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Basic information

Entry
Database: PDB / ID: 3clo
TitleCrystal structure of putative transcriptional regulator containing a LuxR DNA binding domain (NP_811094.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.04 A resolution
ComponentsTranscriptional regulatorTranscriptional regulation
KeywordsTRANSCRIPTION REGULATOR / NP_811094.1 / Putative Transcriptional Regulator Containing a LuxR DNA Binding Domain / Bacterial regulatory proteins / luxR family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / DNA-binding / Transcription regulation
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / PAS domain / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / PAS domain / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.04 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative transcriptional regulator containing a LuxR DNA binding domain (NP_811094.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.04 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
C: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,66213
Polymers90,2763
Non-polymers38610
Water8,899494
1
A: Transcriptional regulator
B: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3617
Polymers60,1842
Non-polymers1775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-13.2 kcal/mol
Surface area23040 Å2
MethodPISA
2
C: Transcriptional regulator
hetero molecules

C: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,60212
Polymers60,1842
Non-polymers41810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area2740 Å2
ΔGint-13.5 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.650, 233.650, 125.273
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYSERAA0 - 761 - 77
21GLYSERBB0 - 761 - 77
31GLYSERCC0 - 761 - 77
42ASPLEUAA84 - 25785 - 258
52ASPLEUBB84 - 25785 - 258
62ASPLEUCC84 - 25785 - 258

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Components

#1: Protein Transcriptional regulator / Transcriptional regulation


Mass: 30091.965 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Species: Bacteroides thetaiotaomicron / Strain: VPI-5482 / DSM 2079 / NCTC 10582 / E50 / Gene: NP_811094.1, BT_2181 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A5Q7
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.64 Å3/Da / Density % sol: 66.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 4.3M NaCl, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97964
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 12, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979641
ReflectionResolution: 2.04→48.45 Å / Num. obs: 82770 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.63 % / Biso Wilson estimate: 36.169 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.04-2.115.660.9981.83448367915100
2.11-2.20.7512.4497788774100
2.2-2.30.5743.2465068179100
2.3-2.420.4384.1462128123100
2.42-2.570.3045.7465518169100
2.57-2.770.2068473738308100
2.77-3.040.13411.4457748048100
3.04-3.480.08217.1469488341100
3.48-4.380.05822.7463958359100
4.38-48.450.05224.846008855599.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.04→48.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.039 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.131
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. CL, NA AND GOL MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 5. THE FOLLOWING REGIONS ARE POORLY ORDERED AND WERE MODELED BASED ON NCS, A70-85, B72-82, C17-27.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4142 5 %RANDOM
Rwork0.187 ---
obs0.189 82770 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.323 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0.49 Å20 Å2
2---0.98 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.04→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 15 494 6629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226251
X-RAY DIFFRACTIONr_bond_other_d0.0020.024281
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9648444
X-RAY DIFFRACTIONr_angle_other_deg0.891310428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0135777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32723.946294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.476151151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4751551
X-RAY DIFFRACTIONr_chiral_restr0.0780.2956
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021242
X-RAY DIFFRACTIONr_nbd_refined0.20.21176
X-RAY DIFFRACTIONr_nbd_other0.1920.24443
X-RAY DIFFRACTIONr_nbtor_refined0.1650.23044
X-RAY DIFFRACTIONr_nbtor_other0.0810.23250
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2321
X-RAY DIFFRACTIONr_metal_ion_refined0.1690.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.228
X-RAY DIFFRACTIONr_mcbond_it1.26433858
X-RAY DIFFRACTIONr_mcbond_other0.68631565
X-RAY DIFFRACTIONr_mcangle_it2.50356227
X-RAY DIFFRACTIONr_scbond_it4.55682453
X-RAY DIFFRACTIONr_scangle_it6.759112213
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1471MEDIUM POSITIONAL0.480.5
2B1471MEDIUM POSITIONAL0.260.5
3C1471MEDIUM POSITIONAL0.50.5
1A1766LOOSE POSITIONAL0.715
2B1766LOOSE POSITIONAL0.465
3C1766LOOSE POSITIONAL0.625
1A1471MEDIUM THERMAL1.342
2B1471MEDIUM THERMAL1.132
3C1471MEDIUM THERMAL1.842
1A1766LOOSE THERMAL2.810
2B1766LOOSE THERMAL2.310
3C1766LOOSE THERMAL3.3710
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 312 -
Rwork0.308 5750 -
all-6062 -
obs--99.98 %
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)
11.8837-0.3258-0.21971.4030.40840.83370.05250.23170.0346-0.0144-0.11170.24850.0007-0.02240.0593-0.08280.0577-0.0339-0.0678-0.0048-0.051810.838948.352132.0392
23.6158-0.4994-2.58580.41250.57792.4676-0.17040.0549-0.40580.1290.105-0.0080.1209-0.08730.0655-0.05730.00560.0762-0.1253-0.0133-0.0336-15.55841.1944.0054
32.1145-0.4595-0.36812.08360.35830.960.090.34920.0328-0.1545-0.0779-0.35050.02020.2592-0.0121-0.07810.0999-0.00770.0415-0.0072-0.002534.02938.323524.5075
44.3335-4.67371.21585.3108-0.81451.25460.17220.32740.0393-0.2547-0.19430.16410.12230.11680.0221-0.05410.1384-0.03980.0158-0.0242-0.094954.711618.481832.7081
51.1724-0.1992-0.04240.8541-0.1061.9588-0.11860.0632-0.1830.0792-0.0398-0.1440.25060.29030.1584-0.06950.0263-0.0113-0.06270.0393-0.046-23.904967.505419.0609
611.14471.1428-2.83781.6005-1.63122.3478-0.2418-0.5023-0.34520.0754-0.2485-0.5553-0.03830.56420.4903-0.1168-0.03280.00650.09050.19750.15994.34172.618410.2427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1971 - 198
2X-RAY DIFFRACTION2AA198 - 257199 - 258
3X-RAY DIFFRACTION3BB0 - 1971 - 198
4X-RAY DIFFRACTION4BB198 - 257199 - 258
5X-RAY DIFFRACTION5CC0 - 1971 - 198
6X-RAY DIFFRACTION6CC198 - 257199 - 258

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