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- PDB-2e1a: crystal structure of FFRP-DM1 -

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Basic information

Entry
Database: PDB / ID: 2e1a
Titlecrystal structure of FFRP-DM1
Components75aa long hypothetical regulatory protein AsnC
KeywordsTRANSCRIPTION / transcriptional regulatory protein / archaea
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SELENOMETHIONINE / 75aa long hypothetical regulatory protein AsnC
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKoike, H. / Suzuki, M.
CitationJournal: Structure / Year: 2007
Title: A Structural Code for Discriminating between Transcription Signals Revealed by the Feast/Famine Regulatory Protein DM1 in Complex with Ligands
Authors: Okamura, H. / Yokoyama, K. / Koike, H. / Yamada, M. / Shimowasa, A. / Kabasawa, M. / Kawashima, T. / Suzuki, M.
History
DepositionOct 19, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 20, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / refine
Item: _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 75aa long hypothetical regulatory protein AsnC
B: 75aa long hypothetical regulatory protein AsnC
C: 75aa long hypothetical regulatory protein AsnC
D: 75aa long hypothetical regulatory protein AsnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8376
Polymers34,4454
Non-polymers3922
Water5,098283
1
A: 75aa long hypothetical regulatory protein AsnC
B: 75aa long hypothetical regulatory protein AsnC
C: 75aa long hypothetical regulatory protein AsnC
D: 75aa long hypothetical regulatory protein AsnC
hetero molecules

A: 75aa long hypothetical regulatory protein AsnC
B: 75aa long hypothetical regulatory protein AsnC
C: 75aa long hypothetical regulatory protein AsnC
D: 75aa long hypothetical regulatory protein AsnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,67412
Polymers68,8908
Non-polymers7844
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area15400 Å2
ΔGint-93 kcal/mol
Surface area22900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.8, 95.8, 95.3
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
75aa long hypothetical regulatory protein AsnC / Lrp/AsnC family protein


Mass: 8611.233 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O73983
#2: Chemical ChemComp-MSE / SELENOMETHIONINE


Type: L-peptide linking / Mass: 196.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2Se
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.66 Å3/Da / Density % sol: 66.43 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.0M LiCl, 10% PEG 6000, 100mM citrate, 20% glycerol, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2002
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.5→81 Å / Num. obs: 35886 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z4P

2z4p


Resolution: 2.5→81 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1740 -RANDOM
Rwork0.1898 ---
obs-32078 99.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 18 283 2693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007475
X-RAY DIFFRACTIONc_angle_deg1.3791

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