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- PDB-1sd4: Crystal Structure of a SeMet derivative of BlaI at 2.0 A -

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Basic information

Entry
Database: PDB / ID: 1sd4
TitleCrystal Structure of a SeMet derivative of BlaI at 2.0 A
ComponentsPENICILLINASE REPRESSOR
KeywordsDNA BINDING PROTEIN / BlaI / MecI / repressor / methicillin / B-lactam
Function / homology
Function and homology information


regulation of gene expression / response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Penicillinase repressor fold / Penicillinase repressor domain / BlaI transcriptional regulatory family / Penicillinase repressor / 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
Penicillinase repressor / Beta-lactamase repressor
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSafo, M.K. / Zhao, Q. / Musayev, F.N. / Robinson, H. / Scarsdale, N. / Archer, G.L.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Crystal structures of the BlaI repressor from Staphylococcus aureus and its complex with DNA: insights into transcriptional regulation of the bla and mec operons
Authors: Safo, M.K. / Zhao, Q. / Ko, T.-P. / Musayev, F.N. / Robinson, H. / Scarsdale, N. / Wang, A.H.-J. / Archer, G.L.
History
DepositionFeb 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PENICILLINASE REPRESSOR
B: PENICILLINASE REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8306
Polymers30,4462
Non-polymers3844
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-83 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.412, 116.362, 40.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe asymmetric unit contains the biological homodimer

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Components

#1: Protein PENICILLINASE REPRESSOR / Regulatory protein blaI / Beta-lactamase repressor protein


Mass: 15222.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q6UB84, UniProt: P0A042*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulfate, glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9792, 0.9795, 0.9611
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Mar 23, 2003
RadiationMonochromator: Channel-cut Si crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
30.96111
ReflectionResolution: 2→30 Å / Num. all: 20786 / Num. obs: 20786 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 52.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.7 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CBASSdata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.3 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.397 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23718 1061 5.1 %RANDOM
Rwork0.20291 ---
all0.2102 19686 --
obs0.20468 19686 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.416 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--1.13 Å20 Å2
3----1.53 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 20 225 2281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222072
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9762774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0555242
X-RAY DIFFRACTIONr_chiral_restr0.0950.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021450
X-RAY DIFFRACTIONr_nbd_refined0.2290.21096
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.220
X-RAY DIFFRACTIONr_mcbond_it1.3041.51212
X-RAY DIFFRACTIONr_mcangle_it2.51821978
X-RAY DIFFRACTIONr_scbond_it3.8093860
X-RAY DIFFRACTIONr_scangle_it6.5234.5796
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.38 77
Rwork0.277 1337
obs-1414
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.80221.71550.66084.09820.56291.1886-0.19230.0416-0.1451-0.31610.3111-0.0425-0.1212-0.0227-0.11880.0722-0.05780.01910.0527-0.01760.02955.657728.805327.3332
21.39120.0806-0.15161.49670.09230.4595-0.110.0941-0.07710.1109-0.0292-0.07170.0926-0.10730.13920.0238-0.02940.01030.0434-0.01940.059452.57351.217227.5276
31.4486-1.24040.23621.70531.38241.13360.09320.18910.05370.1879-0.0943-0.03910.1298-0.17630.00120.0704-0.02960.01780.07830.00050.005528.156616.323331.5582
40.9420.0534-0.29720.9096-0.07870.0655-0.16290.0606-0.0574-0.0675-0.0244-0.10640.0120.00130.18730.0559-0.02880.03270.0468-0.03490.067351.84660.854127.186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 735 - 73
2X-RAY DIFFRACTION2AA74 - 12674 - 126
3X-RAY DIFFRACTION3BB5 - 735 - 73
4X-RAY DIFFRACTION4BB74 - 12674 - 126

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