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- PDB-1nkd: ATOMIC RESOLUTION (1.07 ANGSTROMS) STRUCTURE OF THE ROP MUTANT <2AA> -

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Basic information

Entry
Database: PDB / ID: 1nkd
TitleATOMIC RESOLUTION (1.07 ANGSTROMS) STRUCTURE OF THE ROP MUTANT <2AA>
ComponentsROP
KeywordsTRANSCRIPTION REGULATION / ROP (COLE1 REPRESSOR OF PRIMER) / ATOMIC RESOLUTION STRUCTURE / 4-ALPHA-HELIX BUNDLE
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsVlassi, M. / Kokkinidis, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structural parameters for proteins derived from the atomic resolution (1.09 A) structure of a designed variant of the ColE1 ROP protein.
Authors: Vlassi, M. / Dauter, Z. / Wilson, K.S. / Kokkinidis, M.
#1: 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.
#2: 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.
#3: 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.
History
DepositionSep 23, 1997Processing site: BNL
Revision 1.0Mar 23, 1999Provider: 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 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ROP


Theoretical massNumber of molelcules
Total (without water)7,3791
Polymers7,3791
Non-polymers00
Water2,054114
1
A: ROP

A: ROP


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 area2760 Å2
ΔGint-26 kcal/mol
Surface area6310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.060, 37.880, 31.650
Angle α, β, γ (deg.)90.00, 100.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-138-

HOH

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Components

#1: Protein ROP / COLE1 REPRESSOR OF PRIMER


Mass: 7379.194 Da / Num. of mol.: 1 / Mutation: INS(A-D31-A)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P03051
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.9 Å3/Da / Density % sol: 35 %
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

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.09→23.13 Å / Num. obs: 22361 / % possible obs: 98.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.45 / Net I/σ(I): 18.9
Reflection shellResolution: 1.09→1.19 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 8.2 / % possible all: 97.5
Reflection
*PLUS
Biso Wilson estimate: 9.7 Å2
Reflection shell
*PLUS
% possible obs: 97.5 %

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Processing

Software
NameClassification
SHELXL-93model building
SHELXL-93refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→8 Å / Num. parameters: 5660 / Num. restraintsaints: 5406 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER, 1991.
RfactorNum. reflection% reflectionSelection details
Rfree0.134 4397 20 %0.2
all0.101 21972 --
obs0.104 -98.2 %-
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 1 / Occupancy sum non hydrogen: 1
Refinement stepCycle: LAST / Resolution: 1.09→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms468 0 0 114 582
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.063
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist0.014
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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