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- PDB-3g3z: The structure of NMB1585, a MarR family regulator from Neisseria ... -

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Basic information

Entry
Database: PDB / ID: 3g3z
TitleThe structure of NMB1585, a MarR family regulator from Neisseria meningitidis
ComponentsTranscriptional regulator, MarR family
KeywordsTRANSCRIPTION / MarR / Neisseria meningitidis / transcription factor / Structural Genomics / Oxford Protein Production Facility / OPPF
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #820 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #820 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsNichols, C.E. / Sainsbury, S. / Ren, J. / Walter, T.S. / Verma, A. / Stammers, D.K. / Saunders, N.J. / Owens, R.J. / Oxford Protein Production Facility (OPPF)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: The structure of NMB1585, a MarR-family regulator from Neisseria meningitidis
Authors: Nichols, C.E. / Sainsbury, S. / Ren, J. / Walter, T.S. / Verma, A. / Stammers, D.K. / Saunders, N.J. / Owens, R.J.
History
DepositionFeb 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, MarR family
B: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)32,8592
Polymers32,8592
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-47 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.001, 64.367, 61.066
Angle α, β, γ (deg.)90.00, 91.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 751 - 75
21BB1 - 751 - 75
12AA86 - 11286 - 112
22BB86 - 11286 - 112
13AA121 - 142121 - 142
23BB121 - 142121 - 142

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Transcriptional regulator, MarR family / NMB1585


Mass: 16429.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: MC58 / Gene: NMB1585 / Plasmid: OPPF160 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9JYH5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 25%(w/v) PEG 3350, 0.2M ammonium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.90777, 0.97912, 0.97889
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2004 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.907771
20.979121
30.978891
ReflectionResolution: 2.1→30 Å / Num. obs: 14294 / % possible obs: 89.4 % / Observed criterion σ(I): -1.5 / Redundancy: 3.2 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 1.7 / Num. unique all: 763 / % possible all: 48.1

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.5.0047refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→27.65 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.648 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26581 734 5.1 %RANDOM
Rwork0.20296 ---
obs0.20635 13531 89.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.433 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å2-1.91 Å2
2--3.11 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 0 109 2363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222288
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.9553084
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4495282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.87925.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39515428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.3481514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021698
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.51541402
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.53562246
X-RAY DIFFRACTIONr_scbond_it3.4776886
X-RAY DIFFRACTIONr_scangle_it5.27110838
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
1300MEDIUM POSITIONAL0.220.5
1297LOOSE POSITIONAL0.455
1300MEDIUM THERMAL2.7120
1297LOOSE THERMAL3.5620
2108MEDIUM POSITIONAL0.140.5
297LOOSE POSITIONAL0.345
2108MEDIUM THERMAL2.4920
297LOOSE THERMAL3.8120
388MEDIUM POSITIONAL0.30.5
385LOOSE POSITIONAL1.065
388MEDIUM THERMAL3.3920
385LOOSE THERMAL6.8820
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 35 -
Rwork0.25 505 -
obs--45.8 %
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)
14.5654-2.2391.85392.5793-0.65941.045-0.1873-0.1956-0.03880.23440.12690.1795-0.109-0.02450.06030.15460.02040.07350.1192-0.00550.1192-0.0813.84423.969
20.57930.73210.06892.4625-0.39410.1766-0.0714-0.0119-0.1088-0.31290.0722-0.02230.0528-0.0367-0.00080.14730.01380.00490.1882-0.03070.1388-2.9499.27612.13
32.8947-0.8711-0.28390.90880.07871.7857-0.06150.2292-0.4258-0.0658-0.00450.02670.08250.0740.06590.09890.00220.03830.1057-0.02790.186814.466-3.42215.174
40.91090.8124-0.27013.58730.38480.2436-0.0417-0.0064-0.0537-0.14070.0005-0.0671-0.07380.00770.04120.1950.007-0.01840.11990.01770.09335.32931.38514.388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 25
2X-RAY DIFFRACTION1B116 - 142
3X-RAY DIFFRACTION2B1 - 25
4X-RAY DIFFRACTION2A116 - 142
5X-RAY DIFFRACTION3A26 - 115
6X-RAY DIFFRACTION4B26 - 115

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