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- PDB-2z4p: Crystal structure of FFRP-DM1 -

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Basic information

Entry
Database: PDB / ID: 2z4p
TitleCrystal structure of FFRP-DM1
Components75aa long hypothetical regulatory protein AsnC
KeywordsDNA BINDING PROTEIN / FFRP / feast/famine regulatory protein / transcriptional regulator
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
ISOLEUCINE / 75aa long hypothetical regulatory protein AsnC
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å
AuthorsYamada, M. / Koike, H. / Kudo, N. / 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
DepositionJun 21, 2007Deposition 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

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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)34,7076
Polymers34,4454
Non-polymers2622
Water3,585199
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)69,41512
Polymers68,8908
Non-polymers5254
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area15500 Å2
ΔGint-93 kcal/mol
Surface area23470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.317, 96.317, 95.788
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
75aa long hypothetical regulatory protein AsnC / DM1


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 (bacteria) / Strain (production host): BL21 / References: UniProt: O73983
#2: Chemical ChemComp-ILE / ISOLEUCINE / Isoleucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3.72 Å3/Da / Density % sol: 66.96 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.834 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.834 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 35542 / Biso Wilson estimate: 14.1 Å2

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Processing

Software
NameVersionClassification
CNS1.2refinement
PROCESSdata reduction
PROCESSdata scaling
AMoREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.95→25.35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 417514.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3543 10 %RANDOM
Rwork0.189 ---
obs0.189 35542 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.6441 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å20 Å20 Å2
2---3.3 Å20 Å2
3---6.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.95→25.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 18 199 2609
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.217 500 9.4 %
Rwork0.187 4836 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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