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- PDB-5z7b: Crystal structure of the VanR transcription factor in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5z7b
TitleCrystal structure of the VanR transcription factor in complex with vanillate
ComponentsPadR family transcriptional regulator
KeywordsTRANSCRIPTION / Transcription factor
Function / homologyTranscription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 4-HYDROXY-3-METHOXYBENZOATE / PadR family transcriptional regulator / Predicted transcriptional regulators
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKwak, Y.M. / Park, S.C. / Yoon, S.I.
CitationJournal: FEBS J. / Year: 2018
Title: Crystal structure of the VanR transcription factor and the role of its unique alpha-helix in effector recognition.
Authors: Kwak, Y.M. / Park, S.C. / Na, H.W. / Kang, S.G. / Lee, G.S. / Ko, H.J. / Kim, P.H. / Oh, B.C. / Yoon, S.I.
History
DepositionJan 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: PadR family transcriptional regulator
B: PadR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6654
Polymers44,3302
Non-polymers3342
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-43 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.771, 62.397, 183.950
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-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAGLYGLYAA-3 - 553 - 61
211SERSERGLYGLYBB-4 - 552 - 61
121GLUGLUTYRTYRAA69 - 8575 - 91
221GLUGLUTYRTYRBB69 - 8575 - 91
112GLUGLUTHRTHRAA86 - 10892 - 114
212GLUGLUTHRTHRBB86 - 10892 - 114
113ASNASNLEULEUAA109 - 192115 - 198
213ASNASNLEULEUBB109 - 192115 - 198
114SERSERTHRTHRAA56 - 6862 - 74
214SERSERTHRTHRBB56 - 6862 - 74

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein PadR family transcriptional regulator


Mass: 22165.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: APT58_11555 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0U4XX58, UniProt: Q8NN31*PLUS
#2: Chemical ChemComp-VNL / 4-HYDROXY-3-METHOXYBENZOATE / vanillate / Vanillic acid


Mass: 167.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: calcium acetate, PEG 8000, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 24186 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 23.9
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 1179

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.601 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22354 1180 4.9 %RANDOM
Rwork0.18072 ---
obs0.18281 22947 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 18.572 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 24 175 3259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213162
X-RAY DIFFRACTIONr_bond_other_d0.0010.022187
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9694281
X-RAY DIFFRACTIONr_angle_other_deg0.90235295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7965397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15522.826138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05615536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6331528
X-RAY DIFFRACTIONr_chiral_restr0.0790.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02667
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_it0.5371.51960
X-RAY DIFFRACTIONr_mcbond_other0.1611.5799
X-RAY DIFFRACTIONr_mcangle_it1.04823113
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96431202
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3854.51165
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
1446MEDIUM POSITIONAL0.180.5
1542LOOSE POSITIONAL0.55
1446MEDIUM THERMAL0.482
1542LOOSE THERMAL0.6510
2133MEDIUM POSITIONAL0.090.5
2176LOOSE POSITIONAL0.315
2133MEDIUM THERMAL0.342
2176LOOSE THERMAL0.3510
3499MEDIUM POSITIONAL0.130.5
3659LOOSE POSITIONAL0.465
3499MEDIUM THERMAL0.532
3659LOOSE THERMAL0.7510
475MEDIUM POSITIONAL0.260.5
455LOOSE POSITIONAL0.915
475MEDIUM THERMAL0.622
455LOOSE THERMAL0.6510
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 80 -
Rwork0.199 1639 -
obs--97.01 %
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)
12.2595-0.27290.77171.1204-0.26823.4108-0.03240.23350.0802-0.06790.04320.0029-0.1433-0.1938-0.01080.0515-0.01480.00630.18420.02070.037337.6246.2151.232
20.8954-2.1122-0.27994.55712.53780.80770.22780.1280.1266-0.5462-0.0998-0.1762-0.34210.0374-0.1280.10670.0180.05320.14160.00480.083841.19816.46229.838
30.5263-0.2476-0.52352.01632.41553.9394-0.02070.0818-0.0679-0.0192-0.0240.06850.14820.00220.04470.0238-0.0043-0.00270.1053-0.00840.035835.034-0.64324.836
43.0575-0.6841-0.50893.67160.04142.17990.10190.18510.3174-0.3511-0.0383-0.3017-0.17720.0314-0.06360.09080.01570.03840.12380.01760.044640.44832.97830.837
50.1139-0.2171-1.70381.00412.78196.8060.07530.1187-0.0396-0.201-0.26630.2058-0.4216-0.44630.1910.08580.0471-0.01430.214-0.02750.078140.5055.99218.59
60.6791-0.7642-0.77962.44352.29092.64110.01310.0304-0.01340.0470.03-0.0520.06740.098-0.04310.00620.0069-0.00370.1160.00420.036748.20510.7735.415
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 85
2X-RAY DIFFRACTION2A86 - 108
3X-RAY DIFFRACTION3A109 - 192
4X-RAY DIFFRACTION4B-4 - 85
5X-RAY DIFFRACTION5B86 - 108
6X-RAY DIFFRACTION6B109 - 192

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