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- PDB-1yo7: Re-engineering topology of the homodimeric ROP protein into a sin... -

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Basic information

Entry
Database: PDB / ID: 1yo7
TitleRe-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle
ComponentsRegulatory protein rop
KeywordsREPLICATION REGULATOR / Protein design / re-engineering of topology / four-helix bundle
Function / homologyRegulatory protein Rop / Rop-like superfamily / Rop protein / Alpha-catenin/vinculin-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIR, model building / Resolution: 2.8 Å
AuthorsSagermann, M. / Emery, S.C. / Sander, C.
Citation
Journal: To be Published
Title: Re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle.
Authors: Sagermann, M. / Emery, S.C. / Sander, C.
#1: 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
DepositionJan 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Residues 1-56 were taken from wild type ROP (except for R55S), a new Loop-B (residues ...SEQUENCE Residues 1-56 were taken from wild type ROP (except for R55S), a new Loop-B (residues KKNGQI) was added, then residues 32-56 were added subsequently followed by the new Loop-C (sequence GGS). Finally, wild type ROP residues 3-29 and a terminal AKG sequence were added.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein rop
B: Regulatory protein rop
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4563
Polymers27,3912
Non-polymers651
Water37821
1
A: Regulatory protein rop
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7612
Polymers13,6951
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulatory protein rop


Theoretical massNumber of molelcules
Total (without water)13,6951
Polymers13,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.607, 52.830, 50.360
Angle α, β, γ (deg.)90.00, 94.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Regulatory protein rop / RNA one modulator / ROM


Mass: 13695.465 Da / Num. of mol.: 2 / Mutation: R55S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: The gene for LMROP2 was artificially assembled using cassette mutagenesis and c loned into the expression vector
Gene: rop / Plasmid: pEX70 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K-12 / References: UniProt: P03051
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.29 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 10% PEG 2000, 50mM Tris-HCl pH6.6, 40mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 4, 1994
RadiationMonochromator: Graphite, NI Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→26.4 Å / Num. all: 5376 / Num. obs: 5376 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.74 Å2
Reflection shellResolution: 2.8→2.98 Å / Num. unique all: 783 / Rsym value: 0.11 / % possible all: 85

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
MLPHAREphasing
CNSrefinement
AMoREphasing
CNSphasing
RefinementMethod to determine structure: SIR, model building
Starting model: PDb entry 1ROP

1rop


Resolution: 2.8→26.4 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Data were collected from very flat, plate-like crystals. Only partially occupied platinum atoms could be used to calculate preliminary phases. These initial HA positions were used in ...Details: Data were collected from very flat, plate-like crystals. Only partially occupied platinum atoms could be used to calculate preliminary phases. These initial HA positions were used in combination with molecular replacement to determine the structure.
RfactorNum. reflectionSelection details
Rfree0.31 495 random
Rwork0.216 --
all0.224 5376 -
obs0.224 5376 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.85 Å24.27 Å21.58 Å2
2--0 Å21.11 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.8→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 1 21 1932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_d18

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