterized protein YfhH
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.71 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Kim, D.E. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Bacillus Subtilis YfhH hypothetical protein
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Kim, D.E. / Collart, F.R. / Anderson, W.F.
History
DepositionFeb 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: yfhH hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9973
Polymers14,7661
Non-polymers2312
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.142, 46.486, 50.511
Angle α, β, γ (deg.)90.00, 114.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

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Components

#1: Protein yfhH hypothetical protein


Mass: 14766.347 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yfhH / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: O31576
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.8M Hexanediol, 0.2M Calcium Chloride, 0.5M Sodium Chloride, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 2003
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→25 Å / Num. all: 12888 / Num. obs: 12888 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 39
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 21.6 / Num. unique all: 1260 / % possible all: 99.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.71→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Crystallographic conjugate gradient refinement using maximum likelihood target for amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 664 5.1 %Random
Rwork0.1715 ---
all-12840 --
obs-12840 98 %-
Displacement parametersBiso mean: 17 Å2
Baniso -1Baniso -2Baniso -3
1-2.761 Å20 Å21.201 Å2
2--0.53 Å20 Å2
3----3.291 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.07 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.71→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 2 188 1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.5941.5
X-RAY DIFFRACTIONc_scbond_it2.8392
X-RAY DIFFRACTIONc_mcangle_it2.3192
X-RAY DIFFRACTIONc_scangle_it4.2092.5
LS refinement shellResolution: 1.71→1.76 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2556 60 4.59 %
Rwork0.2059 1035 -
obs-1035 83.78 %

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