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- PDB-3vox: X-ray Crystal Structure of Wild Type HrtR in the Apo Form -

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Basic information

Entry
Database: PDB / ID: 3vox
TitleX-ray Crystal Structure of Wild Type HrtR in the Apo Form
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION / sensor protein / TetR superfamily
Function / homology
Function and homology information


DNA binding / metal ion binding
Similarity search - Function
: / Tetracyclin repressor, C-terminal domain / Tetracycline Repressor, domain 2 / 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
Transcriptional regulator
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsSawai, H. / Sugimoto, H. / Shiro, Y. / Aono, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Basis for the Transcriptional Regulation of Heme Homeostasis in Lactococcus lactis.
Authors: Sawai, H. / Yamanaka, M. / Sugimoto, H. / Shiro, Y. / Aono, S.
History
DepositionFeb 23, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
C: Transcriptional regulator
D: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)91,1064
Polymers91,1064
Non-polymers00
Water00
1
A: Transcriptional regulator
B: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)45,5532
Polymers45,5532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-22 kcal/mol
Surface area18500 Å2
MethodPISA
2
C: Transcriptional regulator
D: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)45,5532
Polymers45,5532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-18 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.837, 190.180, 152.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Transcriptional regulator


Mass: 22776.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: IL1403 / Gene: L53789, LL0661, ygfC / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CHR1

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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: 3.62 Å3/Da / Density % sol: 66.05 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 1.2M sodium citrate, 0.1M HEPES, 0.2M ammonium acetate, pH 7.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 23, 2012
Diffraction measurementDetails: 1.00 degrees, 1.8 sec, detector distance 220.00 mm / Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.099 / Number: 226049
ReflectionResolution: 3.1→30 Å / Num. obs: 24781 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rsym value: 0.086 / Net I/σ(I): 22.5
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 5.14 / Rsym value: 0.429 / % possible all: 100
Cell measurementReflection used: 226049

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.87 Å43.27 Å
Translation2.87 Å43.27 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29.902 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 1249 5.13 %
Rwork0.1841 --
obs0.187 24350 99.83 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.14 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.9485 Å2-0 Å20 Å2
2---15.1963 Å2-0 Å2
3---2.2478 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6109 0 0 0 6109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096301
X-RAY DIFFRACTIONf_angle_d1.2668525
X-RAY DIFFRACTIONf_dihedral_angle_d18.7372331
X-RAY DIFFRACTIONf_chiral_restr0.09902
X-RAY DIFFRACTIONf_plane_restr0.0061073
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1001-3.2240.30711390.2322520100
3.224-3.37060.26391390.22142544100
3.3706-3.5480.28571370.21572530100
3.548-3.76990.3031620.20412533100
3.7699-4.06030.22871270.17712549100
4.0603-4.46770.20731450.14862546100
4.4677-5.11150.22261430.15612578100
5.1115-6.42930.27441340.21192616100
6.4293-29.90380.20261230.1753268599
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)
12.00731.0337-0.45076.7931-0.25962.33710.2876-0.3260.02090.7946-0.03370.47410.3446-0.1894-0.27780.75930.06830.04680.79310.05430.5713-60.496321.3334-2.2581
28.0683-1.4694.28688.842-4.33413.74860.30270.2823-0.0385-0.40350.8051.63790.8419-0.8834-1.18280.66440.0181-0.11911.18760.19681.0633-64.893625.9201-16.2447
32.6295-1.36761.64123.80410.0017.9178-0.15970.07550.4477-0.0612-0.026-0.5269-0.53860.27080.17110.5960.07570.15090.5289-0.01490.684-45.939238.6869-13.6229
41.5402-1.39060.65336.9081-4.35844.7128-0.1032-0.1124-0.1837-0.34650.1343-0.29690.7205-0.1951-0.05860.685-0.0717-0.02720.60090.03550.4514-33.478611.8704-18.279
56.2743-1.7457-1.15126.0532-0.34536.5591-1.19-0.26261.2583-0.08580.38940.1456-0.04050.00840.73530.78170.0548-0.17190.87890.0740.5499-36.138522.4459-10.5496
63.2292-0.1375-0.32799.27481.35725.33470.0352-0.0520.1779-0.13210.71290.6786-0.5143-0.4007-0.79810.51590.09660.05860.69870.13840.3943-48.088830.2128-26.7822
74.0641-2.13840.0564.2405-2.72859.83790.08970.21250.1018-0.81620.1598-0.7090.90330.1936-0.32340.7241-0.11350.28080.5837-0.1760.9841-16.046918.4988-32.3836
86.3231.78870.56275.5682-0.18228.3101-0.1509-0.02620.7922-0.9070.9721-0.9885-0.64790.5702-0.78280.8006-0.24110.06010.7511-0.31180.9838-17.333924.6072-29.7047
93.90252.3423-1.98062.8462-0.92113.5660.4985-0.5331-1.03740.998-0.5427-0.2613-0.0464-0.60950.19261.3151-0.4271-0.15131.0011-0.06561.1764-17.314318.2178-0.7013
103.5099-0.9744-0.41397.53291.89446.5234-0.3897-0.5485-0.07960.52840.1992-0.6755-0.45020.3940.15470.8612-0.0337-0.10340.757-0.21.2439-10.831724.422-14.898
115.08731.3301-1.52412.9764-0.485.49340.0758-0.4887-0.93240.88940.10370.01581.00160.3669-0.19021.456-0.2283-0.19670.78240.11391.1585-4.085321.05271.7778
123.4179-0.85880.75673.3938-0.50314.319-0.1264-0.1147-0.0798-0.3972-0.5906-1.6257-0.64740.76930.69650.69810.15610.10510.83150.19321.662618.787441.4052-25.3335
134.73530.4576-0.40853.9543-1.21848.5421-0.30680.0271-0.2647-1.1141-0.5359-1.4962-0.092-0.49650.76270.72530.22060.26080.66070.01591.277311.98935.9545-26.5889
145.2904-1.20282.34155.3792-2.34672.0321-0.0163-0.73250.75991.0866-0.3454-1.08910.43960.76660.52750.8434-0.0047-0.29240.8923-0.10231.08516.99439.47824.2615
155.8706-0.29960.09618.56651.67397.0824-0.3457-0.62910.602-0.2388-0.21960.3217-0.4586-0.66410.63180.5410.098-0.11330.7654-0.07030.71453.86835.824-14.8041
161.06750.6396-1.48260.3979-0.49143.74110.1227-0.0738-0.59860.5409-0.39730.09531.08220.05830.31461.0017-0.203-0.11150.6541-0.18160.8582.216431.5474-4.172
172.01470.0968-0.30615.2229-2.56062.7132-0.0384-0.2476-0.19030.9378-0.1205-0.51180.4445-0.99780.26820.957-0.2385-0.07651.0029-0.21270.827-8.782639.00724.6625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:122)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 123:138)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 139:188)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 2:113)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 114:138)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 139:186)
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 2:45)
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 46:67)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 68:99)
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 100:138)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 139:186)
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 2:27)
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 28:70)
14X-RAY DIFFRACTION14CHAIN D AND (RESSEQ 71:99)
15X-RAY DIFFRACTION15CHAIN D AND (RESSEQ 100:122)
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 123:157)
17X-RAY DIFFRACTION17CHAIN D AND (RESSEQ 158:186)

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