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- PDB-7fby: Crystal Structure of PH0140 from Pyrococcus horikosii OT3 -

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Basic information

Entry
Database: PDB / ID: 7fby
TitleCrystal Structure of PH0140 from Pyrococcus horikosii OT3
ComponentsTranscriptional regulatory protein
KeywordsTRANSCRIPTION / transcriptional regulator
Function / homology
Function and homology information


sequence-specific DNA binding / identical protein binding
Similarity search - Function
AsnC-type HTH domain profile. / AsnC-type HTH domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ISOLEUCINE / Uncharacterized HTH-type transcriptional regulator PH0140
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsRichard, M. / Ahmad, M. / Pal, R.K. / Biswal, B.K. / Jeyakanthan, J.
CitationJournal: To Be Published
Title: Crystal Structure of PH0140 from Pyrococcus horikosii OT3
Authors: Richard, M. / Ahmad, M. / Pal, R.K. / Biswal, B.K. / Jeyakanthan, J.
History
DepositionJul 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0394
Polymers18,7841
Non-polymers2553
Water1,802100
1
A: Transcriptional regulatory protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)152,31332
Polymers150,2718
Non-polymers2,04224
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_657-x+1,y,-z+21
crystal symmetry operation6_567x,-y+1,-z+21
crystal symmetry operation7_557y,x,-z+21
crystal symmetry operation8_667-y+1,-x+1,-z+21
Buried area36080 Å2
ΔGint-142 kcal/mol
Surface area44590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.790, 102.790, 69.183
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-336-

HOH

21A-377-

HOH

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Components

#1: Protein Transcriptional regulatory protein / Uncharacterized HTH-type transcriptional regulator PH0140


Mass: 18783.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT-3 / Gene: PH0140 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O57880
#2: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M HEPES (PH 7.5), 4.3 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 12806 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 32.54
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.66 / Num. unique obs: 1258

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CYY

2cyy


Resolution: 2.001→25.711 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.096 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2122 646 5.045 %
Rwork0.1733 12160 -
all0.175 --
obs-12806 99.86 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.418 Å2
Baniso -1Baniso -2Baniso -3
1--0.261 Å20 Å2-0 Å2
2---0.261 Å2-0 Å2
3---0.523 Å2
Refinement stepCycle: LAST / Resolution: 2.001→25.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 17 100 1324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131265
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171275
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.6491707
X-RAY DIFFRACTIONr_angle_other_deg1.4291.582932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45220.44168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14415242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2911513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02273
X-RAY DIFFRACTIONr_nbd_refined0.2810.2233
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.21166
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2605
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2693
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.263
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.221
X-RAY DIFFRACTIONr_nbd_other0.2140.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.215
X-RAY DIFFRACTIONr_mcbond_it1.9612.495622
X-RAY DIFFRACTIONr_mcbond_other1.9592.495621
X-RAY DIFFRACTIONr_mcangle_it2.8793.723776
X-RAY DIFFRACTIONr_mcangle_other2.8773.722777
X-RAY DIFFRACTIONr_scbond_it2.7362.918642
X-RAY DIFFRACTIONr_scbond_other2.7342.922643
X-RAY DIFFRACTIONr_scangle_it4.0714.229927
X-RAY DIFFRACTIONr_scangle_other4.0694.233928
X-RAY DIFFRACTIONr_lrange_it5.73129.9451367
X-RAY DIFFRACTIONr_lrange_other5.72929.9691368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.0530.283470.264887X-RAY DIFFRACTION99.5736
2.053-2.1090.266440.206854X-RAY DIFFRACTION100
2.109-2.170.216500.182830X-RAY DIFFRACTION100
2.17-2.2370.206350.174835X-RAY DIFFRACTION100
2.237-2.310.212350.177789X-RAY DIFFRACTION100
2.31-2.3910.222360.171760X-RAY DIFFRACTION100
2.391-2.4810.252470.175737X-RAY DIFFRACTION100
2.481-2.5820.217410.164720X-RAY DIFFRACTION100
2.582-2.6970.234280.196692X-RAY DIFFRACTION100
2.697-2.8280.215350.2649X-RAY DIFFRACTION100
2.828-2.9810.236410.196620X-RAY DIFFRACTION100
2.981-3.1620.253350.186593X-RAY DIFFRACTION100
3.162-3.380.235320.179555X-RAY DIFFRACTION100
3.38-3.650.125270.155534X-RAY DIFFRACTION100
3.65-3.9970.155340.136475X-RAY DIFFRACTION100
3.997-4.4670.102120.119460X-RAY DIFFRACTION100
4.467-5.1550.196240.14392X-RAY DIFFRACTION100
5.155-6.3050.263130.22348X-RAY DIFFRACTION100
6.305-8.8840.273210.212270X-RAY DIFFRACTION100
8.884-250.26790.175160X-RAY DIFFRACTION92.8571
Refinement TLS params.Method: refined / Origin x: 31.6751 Å / Origin y: 30.4912 Å / Origin z: 73.033 Å
111213212223313233
T0.04 Å2-0.0293 Å2-0.0169 Å2-0.0354 Å20.0342 Å2--0.0658 Å2
L0.2467 °20.0635 °20.2627 °2-0.3104 °20.1602 °2--0.3343 °2
S0.056 Å °-0.051 Å °-0.0359 Å °0.0246 Å °0.0204 Å °-0.0135 Å °0.0594 Å °-0.0552 Å °-0.0764 Å °
Refinement TLS groupSelection: ALL

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