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- PDB-1gto: HIGH RESOLUTION STRUCTURE OF A HYPERSTABLE HELICAL BUNDLE PROTEIN... -

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Basic information

Entry
Database: PDB / ID: 1gto
TitleHIGH RESOLUTION STRUCTURE OF A HYPERSTABLE HELICAL BUNDLE PROTEIN MUTANT
ComponentsROP
KeywordsTRANSCRIPTION REGULATION / TURN / HELIX PACKING / CRYSTAL CONTACTS
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 / Resolution: 1.82 Å
AuthorsAgrawal, V. / Predki, P. / Regan, L. / Brunger, A.T.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Amino-acid substitutions in a surface turn modulate protein stability.
Authors: Predki, P.F. / Agrawal, V. / Brunger, A.T. / Regan, L.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Amino-Acid Substitutions in a Surface Turn Modulate Protein Stability
Authors: Predki, P.F. / Agrawal, V. / Brunger, A.T. / Regan, L.
History
DepositionApr 23, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
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
B: ROP
C: ROP


Theoretical massNumber of molelcules
Total (without water)20,9753
Polymers20,9753
Non-polymers00
Water1,63991
1
A: ROP

A: ROP


Theoretical massNumber of molelcules
Total (without water)13,9832
Polymers13,9832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z1
2
B: ROP
C: ROP


Theoretical massNumber of molelcules
Total (without water)13,9832
Polymers13,9832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-28 kcal/mol
Surface area6050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.117, 95.117, 85.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsTHREE ROP PROTOMERS ARE IN THE ASYMMETRIC UNIT, TWO OF WHICH ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD RELATIONSHIP FORMING A ROP DIMER (B/C). THE THIRD ROP PROTOMER (A) FORMS ANOTHER ROP DIMER THROUGH A CRYSTALLOGRAPHIC SYMMETRY MATE.

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Components

#1: Protein ROP / COLE1 REPRESSOR OF PRIMER


Mass: 6991.702 Da / Num. of mol.: 3 / Mutation: M1G, D30G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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
Compound detailsTHE HYPERSTABLE MUTANT, ROP D30G, SHOWED LITTLE INTRAMOLECULAR CHANGE FROM WILD TYPE. THE R.M.S ...THE HYPERSTABLE MUTANT, ROP D30G, SHOWED LITTLE INTRAMOLECULAR CHANGE FROM WILD TYPE. THE R.M.S DEVIATION OF RESIDUE 29-31 BACKBONE ATOMS IS 0.08 ANGSTROMS BETWEEN CHAIN A AND WILD-TYPE. AN ASP AT POSITION 30 WOULD STERICALLY AND ELECTROSTATICALLY HINDER THE OBSERVED PACKING SEEN IN THE MUTANT LATTICE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal grow
*PLUS
pH: 6.8 / Method: unknown / Details: Banner, D.W., (1987) J. Mol. Biol., 196, 657.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein11
20.1 Mphosphate12
30.05 M12NaCl
41 mMdithiothreitol12
530 %MPD12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionRedundancy: 9 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.049
Reflection
*PLUS
Highest resolution: 1.82 Å / Lowest resolution: 20 Å / Num. obs: 17635 / % possible obs: 98.9 %
Reflection shell
*PLUS
Highest resolution: 1.82 Å / Lowest resolution: 1.87 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.241

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOV. 1.3)data reduction
X-PLOR3.8phasing
RefinementResolution: 1.82→20 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1678 9.8 %RANDOM
Rwork0.224 ---
obs0.224 17110 98.9 %-
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å20 Å20 Å2
2--3.15 Å20 Å2
3----6.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.27 Å
Refinement stepCycle: LAST / Resolution: 1.82→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 0 91 1481
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1
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
LS refinement shellResolution: 1.82→1.9 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.35 177 9.1 %
Rwork0.342 1774 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1TOPPAR:PARHCSDX.PROTOPPAR:TOPHCSDX.PRO
X-RAY DIFFRACTION2TOPPAR:PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1

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