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- PDB-3vok: X-ray Crystal Structure of Wild Type HrtR in the Apo Form with th... -

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Basic information

Entry
Database: PDB / ID: 3vok
TitleX-ray Crystal Structure of Wild Type HrtR in the Apo Form with the Target DNA.
Components
  • 5'-D(*AP*TP*GP*AP*CP*AP*CP*TP*GP*TP*GP*TP*CP*AP*T)-3'
  • Transcriptional regulator
KeywordsTRANSCRIPTION/DNA / heme / sensor protein / TetR superfamily / DNA-binding complex / TRANSCRIPTION-DNA complex
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
DNA / DNA (> 10) / Transcriptional regulator
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
DepositionJan 27, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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
U: 5'-D(*AP*TP*GP*AP*CP*AP*CP*TP*GP*TP*GP*TP*CP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)27,3612
Polymers27,3612
Non-polymers00
Water1,45981
1
A: Transcriptional regulator
U: 5'-D(*AP*TP*GP*AP*CP*AP*CP*TP*GP*TP*GP*TP*CP*AP*T)-3'

A: Transcriptional regulator
U: 5'-D(*AP*TP*GP*AP*CP*AP*CP*TP*GP*TP*GP*TP*CP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)54,7214
Polymers54,7214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area6460 Å2
ΔGint-51 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.870, 97.870, 108.695
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Transcriptional regulator


Mass: 22776.600 Da / Num. of mol.: 1
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
#2: DNA chain 5'-D(*AP*TP*GP*AP*CP*AP*CP*TP*GP*TP*GP*TP*CP*AP*T)-3'


Mass: 4583.997 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN U HAS MICROHETEROGENEITY AT POSITION 8(DT/DA)

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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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 1.2M sodium citrate, 0.1M PIPES, pH 7.3, 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 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 23, 2012
Diffraction measurementDetails: 1.00 degrees, 999.0 sec, detector distance 179.58 mm
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.079 / Number: 458505
ReflectionResolution: 2→30 Å / Num. obs: 21224 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 21.5 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 41.584
Reflection shellResolution: 2→2.07 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 6.622 / Rsym value: 0.513 / % possible all: 100
Cell measurementReflection used: 458505

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.87 Å
Translation2.5 Å23.87 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
BSSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QPI

1qpi


Resolution: 2→23.87 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8432 / SU ML: 0.2 / Cross valid method: THROUGHTOUT / σ(F): 0 / Phase error: 21.8 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1070 5.15 %RANDOM
Rwork0.2019 ---
obs0.2037 20763 97.18 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.995 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 147.09 Å2 / Biso mean: 47.2483 Å2 / Biso min: 14.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.4737 Å20 Å2-0 Å2
2--2.4737 Å20 Å2
3----4.9474 Å2
Refinement stepCycle: LAST / Resolution: 2→23.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 325 0 81 1927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071925
X-RAY DIFFRACTIONf_angle_d1.1062671
X-RAY DIFFRACTIONf_chiral_restr0.071286
X-RAY DIFFRACTIONf_plane_restr0.005280
X-RAY DIFFRACTIONf_dihedral_angle_d20.349738
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9992-2.09010.22141220.18892335245794
2.0901-2.20020.22821340.19512333246795
2.2002-2.3380.25841380.20072398253696
2.338-2.51830.28111310.22182440257198
2.5183-2.77140.28371230.23352464258798
2.7714-3.17160.28951590.22162481264099
3.1716-3.99290.22081320.18972556268899
3.9929-23.87190.20081310.19152686281798
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)
10.32240.3115-0.04490.75630.25820.23150.1106-0.16120.00180.11160.0090.06680.04620.0992-0.04240.4642-0.1201-0.10240.3592-0.0290.322334.376647.98284.1551
20.00110.00960.00090.11810.01170.0032-0.06240.03210.0228-0.05360.01780.0316-0.0371-0.01310.01850.5527-0.1488-0.15640.33190.09090.369226.680549.5298-11.0317
30.1450.0460.03180.06580.03080.0816-0.03890.03230.0381-0.06290.0362-0.04290.00440.08690.01130.4302-0.1477-0.12340.27030.0380.349134.556148.0849-3.0229
40.58270.2273-0.00220.1904-0.19390.39660.0531-0.1725-0.13930.2587-0.040.0005-0.0909-0.0357-0.02080.28460.0095-0.00170.1955-0.01560.224615.837622.7628-1.8844
50.11450.08210.03880.11310.09270.0901-0.0317-0.02150.03670.1172-0.05660.0115-0.0527-0.01550.03680.4147-0.0937-0.06570.244-0.02020.328918.149240.3027-4.0382
60.0473-0.01010.08740.08180.03410.2134-0.05920.0942-0.0392-0.06760.0615-0.0104-0.19340.07250.01090.4178-0.0766-0.08760.5333-0.00910.313929.658134.2016-14.1192
70.49920.15990.07410.04990.03770.544-0.01760.0391-0.0294-0.0429-0.0112-0.0748-0.11830.14510.02560.16920.0105-0.02540.18170.01370.213615.549429.3675-13.4047
80.3351-0.1662-0.03110.1143-0.00480.1511-0.0397-0.0319-0.01680.03860.03130.1028-0.0907-0.14140.02550.2050.0607-0.00380.2236-0.02220.26335.495428.4442-9.827
90.0616-0.0040.00330.0139-0.00760.0841-0.029-0.0390.10380.0163-0.0035-0.0494-0.0081-0.01780.02240.16690.0163-0.05050.19010.02690.26071.233613.9852-22.5451
100.049-0.07910.01020.141-0.05580.22770.1689-0.00610.0238-0.01130.2342-0.0262-0.02950.08080.39370.6523-0.172-0.6310.4340.20250.178236.748664.6365-18.1634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:27)A2 - 27
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 28:34)A28 - 34
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 35:70)A35 - 70
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 71:99)A71 - 99
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 100:113)A100 - 113
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 114:138)A114 - 138
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 139:157)A139 - 157
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 158:178)A158 - 178
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 179:189)A179 - 189
10X-RAY DIFFRACTION10CHAIN UU1 - 15

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