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- PDB-3hhf: Structure of CrgA regulatory domain, a LysR-type transcriptional ... -

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Basic information

Entry
Database: PDB / ID: 3hhf
TitleStructure of CrgA regulatory domain, a LysR-type transcriptional regulator from Neisseria meningitidis.
ComponentsTranscriptional regulator, LysR familyTranscriptional regulation
KeywordsTRANSCRIPTION REGULATOR / Neisseria meningitidis / transcription factor / LysR / Structural Genomics / Oxford Protein Production Facility / OPPF / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription
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 ...: / : / 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
HTH-type transcriptional regulator CrgA
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSainsbury, S. / Ren, J. / Owens, R.J. / Stuart, D.I. / Oxford Protein Production Facility (OPPF)
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The structure of CrgA from Neisseria meningitidis reveals a new octameric assembly state for LysR transcriptional regulators
Authors: Sainsbury, S. / Lane, L.A. / Ren, J. / Gilbert, R.J. / Saunders, N.J. / Robinson, C.V. / Stuart, D.I. / Owens, R.J.
History
DepositionMay 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Transcriptional regulator, LysR family
A: Transcriptional regulator, LysR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9504
Polymers46,8792
Non-polymers712
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-37 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.600, 65.600, 63.500
Angle α, β, γ (deg.)90.00, 105.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A95 - 146
2115B95 - 146
1124A155 - 293
2124B155 - 293

NCS ensembles :
ID
1
2

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Components

#1: Protein Transcriptional regulator, LysR family / Transcriptional regulation


Mass: 23439.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: MC58 / Gene: CrgA, NMB1856 / Plasmid: OPPF2152 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9JXW7
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200 mM ammonium acetate, 25% PEG 3350, 0.1M bis-Tris pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9780, 0.9065, 0.9785, 0.9795
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.90651
30.97851
40.97951
ReflectionResolution: 2.3→30 Å / Num. obs: 15951 / % possible obs: 85.8 % / Observed criterion σ(I): -1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.1 / Num. unique all: 636 / % possible all: 34.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.892 / SU B: 15.972 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.768 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25819 770 5 %RANDOM
Rwork0.20146 ---
obs0.20417 14781 84.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.523 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20.57 Å2
2--1.16 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 2 203 3344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223206
X-RAY DIFFRACTIONr_bond_other_d0.0010.022175
X-RAY DIFFRACTIONr_angle_refined_deg11.9774350
X-RAY DIFFRACTIONr_angle_other_deg0.94735301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5955403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.60623.617141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07715530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7281522
X-RAY DIFFRACTIONr_chiral_restr0.1180.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02647
X-RAY DIFFRACTIONr_nbd_refined0.1840.2621
X-RAY DIFFRACTIONr_nbd_other0.1790.22218
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21522
X-RAY DIFFRACTIONr_nbtor_other0.0810.21669
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6822505
X-RAY DIFFRACTIONr_mcbond_other0.0852822
X-RAY DIFFRACTIONr_mcangle_it0.8733243
X-RAY DIFFRACTIONr_scbond_it1.53241311
X-RAY DIFFRACTIONr_scangle_it2.29961107
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1308medium positional0.12
21831medium positional0.382
1389loose positional0.5810
1308medium thermal1.658
21831medium thermal18
1389loose thermal1.920
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 24 -
Rwork0.278 389 -
obs--29.97 %
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)
14.57880.41820.07522.59320.18142.2840.011-0.16760.10950.2299-0.0598-0.1361-0.09480.04920.0488-0.0447-0.00340.0042-0.03140.0114-0.065324.398735.423948.6081
22.83250.7502-0.85882.21180.23411.7965-0.02020.02720.0106-0.13930.0516-0.07830.05720.1308-0.0313-0.11310.00140.0236-0.14980.0186-0.161717.016930.930822.1654
34.0486-0.2243-0.73691.9017-0.7142.0803-0.0194-0.09310.2381-0.05420.04160.0618-0.2514-0.1092-0.0222-0.02870.01370.0138-0.0658-0.0043-0.0166-4.625139.514631.0215
42.15280.4196-0.59021.7016-0.10811.7357-0.0089-0.1086-0.07490.080.00360.00470.08330.0070.0053-0.04290.00490.0004-0.01810.0272-0.06612.461723.445252.7737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 161
2X-RAY DIFFRACTION1A267 - 294
3X-RAY DIFFRACTION2A162 - 266
4X-RAY DIFFRACTION3B90 - 161
5X-RAY DIFFRACTION3B267 - 294
6X-RAY DIFFRACTION4B162 - 266

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