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- PDB-1rop: STRUCTURE OF THE COL*E1 ROP PROTEIN AT 1.7 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1rop
TitleSTRUCTURE OF THE COL*E1 ROP PROTEIN AT 1.7 ANGSTROMS RESOLUTION
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: 1.7 Å
AuthorsKokkinidis, M. / Banner, D.W. / Tsernoglou, D.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Structure of the ColE1 rop protein at 1.7 A resolution
Authors: Banner, D.W. / Kokkinidis, M. / Tsernoglou, D.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Crystallization of the Cole1 Rop Protein
Authors: Banner, D.W. / Cesareni, G. / Tsernoglou, D.
History
DepositionApr 2, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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)7,2371
Polymers7,2371
Non-polymers00
Water86548
1
A: ROP PROTEIN

A: ROP PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,4742
Polymers14,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area2680 Å2
ΔGint-28 kcal/mol
Surface area6120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.380, 40.390, 27.730
Angle α, β, γ (deg.)90.00, 105.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ROP PROTEIN


Mass: 7237.039 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.: 48 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A VERY TIGHT BEND (RESIDUES ASP 30 AND ALA 31) IN EACH MONOMER. IT IS NOT LISTED ON A ...THERE IS A VERY TIGHT BEND (RESIDUES ASP 30 AND ALA 31) IN EACH MONOMER. IT IS NOT LISTED ON A *TURN* RECORD BECAUSE EACH RESIDUE IS INTEGRATED IN THE HYDROGEN BONDING NETWORK OF HELICES H1 AND H2.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.29 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→5 Å /
RfactorNum. reflection
obs0.182 6725
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms447 0 0 48 495
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0290.015
X-RAY DIFFRACTIONp_angle_d0.0340.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.761
X-RAY DIFFRACTIONp_mcangle_it2.361.5
X-RAY DIFFRACTIONp_scbond_it3.071
X-RAY DIFFRACTIONp_scangle_it4.71.5
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.2430.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.5
X-RAY DIFFRACTIONp_multtor_nbd0.240.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.220.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.23
X-RAY DIFFRACTIONp_staggered_tor16.715
X-RAY DIFFRACTIONp_orthonormal_tor44.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 5 Å / Num. reflection obs: 6725 / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS

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