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- PDB-4ejo: Crystal structure of padr family transcriptional regulator from E... -

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Basic information

Entry
Database: PDB / ID: 4ejo
TitleCrystal structure of padr family transcriptional regulator from Eggerthella lenta DSM 2243
ComponentsTranscriptional regulator, PadR-like family
KeywordsTRANSCRIPTION REGULATOR / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / TRANSCRIPTIONAL REGULATOR
Function / homology
Function and homology information


: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / 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
ETHANOL / Transcriptional regulator, PadR-like family
Similarity search - Component
Biological speciesEggerthella lenta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsChang, C. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of padr family transcriptional regulator from Eggerthella lenta DSM 2243
Authors: Chang, C. / Li, H. / Bearden, J. / Joachimiak, A.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionApr 25, 2012ID: 3RI2
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / 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.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, PadR-like family
B: Transcriptional regulator, PadR-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2673
Polymers28,2212
Non-polymers461
Water39622
1
A: Transcriptional regulator, PadR-like family
hetero molecules

A: Transcriptional regulator, PadR-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3134
Polymers28,2212
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area3830 Å2
ΔGint-34 kcal/mol
Surface area12890 Å2
MethodPISA
2
B: Transcriptional regulator, PadR-like family

B: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)28,2212
Polymers28,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4260 Å2
ΔGint-39 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.783, 55.783, 132.425
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11B-206-

HOH

Detailsunit A makes dimer with operator (x,y,z) (1-x,1-y,z) unit B makes dimer with operator (x,y,z) (-x,-y,z)

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Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 14110.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eggerthella lenta (bacteria)
Strain: ATCC 25559 / DSM 2243 / JCM 9979 / NCTC 11813 / VPI 0255
Gene: Elen_1533 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) MAGIC / References: UniProt: C8WHB0
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 1.83 Å3/Da / Density % sol: 32.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M PHOSPHATE-CITRATE PH 4.2, 40% ETHANOL, 5% PEG 1000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE, temperature 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948, 0.97959
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2010
RadiationMonochromator: SI(111)DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979481
20.979591
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.588
11K, H, -L20.412
ReflectionResolution: 2.1→50 Å / Num. all: 11881 / Num. obs: 11880 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 33.9
Reflection shellResolution: 2.1→2.12 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.543 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 532 4.5 %RANDOM
Rwork0.181 ---
obs0.1833 11854 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.83 Å2 / Biso mean: 44.9808 Å2 / Biso min: 6.08 Å2
Baniso -1Baniso -2Baniso -3
1-15.51 Å20 Å20 Å2
2--15.51 Å20 Å2
3----31.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 3 22 1792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021862
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.992519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9415232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88922.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92115342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0551522
X-RAY DIFFRACTIONr_chiral_restr0.1040.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211398
X-RAY DIFFRACTIONr_rigid_bond_restr5.43531862
X-RAY DIFFRACTIONr_sphericity_free29.42856
X-RAY DIFFRACTIONr_sphericity_bonded28.2951846
LS refinement shellResolution: 2.096→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 52 -
Rwork0.184 839 -
all-891 -
obs-893 98.34 %
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)
10.10361.37640.157526.8957-5.97698.45970.03710.03160.07010.2360.38871.21350.3805-0.2922-0.42580.15310.01760.02340.25930.08040.318319.72614.9479.901
21.8825-1.9299-1.03584.92390.72240.6162-0.0107-0.0241-0.0211-0.18480.04110.16740.06080.0027-0.03040.1909-0.0053-0.05760.1893-0.01260.305521.51735.6115.737
311.6429-4.7078.48491.9074-3.43226.1879-0.3679-0.25340.22080.14830.1219-0.1031-0.3024-0.18130.2460.22260.03660.00480.1953-0.04710.461810.33746.0317.717
416.678314.597512.663413.690712.818212.90710.5655-0.0861-0.45770.3822-0.1909-0.42260.2045-0.2718-0.37460.14070.1153-0.1490.1163-0.13550.458411.06535.4214.625
54.11642.5886-1.39855.5687-0.71740.4843-0.1806-0.4418-0.2434-0.30430.05750.15390.06160.14620.12310.20610.0449-0.02540.22820.02130.319317.64937.7115.314
65.5255-0.19552.61520.89550.07021.27190.0246-0.56350.18170.0892-0.11820.08810.0411-0.26570.09350.2030.0033-0.0060.2341-0.04570.321714.60850.30513.229
70.2941-1.3596-0.35797.8232.59261.1736-0.01260.01010.06680.02080.153-0.1179-0.0335-0.0475-0.14030.15880.0101-0.00030.2790.0810.350729.39344.8311.803
83.4566-7.2655-2.693919.79814.42482.5235-0.2599-0.216-0.13140.02290.12790.18790.19830.28550.1320.2403-0.01020.02250.17440.02240.273234.00626.105-3.575
92.72351.5614-1.020516.5687.70375.20880.06310.0253-0.42320.3994-0.2387-0.39710.2929-0.30550.17570.17160.00670.04990.2364-0.04120.34547.617-13.813-7.288
101.68823.1803-0.21247.09471.8894.8675-0.3268-0.14790.1706-0.5899-0.31910.59720.3836-0.16440.64590.2780.026-0.02370.20580.00840.43226.2577.598-3.3
1123.7477-1.50179.18050.096-0.58183.5507-0.12670.5956-0.05380.0220.0395-0.0121-0.09220.23790.08720.2247-0.06980.00030.13940.06520.424117.59918.087-5.242
1212.1787-2.19471.89217.5995-22.948230.0033-0.0967-0.8-0.12790.11920.40870.2829-0.1371-0.4325-0.3120.1262-0.0190.01970.17310.00030.388116.7297.632-2.138
134.4744-17.7931-0.98670.79133.92130.2173-0.07590.0911-0.3510.7808-0.1351.29180.0423-0.01530.21090.5704-0.67140.1910.818-0.29110.3459.19110.658-12.521
141.9469-0.4945-1.412.4418-1.79323.01970.0820.10950.0875-0.1203-0.0018-0.00060.0256-0.1075-0.08010.1717-0.0172-0.02140.21120.01870.306813.26922.456-10.855
155.2432-0.9421-2.94769.3223-4.35984.27020.1171-0.041-0.2680.1215-0.26830.0862-0.1440.18520.15120.14130.00070.01380.23170.08260.3837-1.44916.8640.743
163.7298-0.2526-1.50314.6798-1.4950.7809-0.08930.33860.0670.75790.14710.0608-0.0409-0.1605-0.05780.1489-0.0205-0.01660.20910.02810.2957-6.492-2.7946.393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 12
2X-RAY DIFFRACTION2A13 - 28
3X-RAY DIFFRACTION3A29 - 34
4X-RAY DIFFRACTION4A35 - 45
5X-RAY DIFFRACTION5A46 - 59
6X-RAY DIFFRACTION6A60 - 83
7X-RAY DIFFRACTION7A84 - 95
8X-RAY DIFFRACTION8A96 - 111
9X-RAY DIFFRACTION9B0 - 12
10X-RAY DIFFRACTION10B13 - 28
11X-RAY DIFFRACTION11B29 - 34
12X-RAY DIFFRACTION12B35 - 45
13X-RAY DIFFRACTION13B46 - 59
14X-RAY DIFFRACTION14B60 - 83
15X-RAY DIFFRACTION15B84 - 95
16X-RAY DIFFRACTION16B96 - 115

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