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- PDB-6wah: Crystal Structure of SmcR L139R from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 6wah
TitleCrystal Structure of SmcR L139R from Vibrio vulnificus
ComponentsLuxR family transcriptional regulator
KeywordsTRANSCRIPTION / quorum-sensing / transcription factor / DNA-binding protein
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Quorum-sensing regulator of virulence HapR
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsNewman, J.D. / Russell, M.M. / Gonzalez-Gutierrez, G. / van Kessel, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124698 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is flexible and binds diverse DNA sequences.
Authors: Newman, J.D. / Russell, M.M. / Fan, L. / Wang, Y.X. / Gonzalez-Gutierrez, G. / van Kessel, J.C.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 18, 2023Group: 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LuxR family transcriptional regulator
B: LuxR family transcriptional regulator
C: LuxR family transcriptional regulator
D: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0667
Polymers103,8464
Non-polymers2203
Water2,900161
1
A: LuxR family transcriptional regulator
B: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0814
Polymers51,9232
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-14 kcal/mol
Surface area19420 Å2
MethodPISA
2
C: LuxR family transcriptional regulator
D: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9853
Polymers51,9232
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-23 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.971, 98.998, 129.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
LuxR family transcriptional regulator / SmcR / SmcR-like protein / TetR/AcrR family transcriptional regulator / VvpR


Mass: 25961.398 Da / Num. of mol.: 4 / Mutation: L139R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria)
Gene: smcR, vvpR, CRN32_08135, CRN52_17705, D8T54_02235, D8T65_23975, JS86_16400
Production host: Escherichia coli (E. coli) / References: UniProt: Q9L8G8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M of Lithium Sulfate, 0.1 M Imidazole buffer pH 7.6-8 and 6-10% PEG3350
PH range: 7.6 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.55→46.22 Å / Num. obs: 33302 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.98 / Rpim(I) all: 0.155 / Rrim(I) all: 0.373 / Rsym value: 0.315 / Net I/σ(I): 7.7
Reflection shellResolution: 2.55→2.63 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4024 / CC1/2: 0.786 / Rpim(I) all: 0.588 / Rrim(I) all: 1.512 / Rsym value: 1.265 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kz9

3kz9


Resolution: 2.55→46.218 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.75
RfactorNum. reflection% reflection
Rfree0.3031 1566 4.74 %
Rwork0.228 --
obs0.2315 33033 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→46.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 13 161 6724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086690
X-RAY DIFFRACTIONf_angle_d0.8569068
X-RAY DIFFRACTIONf_dihedral_angle_d2.0243144
X-RAY DIFFRACTIONf_chiral_restr0.0471019
X-RAY DIFFRACTIONf_plane_restr0.0061181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.63240.37341470.3112738X-RAY DIFFRACTION97
2.6324-2.72650.3551450.28532777X-RAY DIFFRACTION98
2.7265-2.83560.33631470.26712807X-RAY DIFFRACTION99
2.8356-2.96460.3671370.26252853X-RAY DIFFRACTION100
2.9646-3.12090.3481450.2582839X-RAY DIFFRACTION100
3.1209-3.31640.35951260.23542871X-RAY DIFFRACTION100
3.3164-3.57240.32821420.22352847X-RAY DIFFRACTION100
3.5724-3.93170.26631380.20952885X-RAY DIFFRACTION100
3.9317-4.50020.25991470.18532896X-RAY DIFFRACTION100
4.5002-5.66820.25241420.20422905X-RAY DIFFRACTION100
5.6682-46.2180.27861500.21893049X-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)
12.53472.96010.58223.59810.3061.18880.238-0.61290.06780.1316-0.6442-0.218-0.12720.10360.27620.392-0.0253-0.07240.471-0.01810.431534.124924.5331-1.5022
22.47580.09830.54741.85880.83432.54140.01290.0560.17250.0829-0.0580.1299-0.1372-0.19550.02670.25450.0636-0.01430.4174-0.04710.274917.16778.4581-13.0424
31.66450.7827-0.40011.6948-0.79712.29370.46180.12720.41140.5556-0.0454-0.5471-0.2455-0.0746-0.20840.6880.37360.11260.17990.27840.622759.8093-2.6104-11.5944
48.9653-2.7973-1.17085.1508-0.54573.5301-0.6728-0.7489-0.13240.15470.51150.2588-0.1416-0.79740.09870.2787-0.0351-0.04340.5795-0.03160.313353.034-0.4943-18.0099
53.2512.1681-0.66823.0806-2.00255.6760.07340.36690.91870.3074-0.2149-0.0494-0.90430.2970.29670.33310.0945-0.02530.73340.02550.498757.48967.0393-17.2315
64.47062.26450.06894.8961.15822.691-0.25430.9237-0.0832-0.40790.4203-0.37510.17260.3921-0.18330.24170.06580.01590.79730.02710.320243.52890.1709-26.7719
70.1829-0.5234-0.65482.2520.38465.74840.16020.07610.0458-0.1904-0.01130.38730.7683-0.8324-0.09930.30710.02810.00850.53750.09140.404927.6295-10.7326-24.2868
84.0192-0.251-0.03481.92580.222.8318-0.0177-0.38510.58890.02940.0911-0.0777-0.09230.5857-0.1050.24640.03550.01870.81020.00350.335438.24565.6588-21.8189
99.10080.02040.98541.7397-0.24012.55440.3221.1307-0.38950.2691-0.14580.1114-0.1751-0.6295-0.27060.37140.01580.00610.5471-0.03830.274626.3291-1.6179-34.5503
103.2177-0.67123.33041.02-1.57865.5680.0960.0892-0.0936-0.1981-0.07580.15790.6448-0.44750.05930.33560.0493-0.01410.48770.05940.300222.28160.5506-25.3695
113.22611.81782.46463.03061.95834.90330.0508-0.3621-0.6138-0.17570.0994-0.3939-0.1504-0.5667-0.18260.3639-0.1664-0.0070.4122-0.00180.303324.1671-7.5483-11.795
122.4010.3753-0.938.79830.18670.37850.22250.515-0.6372-1.34970.52540.62310.1457-0.3666-0.45820.54460.0301-0.14050.6402-0.20750.503612.1748-9.0232-28.7492
132.78970.72621.18882.90020.84112.34790.0034-0.57230.058-0.22460.092-0.0782-0.2168-0.4346-0.10880.4238-0.119-0.05820.5542-0.07960.411620.12-23.80370.2845
142.76860.23440.19711.89150.12242.9977-0.00130.22450.04830.092-0.03710.0303-0.2124-0.0290.03050.2431-0.00870.01910.1849-0.06220.21670.2104-40.4152-10.2742
153.43190.3923-1.42192.29921.14824.3806-0.1653-1.73330.7080.32030.4549-0.3416-0.10630.1558-0.29230.3749-0.0039-0.02590.8099-0.14490.457638.5997-48.7079-15.7791
163.7889-0.8699-0.06511.6961-0.63832.9834-0.02440.2753-0.0228-0.00880.1048-0.19850.15010.4661-0.03140.29380.02680.05670.3845-0.02350.239416.8374-51.18-25.0492
172.91220.44460.19781.7949-0.94852.1823-0.0744-0.1596-0.2016-0.0820.00540.01130.1751-0.04990.11270.3143-0.01580.05290.3741-0.10320.27173.3279-53.7567-20.586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 205 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 13 )
4X-RAY DIFFRACTION4chain 'B' and (resid 14 through 32 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 59 )
6X-RAY DIFFRACTION6chain 'B' and (resid 60 through 82 )
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 105 )
8X-RAY DIFFRACTION8chain 'B' and (resid 106 through 133 )
9X-RAY DIFFRACTION9chain 'B' and (resid 134 through 149 )
10X-RAY DIFFRACTION10chain 'B' and (resid 150 through 177 )
11X-RAY DIFFRACTION11chain 'B' and (resid 178 through 196 )
12X-RAY DIFFRACTION12chain 'B' and (resid 197 through 203 )
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 59 )
14X-RAY DIFFRACTION14chain 'C' and (resid 60 through 205 )
15X-RAY DIFFRACTION15chain 'D' and (resid 5 through 59 )
16X-RAY DIFFRACTION16chain 'D' and (resid 60 through 149 )
17X-RAY DIFFRACTION17chain 'D' and (resid 150 through 203 )

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