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- PDB-1qx8: Crystal structure of a five-residue deletion mutant of the Rop protein -

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Basic information

Entry
Database: PDB / ID: 1qx8
TitleCrystal structure of a five-residue deletion mutant of the Rop protein
ComponentsRegulatory protein ROP
KeywordsTRANSCRIPTION / REPLICATION / INITIATION OF TRANSCRIPTION / RNA PRIMER / X-RAY
Function / homologyRegulatory protein rop / Regulatory protein Rop / Rop-like superfamily / Rop protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsGlykos, N.M. / Vlassi, M. / Papanikolaou, Y. / Kotsifaki, D. / Cesareni, G. / Kokkinidis, M.
Citation
Journal: Biochemistry / Year: 2006
Title: Loopless Rop: structure and dynamics of an engineered homotetrameric variant of the repressor of primer protein.
Authors: Glykos, N.M. / Papanikolau, Y. / Vlassi, M. / Kotsifaki, D. / Cesareni, G. / Kokkinidis, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Ionic strength reducers: an efficient approach to protein purification and crystallization. Application to two Rop variants
History
DepositionSep 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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


Theoretical massNumber of molelcules
Total (without water)13,3572
Polymers13,3572
Non-polymers00
Water97354
1
A: Regulatory protein ROP
B: Regulatory protein ROP

A: Regulatory protein ROP
B: Regulatory protein ROP


Theoretical massNumber of molelcules
Total (without water)26,7144
Polymers26,7144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9370 Å2
ΔGint-117 kcal/mol
Surface area10340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.476, 42.565, 51.722
Angle α, β, γ (deg.)90.00, 104.68, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsHomotetramer. Apply -x,y,-z to chains A & B to generate.

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Components

#1: Protein Regulatory protein ROP / RNA I inhibition modulator protein / RNA ONE modulator / rom / gtg start codon / regulatory protein ...RNA I inhibition modulator protein / RNA ONE modulator / rom / gtg start codon / regulatory protein rop / Repressor of primer


Mass: 6678.543 Da / Num. of mol.: 2 / Mutation: Deletion [30D-34Q]
Source method: isolated from a genetically manipulated source
Details: five residues (30D-34Q) deleted / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rop / Production host: Escherichia coli (E. coli) / Strain (production host): K38 / References: UniProt: P03051
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: NaCl, methanol, Bis-Tris, DTT, EDTA, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: May 30, 1997 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→33 Å / Num. all: 7271 / Num. obs: 7271 / % possible obs: 95.32 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 7.8
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.2 / Num. unique all: 555 / Rsym value: 0.312 / % possible all: 76

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMAC5.1.24refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RPO

1rpo


Resolution: 2.02→33 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.974 / SU B: 5.206 / SU ML: 0.137 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.199 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Used TLS parameterisation for each of the two helices
RfactorNum. reflection% reflectionSelection details
Rfree0.21218 361 5 %RANDOM
Rwork0.18946 ---
all0.19057 7270 --
obs0.19057 6909 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.113 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å2-0.75 Å2
2--0.51 Å20 Å2
3---1.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.157 Å0.199 Å
Refinement stepCycle: LAST / Resolution: 2.02→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 0 0 54 843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021823
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9781108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.814596
X-RAY DIFFRACTIONr_chiral_restr0.0910.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02592
X-RAY DIFFRACTIONr_nbd_refined0.2110.2307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.212
X-RAY DIFFRACTIONr_mcbond_it2.8842493
X-RAY DIFFRACTIONr_mcangle_it5.4955795
X-RAY DIFFRACTIONr_scbond_it7.7025330
X-RAY DIFFRACTIONr_scangle_it11.3528313
LS refinement shellResolution: 2.02→2.073 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.295 12
Rwork0.324 379
obs-391
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.242-1.67036.634-0.3996-1.01575.2749-0.14290.3462-0.3056-0.04040.0877-0.1585-0.0219-0.01430.05510.1327-0.0452-0.00720.0392-0.03330.07510.4323-3.3259-4.7916
23.63540.34360.8869-0.07960.30320.6521-0.1599-0.17380.1627-0.0220.02610.0124-0.0245-0.0590.13390.1194-0.00040.05320.00020.00570.1637-1.11563.68213.4525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 515 - 51
2X-RAY DIFFRACTION2BB1 - 511 - 51

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