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- PDB-3vp5: X-ray Crystal Structure of Wild Type HrtR in the Holo Form -

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Basic information

Entry
Database: PDB / ID: 3vp5
TitleX-ray Crystal Structure of Wild Type HrtR in the Holo Form
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION / heme / sensor protein / transcriptional regulator / 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
CACODYLATE ION / PROTOPORPHYRIN IX CONTAINING FE / Transcriptional regulator
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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
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 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5303
Polymers22,7771
Non-polymers7532
Water79344
1
A: Transcriptional regulator
hetero molecules

A: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0606
Polymers45,5532
Non-polymers1,5074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5640 Å2
ΔGint-50 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.140, 51.998, 87.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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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: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 19 % (w/v) polyethylene glycol 4000, 0.1M sodium cacodylate, 0.2M magnesium chloride, pH 6.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MarMosaic225 Rayonix / Detector: CCD / Date: Dec 15, 2010
Diffraction measurementDetails: 0.40 degrees, 1.6 sec, detector distance 169.744 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: 0.04 / Number: 121099
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.082097.110.0240.6466.7
3.254.0899.910.0421.0487.1
2.843.2510010.0441.0527.2
2.582.8410010.0430.917.3
2.392.5810010.060.9167.3
2.252.3910010.0810.937.2
2.142.2599.310.1060.9267
2.052.149410.1360.846.8
1.972.0588.310.1950.7826.7
1.91.9782.110.2410.7556.7
ReflectionResolution: 1.9→20 Å / Num. obs: 17259 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 32.961
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 5.691 / Rsym value: 0.241 / % possible all: 82.1
Cell measurementReflection used: 121099

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.97 Å26.01 Å
Translation1.97 Å26.01 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
BSSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→17.663 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 0 / Phase error: 32.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 832 4.84 %
Rwork0.2108 --
obs0.2134 17194 95.93 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.558 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-32.2098 Å2-0 Å2-0 Å2
2---21.4075 Å20 Å2
3----10.8023 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 48 44 1667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131683
X-RAY DIFFRACTIONf_angle_d1.2972296
X-RAY DIFFRACTIONf_dihedral_angle_d15.779612
X-RAY DIFFRACTIONf_chiral_restr0.087236
X-RAY DIFFRACTIONf_plane_restr0.006286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-2.01890.34061340.2836230984
2.0189-2.17450.2831330.2465264494
2.1745-2.39290.31561270.23952806100
2.3929-2.7380.29291430.23672827100
2.738-3.44540.28391460.21982845100
3.4454-17.66340.22641490.1821293198
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)
15.53430.1595-0.5793.29370.36514.091-0.24430.079-0.18710.0550.0852-0.14410.20370.55880.00610.4244-0.0421-0.01320.34940.01160.263622.025426.161235.7427
24.23031.33690.91075.84060.1955.5167-0.36030.1570.4698-0.23840.14330.2337-0.7970.13060.22580.4993-0.0317-0.0270.28920.02850.328516.087834.809233.7925
31.41613.36020.76416.96452.71082.34930.23890.2451-0.52340.0629-0.1708-0.55910.16780.2358-0.09370.2586-0.0038-0.08380.3358-0.02810.439915.462914.153829.821
44.19210.31030.42457.497-0.16256.58190.7385-0.4454-0.71811.4047-0.185-0.66860.9505-0.0827-0.6270.6856-0.0479-0.2680.36330.08060.48059.1641-0.232335.9668
55.44451.16351.94793.6238-0.03298.7081-0.1565-0.53930.3073-0.1974-0.10080.34610.4589-0.48130.16010.4028-0.06350.02970.3037-0.05650.41394.930318.03734.7483
62.08881.3707-3.88373.78091.27689.6258-0.20610.81440.5109-1.04290.32290.5131-0.73350.523-0.13921.0205-0.145-0.21450.57150.07990.53848.411724.30419.4022
76.2762-2.48141.04153.9933-3.76597.07960.38111.2983-0.8327-0.6218-1.7193-0.2861-0.37021.86511.38750.7671-0.03850.13511.02710.03481.008716.12897.657519.91
82.8625-0.6050.75778.2931.48476.47950.1632-0.4063-0.1380.7628-0.27140.52290.7611-0.57190.0350.3192-0.1063-0.04780.37860.00890.3041-0.89134.884430.5705
93.39524.6006-2.95746.1296-3.95242.51940.6224-0.11590.3875-0.24310.1587-1.184-1.85810.72430.15950.8776-0.0762-0.16640.37270.05890.5004-7.0372-10.386123.6622
100.0126-0.0157-0.0037-0.00340.00050.0085-0.20890.0080.0162-0.4172-0.0686-0.0699-0.1970.013700.31760.0330.0330.3139-0.00890.34358.926910.659125.2861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:27)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 28:55)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 56:80)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 81:98)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 99:113)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 114:126)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 127:138)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 139:178)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 179:186)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 201:201)

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