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- PDB-6gy3: Crystal Structure of C. glutamicum AmtR bound to glnA operator DNA -

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Basic information

Entry
Database: PDB / ID: 6gy3
TitleCrystal Structure of C. glutamicum AmtR bound to glnA operator DNA
Components
  • AmtR protein
  • DNA (5'-D(*GP*TP*CP*TP*AP*TP*AP*GP*AP*TP*CP*GP*AP*TP*AP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*TP*AP*TP*CP*GP*AP*TP*CP*TP*AP*TP*AP*GP*AP*C)-3')
KeywordsTRANSCRIPTION / transcription regulator / TetR family / nitrogen regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / AmtR protein / Repressor of the high-affinity (Methyl) ammonium uptake system
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsSevvana, M. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP1395 Germany
CitationJournal: To be published
Title: The role of DNA flexibility in transcription regulator AmtR-DNA interaction
Authors: Schwab, C. / Sevvana, M. / Seidel, G. / Sandmann, A. / Grau, F.C. / Muller, Y.A.
History
DepositionJun 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmtR protein
B: AmtR protein
C: DNA (5'-D(*GP*TP*CP*TP*AP*TP*AP*GP*AP*TP*CP*GP*AP*TP*AP*GP*AP*C)-3')
D: DNA (5'-D(*GP*TP*CP*TP*AP*TP*CP*GP*AP*TP*CP*TP*AP*TP*AP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)55,6854
Polymers55,6854
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-61 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.320, 76.150, 117.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B
112(CHAIN C AND (RESID 1 THROUGH 6 OR RESID 8 THROUGH 11 OR RESID 13 THROUGH 18))
212(CHAIN D AND (RESID 1 THROUGH 6 OR RESID 8 THROUGH 11 OR RESID 13 THROUGH 18))

NCS ensembles :
ID
1
2

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Components

#1: Protein AmtR protein


Mass: 22327.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: first 14 residues cleaved off due to factor Xa protease treatment electron density allowed tracing of residues 19-220 in both protomers
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: amtR / Plasmid: pMALc2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H7C699, UniProt: Q79VH8*PLUS
#2: DNA chain DNA (5'-D(*GP*TP*CP*TP*AP*TP*AP*GP*AP*TP*CP*GP*AP*TP*AP*GP*AP*C)-3')


Mass: 5539.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Corynebacterium glutamicum (bacteria)
#3: DNA chain DNA (5'-D(*GP*TP*CP*TP*AP*TP*CP*GP*AP*TP*CP*TP*AP*TP*AP*GP*AP*C)-3')


Mass: 5490.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Corynebacterium glutamicum (bacteria)

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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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M ammonium acetate, 0.1 M Tris-HCl, pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.68→33.289 Å / Num. obs: 16335 / % possible obs: 98.8 % / Redundancy: 6.964 % / Biso Wilson estimate: 53.68 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.46
Reflection shellResolution: 2.68→2.75 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 3.39 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MQQ

5mqq


Resolution: 2.68→33.29 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 28.07
RfactorNum. reflection% reflection
Rfree0.251 812 4.99 %
Rwork0.208 --
obs0.21 16275 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.1 Å2
Refinement stepCycle: LAST / Resolution: 2.68→33.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 732 0 0 3872
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A1230X-RAY DIFFRACTIONPOSITIONAL
12B1230X-RAY DIFFRACTIONPOSITIONAL
21C300X-RAY DIFFRACTIONPOSITIONAL
22D300X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6802-2.8480.34311290.27612448X-RAY DIFFRACTION95
2.848-3.06780.30151340.26862545X-RAY DIFFRACTION100
3.0678-3.37630.30071320.25372545X-RAY DIFFRACTION98
3.3763-3.86420.29121350.22042569X-RAY DIFFRACTION99
3.8642-4.8660.23871370.18272615X-RAY DIFFRACTION99
4.866-33.29150.19121450.1742741X-RAY DIFFRACTION99
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)
10.25550.0523-0.29410.1628-0.35680.94070.140.06580.06810.23570.2523-0.0478-0.4871-0.39270.0620.58280.01020.04340.3901-0.12450.321413.791738.388921.1523
20.03350.0513-0.01110.06650.0190.02930.39530.42410.2505-0.17340.17840.3582-0.10040.27280.00050.58650.0811-0.01720.49690.09520.393916.197836.9551-8.08
30.10010.0752-0.02860.14230.02060.04830.1241-0.1337-0.04130.5713-0.30360.55680.07880.2104-0.00060.40350.05180.08730.4519-0.0560.38629.684920.140721.9917
40.02510.0134-0.00660.0326-0.02480.0203-0.23870.30990.2990.5788-0.0003-0.04980.3852-0.2828-0.00050.43130.0358-0.07940.4916-0.04740.362213.107528.997127.1467
50.11720.03550.06790.01120.01850.0303-0.0175-0.3164-0.03670.1198-0.0518-0.22660.23210.076900.58040.1136-0.10670.5038-0.01570.498322.96257.751325.9812
60.15840.0870.01290.10230.04820.0598-0.215-0.2592-0.2850.32970.11660.18840.65810.1416-0.0580.96310.06970.11120.49260.06840.49717.7798-4.18524.1274
70.21380.02320.01820.00260.00280.00170.06260.2055-0.2588-0.04540.1361-0.1054-0.03020.30590.00210.3835-0.0302-0.03050.57090.04230.460124.69713.859413.9732
80.0411-0.00430.01640.015-0.0220.071-0.10960.1198-0.1499-0.07360.0542-0.06270.10420.260.00050.72320.1476-0.16350.61910.04560.749929.7259-1.852618.7329
90.04430.03080.05590.18860.13750.11980.4902-0.24420.14770.43790.0064-0.08740.1885-0.00760.0160.56290.02950.12880.3031-0.05740.508522.3505-6.325912.5593
100.1620.1062-0.02240.07610.01150.0766-0.1759-0.163-0.38320.08-0.03770.01160.3978-0.0418-0.55610.6973-0.17120.4050.30030.05150.55279.483-5.399722.3712
110.0008-00.00050.0002-0.0004-0.00010.0209-0.107-0.0140.2635-0.04450.1536-0.0306-0.0697-0.17681.22720.06640.34850.48150.28660.736619.9082-20.45320.8193
121.02830.04430.27960.15620.20870.3249-0.0761-0.262-0.5591-0.1360.07210.08030.14850.41180.09691.66090.06790.28640.76040.29080.781718.2164-11.723933.3309
130.0824-0.1458-0.13790.59960.26780.2480.06420.15020.2027-0.2148-0.2723-0.1769-0.26740.0373-0.01450.23830.0132-0.06020.37480.01490.265221.79621.9456-6.078
140.11270.1991-0.1480.3675-0.23390.3922-0.15310.5232-0.3407-0.21730.03750.05470.2729-0.1896-0.29920.2215-0.0384-0.05940.4685-0.18490.639710.71235.7887-7.0367
150.71260.20580.41581.2815-1.04841.43980.01370.2779-0.1661-0.3192-0.25190.34020.6019-0.0754-1.27120.2827-0.10860.07120.2785-0.17710.538915.0485-5.6072-1.0423
160.135-0.02330.01780.1675-0.13240.08630.1137-0.2049-0.0157-0.34250.20820.1486-0.14430.1448-0.00010.4646-0.01590.13750.48680.13470.419217.731637.4666-4.6294
170.03120.0072-0.02710.01690.01250.01590.17880.03770.2418-0.06730.1657-0.2558-0.4854-0.1210.00030.6961-0.0430.00210.5031-0.07520.339815.47538.180424.8528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'D' AND (RESID 1 THROUGH 10 )
2X-RAY DIFFRACTION2CHAIN 'D' AND (RESID 11 THROUGH 18 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 19 THROUGH 49 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 50 THROUGH 62 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 63 THROUGH 87 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 88 THROUGH 117 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 118 THROUGH 128 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 129 THROUGH 150 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 151 THROUGH 168 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 169 THROUGH 199 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 200 THROUGH 207 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 208 THROUGH 220 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 19 THROUGH 62 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 63 THROUGH 87 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 88 THROUGH 220 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 1 THROUGH 10 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 11 THROUGH 18 )

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