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- PDB-1rpo: RESTORED HEPTAD PATTERN CONTINUITY DOES NOT ALTER THE FOLDING OF ... -

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Basic information

Entry
Database: PDB / ID: 1rpo
TitleRESTORED HEPTAD PATTERN CONTINUITY DOES NOT ALTER THE FOLDING OF A 4-ALPHA-HELICAL BUNDLE
ComponentsROP PROTEIN
KeywordsTRANSCRIPTION REGULATION
Function / homologyHelix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsVlassi, M. / Kokkinidis, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Restored heptad pattern continuity does not alter the folding of a four-alpha-helix bundle.
Authors: Vlassi, M. / Steif, C. / Weber, P. / Tsernoglou, D. / Wilson, K.S. / Hinz, H.J. / Kokkinidis, M.
#1: Journal: Proteins / Year: 1993
Title: Correlation between Protein Stability and Crystal Properties of Designed Rop Variants
Authors: Kokkinidis, M. / Vlassi, M. / Papanikolaou, Y. / Kotsifaki, D. / Kingswell, A. / Tsernoglou, D. / Hinz, H.J.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of the Col(Asterisk)E1 (Asterisk)Rop Protein at 1.7 Angstroms Resolution
Authors: Banner, D.W. / Kokkinidis, M. / Tsernoglou, D.
History
DepositionAug 25, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ROP PROTEIN


Theoretical massNumber of molelcules
Total (without water)7,3791
Polymers7,3791
Non-polymers00
Water1,63991
1
A: ROP PROTEIN

A: ROP PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,7582
Polymers14,7582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2800 Å2
ΔGint-27 kcal/mol
Surface area6600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.960, 37.940, 31.840
Angle α, β, γ (deg.)90.00, 101.04, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE MOLECULE EXISTS IN SOLUTION AS A DIMER WHICH IS FORMED IN THE CRYSTAL BY THE CRYSTALLOGRAPHIC DYAD AXIS. THE SECOND MONOMER RESULTS FROM THE TRANSFORMATION: W' = R W +T WHERE W IS THE COLUMN VECTOR XSUB,YSUB,ZSUB R IS THE ROTATION MATRIX: SYMTY1 1 -0.999780 0.000000 0.000230 40.86282 SYMTY2 1 0.000000 1.000000 0.000000 0.00000 SYMTY3 1 0.000000 0.000000 -1.000020 31.25076

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Components

#1: Protein ROP PROTEIN


Mass: 7379.194 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P03051
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.79 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 5.4 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
2100 mMsodium acetate1drop
30.8 Mammonium sulfate1drop
41.6 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. obs: 10456 / % possible obs: 96 % / Rmerge(I) obs: 0.043

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.4→6 Å / σ(I): 1.5 /
RfactorNum. reflection
Rwork0.189 -
obs0.189 9994
Refinement stepCycle: LAST / Resolution: 1.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms484 0 0 91 575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d0.008
X-RAY DIFFRACTIONx_plane_restr0.021

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