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- PDB-1b6q: ALANINE 31 PROLINE MUTANT OF ROP PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1b6q
TitleALANINE 31 PROLINE MUTANT OF ROP PROTEIN
ComponentsROP
KeywordsTRANSCRIPTION REGULATION
Function / homology
Function and homology information


DNA-templated transcription / identical protein binding
Similarity search - Function
Helix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein rop
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGlykos, N. / Cesareni, G. / Kokkinidis, M.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Protein plasticity to the extreme: changing the topology of a 4-alpha-helical bundle with a single amino acid substitution.
Authors: Glykos, N.M. / Cesareni, G. / Kokkinidis, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Meaningful Refinement of Poly-Alanine Models Using Rigid-Body Simulated Annealing : Application to the Structure Determination of the A31P Rop Mutant
History
DepositionJan 16, 1999Processing site: BNL
Revision 1.0Jul 9, 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 16, 2011Group: Atomic model
Revision 1.4Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.5Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.6Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.7May 22, 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


Theoretical massNumber of molelcules
Total (without water)7,2631
Polymers7,2631
Non-polymers00
Water99155
1
A: ROP

A: ROP


Theoretical massNumber of molelcules
Total (without water)14,5262
Polymers14,5262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3070 Å2
ΔGint-38 kcal/mol
Surface area7350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)30.400, 42.100, 81.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-103-

HOH

21A-143-

HOH

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Components

#1: Protein ROP / ROM


Mass: 7263.076 Da / Num. of mol.: 1 / Mutation: A31P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Gene: ROP / Plasmid: PEX43 / Production host: Escherichia coli (E. coli) / Strain (production host): 71/72 (71/18 PLUS PCI857) / References: UniProt: P03051
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.8 Å3/Da / Density % sol: 35 %
Crystal growpH: 4.3 / Details: pH 4.3
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
3100 mMammonium sulfate1drop
41.6 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Details: MONOCHROMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40.825 Å / Num. obs: 5103 / % possible obs: 99.9 % / Redundancy: 1 % / Biso Wilson estimate: 28.9 Å2 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1 % / Mean I/σ(I) obs: 2.48 / % possible all: 99.6
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
CAD4data reduction
CAD4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: POLY-ALANINE MODEL FROM PDB ENTRY 1ROP

1rop


Resolution: 1.8→40.825 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESOLUTION-DEPENDENT TWO-LINE WEIGHTING SCHEME AS SUGGESTED BY DAVID SMITH, PROCEEDINGS OF THE CCP4 STUDY WEEKEND, 1996.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 286 5 %RANDOM
Rwork0.189 ---
obs0.189 5103 99.9 %-
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-6.2422 Å20 Å20 Å2
2---1.7673 Å20 Å2
3----4.4617 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 40.8 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms440 0 0 55 495
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg0.909
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.53
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it2.73
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4 31 5 %
Rwork0.332 588 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1TOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
X-RAY DIFFRACTION3PROTEIN_REP.PARAM
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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