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- PDB-2zny: Crystal structure of the FFRP -

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Basic information

Entry
Database: PDB / ID: 2zny
TitleCrystal structure of the FFRP
ComponentsUncharacterized HTH-type transcriptional regulator PH1519
KeywordsDNA BINDING PROTEIN / transcription / DNA-binding / Transcription regulation
Function / homology
Function and homology information


sequence-specific DNA binding / identical protein binding
Similarity search - Function
AsnC-type helix-turn-helix domain / AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel ...AsnC-type helix-turn-helix domain / AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ARGININE / HTH-type transcriptional regulator FL11
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsYamada, M. / Suzuki, M.
CitationJournal: Proteins / Year: 2009
Title: Interactions between the archaeal transcription repressor FL11 and its coregulators lysine and arginine.
Authors: Yamada, M. / Ishijima, S.A. / Suzuki, M.
History
DepositionMay 2, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized HTH-type transcriptional regulator PH1519
B: Uncharacterized HTH-type transcriptional regulator PH1519
C: Uncharacterized HTH-type transcriptional regulator PH1519
D: Uncharacterized HTH-type transcriptional regulator PH1519
E: Uncharacterized HTH-type transcriptional regulator PH1519
F: Uncharacterized HTH-type transcriptional regulator PH1519
G: Uncharacterized HTH-type transcriptional regulator PH1519
H: Uncharacterized HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,26114
Polymers153,2108
Non-polymers1,0516
Water4,234235
1
A: Uncharacterized HTH-type transcriptional regulator PH1519
B: Uncharacterized HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4783
Polymers38,3022
Non-polymers1751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-35 kcal/mol
Surface area14150 Å2
MethodPISA
2
C: Uncharacterized HTH-type transcriptional regulator PH1519
D: Uncharacterized HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6534
Polymers38,3022
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-35 kcal/mol
Surface area14290 Å2
MethodPISA
3
E: Uncharacterized HTH-type transcriptional regulator PH1519
F: Uncharacterized HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6534
Polymers38,3022
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-37 kcal/mol
Surface area14210 Å2
MethodPISA
4
G: Uncharacterized HTH-type transcriptional regulator PH1519
H: Uncharacterized HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4783
Polymers38,3022
Non-polymers1751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-34 kcal/mol
Surface area14420 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.310, 73.500, 103.060
Angle α, β, γ (deg.)90.00, 98.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized HTH-type transcriptional regulator PH1519 / archaeal transcription repressor


Mass: 19151.221 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1519 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O59188
#2: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG 3350, 0.3M CaCl2, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 49860 / Num. obs: 47467 / % possible obs: 95.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.1
Reflection shellResolution: 2.59→2.68 Å / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.8 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RI7

1ri7


Resolution: 2.59→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 4746 -random
Rwork0.254 ---
obs0.254 47467 95.2 %-
all-49860 --
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9184 0 72 235 9491

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