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- PDB-1f4m: P3(2) CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A RE... -

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Basic information

Entry
Database: PDB / ID: 1f4m
TitleP3(2) 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: 2.25 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_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.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.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.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

Downloads & links

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Assembly

Deposited unit
A: ROP ALA2ILE2-6
B: ROP ALA2ILE2-6
C: ROP ALA2ILE2-6
D: ROP ALA2ILE2-6
E: ROP ALA2ILE2-6
F: ROP ALA2ILE2-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,56312
Polymers42,3236
Non-polymers2406
Water2,000111
1
A: ROP ALA2ILE2-6
B: ROP ALA2ILE2-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1884
Polymers14,1082
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-43 kcal/mol
Surface area5890 Å2
MethodPISA
2
C: ROP ALA2ILE2-6
D: ROP ALA2ILE2-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1884
Polymers14,1082
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-45 kcal/mol
Surface area6100 Å2
MethodPISA
3
E: ROP ALA2ILE2-6
F: ROP ALA2ILE2-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1884
Polymers14,1082
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-44 kcal/mol
Surface area5790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.092, 73.092, 65.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThe biological assembly is a dimer of which there are three in the asymmetric unit

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Components

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


Mass: 7053.767 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54128
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54128 Å / Relative weight: 1
ReflectionResolution: 2.1→45.66 Å / Num. all: 20062 / Num. obs: 20062 / % possible obs: 87.2 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.238 / Num. unique all: 909 / % possible all: 40
Reflection shell
*PLUS
% possible obs: 63.5 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.25→45.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2893541.94 / 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
Rfree0.282 3362 9.6 %RANDOM
Rwork0.233 ---
all-34854 --
obs-34854 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.39 Å2 / ksol: 0.449 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.33 Å26 Å20 Å2
2--7.33 Å20 Å2
3----14.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.25→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 6 111 2735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d15.2
X-RAY DIFFRACTIONc_improper_angle_d0.56
X-RAY DIFFRACTIONc_mcbond_it3.031.5
X-RAY DIFFRACTIONc_mcangle_it4.342
X-RAY DIFFRACTIONc_scbond_it6.252
X-RAY DIFFRACTIONc_scangle_it7.762.5
LS refinement shellResolution: 2.25→2.35 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.348 284 9.2 %
Rwork0.303 2816 -
obs--65.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.6 % / Rfactor obs: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.56
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: 0.348 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.303

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