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- PDB-3onm: Effector binding Domain of LysR-Type transcription factor RovM fr... -

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Basic information

Entry
Database: PDB / ID: 3onm
TitleEffector binding Domain of LysR-Type transcription factor RovM from Y. pseudotuberculosis
ComponentsTranscriptional regulator LrhA
KeywordsTRANSCRIPTION / LysR / RovM / transcription factor / virulence factor
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator LrhA / Transcriptional regulator LrhA
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsQuade, N. / Diekmann, M. / Haffke, M. / Heroven, A.K. / Dersch, P. / Heinz, D.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of the effector-binding domain of the LysR-type transcription factor RovM from Yersinia pseudotuberculosis.
Authors: Quade, N. / Dieckmann, M. / Haffke, M. / Heroven, A.K. / Dersch, P. / Heinz, D.W.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator LrhA
B: Transcriptional regulator LrhA


Theoretical massNumber of molelcules
Total (without water)52,3172
Polymers52,3172
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-12 kcal/mol
Surface area17670 Å2
MethodPISA
2
A: Transcriptional regulator LrhA
B: Transcriptional regulator LrhA

A: Transcriptional regulator LrhA
B: Transcriptional regulator LrhA


Theoretical massNumber of molelcules
Total (without water)104,6354
Polymers104,6354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455-x-1,-y,z1
Buried area7300 Å2
ΔGint-38 kcal/mol
Surface area31420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.468, 69.468, 351.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Transcriptional regulator LrhA


Mass: 26158.682 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 92-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Strain: IP 31758 / Gene: lrhA, RovM, YpsIP31758_1452 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7FGQ3, UniProt: A0A0U1QVR9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M HEPES pH 8.0, 12.5% (w/v) PEG 6000, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF ID2910.9793
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMay 2, 2010
RIGAKU SATURN 944+2CCDJan 1, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111) Si (311)SINGLE WAVELENGTHMx-ray1
2VariMaxSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21.541
ReflectionRedundancy: 10.4 % / Av σ(I) over netI: 6.18 / Number: 182284 / Rsym value: 0.074 / D res high: 2.4 Å / D res low: 87.804 Å / Num. obs: 17557 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.5942.8797.710.0390.0399.3
5.377.5910010.0550.05510.4
4.385.3710010.0640.06410.8
3.794.3810010.0720.07211.1
3.393.7910010.0810.08111.1
3.13.3910010.1020.10211.1
2.873.110010.1380.13810.8
2.682.8710010.2060.20610.4
2.532.6810010.3440.3449.6
2.42.5310010.540.549.2
ReflectionResolution: 2.4→87.8 Å / Num. all: 17557 / Num. obs: 17557 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rsym value: 0.074 / Net I/σ(I): 16.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.5 / Num. measured all: 22745 / Num. unique all: 2485 / Rsym value: 0.54 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→42.87 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.291 / WRfactor Rwork: 0.2206 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7968 / SU B: 19.941 / SU ML: 0.216 / SU R Cruickshank DPI: 0.4017 / SU Rfree: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2946 909 5.2 %RANDOM
Rwork0.2205 ---
obs0.2243 17503 99.76 %-
all-17557 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 174.08 Å2 / Biso mean: 59.3615 Å2 / Biso min: 18.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2--1.81 Å20 Å2
3----3.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 0 70 2857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222847
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.9893893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53822.857105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4615446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6421523
X-RAY DIFFRACTIONr_chiral_restr0.1050.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222124
X-RAY DIFFRACTIONr_mcbond_it0.681.51855
X-RAY DIFFRACTIONr_mcangle_it1.25622998
X-RAY DIFFRACTIONr_scbond_it2.0353992
X-RAY DIFFRACTIONr_scangle_it3.224.5895
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 64 -
Rwork0.229 1210 -
all-1274 -
obs--100 %
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)
14.60810.5994-0.43695.23190.98153.65070.0116-0.23020.16970.36110.0058-0.2234-0.24030.1192-0.01740.12590.0102-0.02180.19410.03730.2788-25.2434-1.2255-0.1241
21.75550.457-0.90014.930.92743.1562-0.05080.0730.258-0.32030.00150.2589-0.4008-0.16810.04930.1738-0.0164-0.05710.12230.00140.2255-26.68119.8059-13.6266
38.8056-1.07965.804714.2691-5.13254.91820.32250.1354-0.50060.4818-0.1573-0.23620.07820.3634-0.16530.05310.1321-0.03590.5690.11620.4146-16.5219-5.91960.6725
44.46630.3480.32062.6425-0.52428.61830.00340.24020.5024-0.2282-0.03030.5005-0.6188-0.56520.02680.3291-0.0039-0.03080.176-0.00590.3837-36.313515.1502-39.8572
52.3817-0.1564-0.01282.46140.35882.6520.0057-0.05610.02930.0455-0.0585-0.1456-0.13250.28990.05280.1604-0.02510.0070.15630.00940.1267-20.45663.5331-30.6736
6-1.05052.0840.95892.75442.1417-6.4912-1.24340.92260.274-0.43730.80310.0299-0.10940.01310.44032.6489-0.484-0.63541.32380.21691.1048-39.080128.3348-44.4739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A99 - 166
2X-RAY DIFFRACTION2A167 - 263
3X-RAY DIFFRACTION3A264 - 289
4X-RAY DIFFRACTION4B100 - 160
5X-RAY DIFFRACTION5B161 - 269
6X-RAY DIFFRACTION6B270 - 280

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