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- PDB-1f4n: C2 CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPAC... -

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Basic information

Entry
Database: PDB / ID: 1f4n
TitleC2 CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPACKED HYDROPHOBIC CORE AND A NEW FOLD.
ComponentsROP ALA2ILE2-6
KeywordsTRANSCRIPTION / Rop / dimer / homodimer / helix-turn-helix / transcription regulation / hydrophobic core packing / thermodynamic stability
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: 1.9 Å
AuthorsWillis, M.A. / Bishop, B. / Regan, L. / Brunger, A.T.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core.
Authors: Willis, M.A. / Bishop, B. / Regan, L. / Brunger, A.T.
History
DepositionJun 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ROP ALA2ILE2-6
B: ROP ALA2ILE2-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3867
Polymers14,1082
Non-polymers2785
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-53 kcal/mol
Surface area6190 Å2
MethodPISA
2
A: ROP ALA2ILE2-6
B: ROP ALA2ILE2-6
hetero molecules

A: ROP ALA2ILE2-6
B: ROP ALA2ILE2-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,77214
Polymers28,2154
Non-polymers55710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area6740 Å2
ΔGint-122 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.617, 36.488, 47.727
Angle α, β, γ (deg.)90.00, 121.205, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-104-

CA

21B-188-

HOH

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Components

#1: Protein ROP ALA2ILE2-6 / REGULATORY PROTEIN ROP / ROM


Mass: 7053.767 Da / Num. of mol.: 2 / Mutation: M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid details: PMR101 / Production host: Escherichia coli (E. coli) / References: UniProt: P03051
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, calcium chloride, sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
218-22 %MPD1reservoir
350-100 mM1reservoirCaCl2
4100 mMsodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54128
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54128 Å / Relative weight: 1
ReflectionResolution: 1.9→40.82 Å / Num. all: 9460 / Num. obs: 9460 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.238 / Num. unique all: 806 / % possible all: 84
Reflection shell
*PLUS
% possible obs: 84 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.9→40.82 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 906866.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1769 9.6 %RANDOM
Rwork0.204 ---
all-18445 --
obs-18445 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.16 Å2 / ksol: 0.435 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.94 Å20 Å2-4.67 Å2
2--4.43 Å20 Å2
3----0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 4 106 965
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d15.7
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it2.551.5
X-RAY DIFFRACTIONc_mcangle_it3.332
X-RAY DIFFRACTIONc_scbond_it6.392
X-RAY DIFFRACTIONc_scangle_it8.752.5
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.344 167 8.1 %
Rwork0.273 1892 -
obs--88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4MPD_NEW.PARMPD_NEW.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.6 % / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.344 / % reflection Rfree: 8.1 % / Rfactor Rwork: 0.273

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