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- PDB-3mlf: Putative transcriptional regulator from Staphylococcus aureus. -

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Basic information

Entry
Database: PDB / ID: 3mlf
TitlePutative transcriptional regulator from Staphylococcus aureus.
Componentstranscriptional regulator
Keywordstranscription regulator / structural genomics / Helix-turn-helix XRE-family like protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologylambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsOsipiuk, J. / Tesar, C. / Gornicki, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative transcriptional regulator from Staphylococcus aureus.
Authors: Osipiuk, J. / Tesar, C. / Gornicki, P. / Joachimiak, A.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: transcriptional regulator
B: transcriptional regulator
C: transcriptional regulator
D: transcriptional regulator
E: transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)65,6065
Polymers65,6065
Non-polymers00
Water2,306128
1
A: transcriptional regulator
B: transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,2422
Polymers26,2422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-18 kcal/mol
Surface area10830 Å2
MethodPISA
2
C: transcriptional regulator
D: transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,2422
Polymers26,2422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-17 kcal/mol
Surface area10590 Å2
MethodPISA
3
E: transcriptional regulator

E: transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,2422
Polymers26,2422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+3/21
Buried area2030 Å2
ΔGint-16 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.776, 159.776, 69.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsputative biological unit is a dimer

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Components

#1: Protein
transcriptional regulator


Mass: 13121.135 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: USA300_TCH1516 / Gene: USA300HOU_2003 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8Z4R3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M TRIS buffer, 1.4 M di-ammonium tartrate, 1 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→44.3 Å / Num. all: 27459 / Num. obs: 27459 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 59.3 Å2 / Rmerge(I) obs: 0.146 / Χ2: 3.038 / Net I/σ(I): 8.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1386 / Χ2: 1.161 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→44.3 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 20.812 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.349 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1376 5 %RANDOM
Rwork0.208 ---
all0.21 27422 --
obs0.21 27422 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.1 Å2 / Biso mean: 24.902 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 0 128 3902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223920
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9685252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54125.9200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.13715823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3521512
X-RAY DIFFRACTIONr_chiral_restr0.1130.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022874
X-RAY DIFFRACTIONr_mcbond_it0.7371.52309
X-RAY DIFFRACTIONr_mcangle_it1.47523737
X-RAY DIFFRACTIONr_scbond_it2.61431611
X-RAY DIFFRACTIONr_scangle_it4.3334.51502
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 110 -
Rwork0.311 1864 -
all-1974 -
obs-1974 97.19 %
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)
12.1614-3.2109-0.29615.48642.74927.51840.16450.15960.1958-0.3673-0.1916-0.2962-0.46560.11340.0270.12210.06380.0110.17050.0280.139822.38941.782231.6565
20.88881.36941.00735.0739-0.79713.02260.1370.1523-0.1678-0.0433-0.0397-0.37130.26550.3955-0.09730.17270.0358-0.01850.09990.00140.122817.880856.912321.5078
30.1156-0.3697-0.58917.0591-0.03883.65590.04150.093-0.0189-0.0414-0.01790.3561-0.0997-0.57-0.02360.1672-0.00210.01260.09830.01630.1347.54336.024457.3224
43.9139-2.32971.10771.5021-1.33044.34480.15490.2316-0.318-0.1698-0.08590.19540.5945-0.242-0.0690.16010.0159-0.0110.1636-0.03710.10310.543250.143967.9287
50.68171.44680.53854.3083-0.56283.14880.0447-0.10440.09120.1119-0.0220.2504-0.0927-0.2547-0.02260.1094-0.0107-0.02740.0774-0.00950.11122.14019.93155.1258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-9 - 85
2X-RAY DIFFRACTION1A88 - 127
3X-RAY DIFFRACTION2B-7 - 84
4X-RAY DIFFRACTION2B88 - 112
5X-RAY DIFFRACTION3C-7 - 84
6X-RAY DIFFRACTION3C88 - 126
7X-RAY DIFFRACTION4D-7 - 85
8X-RAY DIFFRACTION4D88 - 125
9X-RAY DIFFRACTION5E0 - 85
10X-RAY DIFFRACTION5E88 - 128

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