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- PDB-6xtu: FULL-LENGTH LTTR LYSG FROM CORYNEBACTERIUM GLUTAMICUM -

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Basic information

Entry
Database: PDB / ID: 6xtu
TitleFULL-LENGTH LTTR LYSG FROM CORYNEBACTERIUM GLUTAMICUM
ComponentsLysine export transcriptional regulatory protein LysG
KeywordsTRANSCRIPTION / LTTR HELIX-TURN-HELIX TRANSCRIPTION REGULATION
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
HTH-type transcriptional regulator ArgP / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Lysine export transcriptional regulatory protein LysG
Similarity search - Component
Biological speciesCorynebacterium glutamicum MB001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsHofmann, E. / Syberg, F. / Schlicker, C. / Eggeling, L. / Schendzielorz, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Nat Commun / Year: 2020
Title: Engineering and application of a biosensor with focused ligand specificity.
Authors: Della Corte, D. / van Beek, H.L. / Syberg, F. / Schallmey, M. / Tobola, F. / Cormann, K.U. / Schlicker, C. / Baumann, P.T. / Krumbach, K. / Sokolowsky, S. / Morris, C.J. / Grunberger, A. / ...Authors: Della Corte, D. / van Beek, H.L. / Syberg, F. / Schallmey, M. / Tobola, F. / Cormann, K.U. / Schlicker, C. / Baumann, P.T. / Krumbach, K. / Sokolowsky, S. / Morris, C.J. / Grunberger, A. / Hofmann, E. / Schroder, G.F. / Marienhagen, J.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine export transcriptional regulatory protein LysG
B: Lysine export transcriptional regulatory protein LysG


Theoretical massNumber of molelcules
Total (without water)67,1892
Polymers67,1892
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-22 kcal/mol
Surface area28880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.980, 124.980, 111.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISchain 'A'AA0 - 19120 - 211
12ASPASPchain 'A'AA197 - 290217 - 310
23HISHISchain 'B'BB0 - 19120 - 211
24ASPASPchain 'B'BB197 - 290217 - 310

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Components

#1: Protein Lysine export transcriptional regulatory protein LysG


Mass: 33594.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum MB001 (bacteria)
Gene: lysG, Cgl1263, cg1425 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P94632
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17.5% PEG4000, 0.1 M AMMONIUMSULFATE, 0.1 M TRIS-HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.044 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 2.52→49.94 Å / Num. obs: 30335 / % possible obs: 99.92 % / Redundancy: 9.6 % / Biso Wilson estimate: 62.72 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.067 / Net I/σ(I): 25.02
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.206 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 2992 / CC1/2: 0.742 / Rrim(I) all: 1.273 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSNovember 3, 2014qdata reduction
XSCALENovember 3, 2014 BUILT=20141118data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ISP

3isp


Resolution: 2.52→49.94 Å / SU ML: 0.3933 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.1509
RfactorNum. reflection% reflection
Rfree0.2274 2914 5.13 %
Rwork0.1947 --
obs0.1964 30333 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 70.2 Å2
Refinement stepCycle: LAST / Resolution: 2.52→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 0 20 4372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00584430
X-RAY DIFFRACTIONf_angle_d0.81726026
X-RAY DIFFRACTIONf_chiral_restr0.048706
X-RAY DIFFRACTIONf_plane_restr0.0055784
X-RAY DIFFRACTIONf_dihedral_angle_d13.70011646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.560.431410.36372586X-RAY DIFFRACTION100
2.56-2.610.3661370.32662609X-RAY DIFFRACTION100
2.61-2.650.34971350.30992548X-RAY DIFFRACTION99.96
2.65-2.70.33441420.29092555X-RAY DIFFRACTION100
2.7-2.760.33191360.29352546X-RAY DIFFRACTION100
2.76-2.820.33871390.28252575X-RAY DIFFRACTION100
2.82-2.880.27941380.26522576X-RAY DIFFRACTION100
2.88-2.960.25931440.25452534X-RAY DIFFRACTION100
2.96-3.040.31021500.2592595X-RAY DIFFRACTION99.96
3.04-3.130.29561490.26892535X-RAY DIFFRACTION100
3.13-3.230.31881400.26052573X-RAY DIFFRACTION100
3.23-3.340.2871580.2442568X-RAY DIFFRACTION100
3.34-3.480.24051570.22512556X-RAY DIFFRACTION100
3.48-3.630.26941540.2042538X-RAY DIFFRACTION100
3.63-3.830.23011570.2012538X-RAY DIFFRACTION100
3.83-4.070.21521430.17922588X-RAY DIFFRACTION100
4.07-4.380.17031080.15182564X-RAY DIFFRACTION100
4.38-4.820.15511260.13192603X-RAY DIFFRACTION100
4.82-5.520.17911100.15482584X-RAY DIFFRACTION100
5.52-6.940.20031200.17382603X-RAY DIFFRACTION100
6.95-49.940.15021300.13672555X-RAY DIFFRACTION99.22
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)
11.514035489730.849415394342-1.409201444433.00801157502-1.31014556196.53637545640.01831830623060.06578402606150.0172575314075-0.2791871591180.05052859590090.1101492889650.245087764406-0.0989466669577-0.04222651719970.5163881283870.0437642394221-0.05764795344360.4418263984460.01560379731680.55288640853134.0375941592-3.20994173896-6.05532029982
22.265998440090.959307653681-0.01105997931294.09960463226-0.3948611233341.0222717119-0.101287279623-0.0192185221356-0.2440058842530.06635750440450.0791640474660.01938032318320.06057611110880.03878682548160.0421001263340.4480288470330.01097172881420.0231904464150.469895741315-0.02378215052040.46768541124336.380679613618.7650610616-18.9469604269
36.890936767480.776659667756-1.275161152025.26344254519-0.2668790100132.429981593350.0312554350313-0.4570135336590.5672635677770.01510461608670.0512055305053-0.128986722709-0.4671515203720.0460220180646-0.06165104807770.5182253163940.0298114552709-0.08710003006310.519176711875-0.04146394234670.46447973676226.755088668244.3287134056-15.3210502865
42.947533226991.60182024575-0.1409703578688.9912320411-1.122772701382.67486693314-0.1500619790710.0419866221199-0.141296713645-0.1691377675850.125481640956-0.4279491133970.1459329504020.1427789696380.03316501091680.304901660312-0.01034615046650.004563910009460.4746877323270.01059543995770.44499732039643.991527018419.7154075497-20.5815398612
52.35689009606-1.86113688368-0.2852775365727.004223227941.884651115445.449549815060.06834767016230.444732894365-0.193861536997-1.05372824538-0.327174562626-0.118045927640.2191790498090.3367054703010.1853913262560.5635448604870.006104364037860.1683194784540.5797719145550.003106417292820.58665192267752.0711917175-12.0857821111-18.1273964765
61.535307659-0.275763994743-0.7528614546212.192052962781.05654288474.52736886984-0.188488874156-0.128686352164-0.3586447125680.38442987359-0.1452498293850.05170234573690.387077628838-0.3184942298160.3303992127780.6165944433310.002805442414260.08067614491730.3835032808380.0774422249070.46096524129330.48642559978.7407663115319.1733150586
73.59045993835-1.231716104530.2818401775545.33038379845-1.410694206874.34078051656-0.17921354694-0.616306889057-0.4181078605380.7361372602050.2875540347880.8675582932320.39209762322-0.516135141507-0.04170051575260.76985008244-0.06270374826070.230463848260.628740307720.09324752824420.55488849855713.83612915122.044632528136.4751858777
85.012572815692.3198361931-2.696286322351.978225735110.1694005840726.80038415943-0.123907460634-0.536526115289-0.4874051988930.7362264107820.130291583343-0.3319441332291.29031483670.4227945422890.1059856895241.01482409070.1197695328790.001423585368560.4716179916860.1954980350860.69048034663933.96136791742.9813237297223.8001399433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 256 )
4X-RAY DIFFRACTION4chain 'A' and (resid 257 through 290 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 82 )
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 164 )
7X-RAY DIFFRACTION7chain 'B' and (resid 165 through 256 )
8X-RAY DIFFRACTION8chain 'B' and (resid 257 through 290 )

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