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- PDB-3mlg: 2ouf-2x, a designed knotted protein -

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Basic information

Entry
Database: PDB / ID: 3mlg
Title2ouf-2x, a designed knotted protein
Components2X chimera of Helicobacter pylori protein HP0242
KeywordsDE NOVO PROTEIN / knot / designed protein / fusion protein / chimera protein
Function / homologyKnotted protein, ribbon-helix-helix DNA-binding domain / Protein of unknown function DUF2018 / HP0242-like superfamily / Domain of unknown function (DUF2018) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / metal ion binding / DUF2018 family protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.29 Å
AuthorsKing, N.P. / Sawaya, M.R. / Jacobitz, A.W. / Yeates, T.O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure and folding of a designed knotted protein.
Authors: King, N.P. / Jacobitz, A.W. / Sawaya, M.R. / Goldschmidt, L. / Yeates, T.O.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Jul 26, 2017Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / software / struct / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct.pdbx_descriptor / _struct_keywords.text / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.4Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2X chimera of Helicobacter pylori protein HP0242
B: 2X chimera of Helicobacter pylori protein HP0242


Theoretical massNumber of molelcules
Total (without water)43,9242
Polymers43,9242
Non-polymers00
Water90150
1
A: 2X chimera of Helicobacter pylori protein HP0242


Theoretical massNumber of molelcules
Total (without water)21,9621
Polymers21,9621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2X chimera of Helicobacter pylori protein HP0242


Theoretical massNumber of molelcules
Total (without water)21,9621
Polymers21,9621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 2X chimera of Helicobacter pylori protein HP0242

B: 2X chimera of Helicobacter pylori protein HP0242


Theoretical massNumber of molelcules
Total (without water)43,9242
Polymers43,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area1220 Å2
ΔGint-14 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.942, 75.390, 118.573
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2X chimera of Helicobacter pylori protein HP0242


Mass: 21961.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The designed gene is a tandem repeat of the Helicobacter pylori gene HP0242
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_0242 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25025
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 8% PEG 8000, 0.1 M Na+/K+ phosphate pH 6.2, 0.1 M sodium chloride, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.29→90 Å / Num. all: 17338 / Num. obs: 17338 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.068 / Χ2: 1.007 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.386.50.4518051.02143.2
2.38-2.4870.48914481.008179
2.48-2.5970.46718440.979199.5
2.59-2.7370.31318480.9471100
2.73-2.970.20918670.953199.9
2.9-3.1270.1318580.9711100
3.12-3.4470.0819011.029199.9
3.44-3.936.80.0718850.971100
3.93-4.956.70.05619341.1731100
4.95-906.20.03719481.032195.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å46.55 Å
Translation3.5 Å46.55 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data processing
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OUF

2ouf
PDB Unreleased entry


Resolution: 2.29→21.99 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 873 5.06 %RANDOM
Rwork0.248 ---
all0.25 17260 --
obs0.25 17260 --
Displacement parametersBiso max: 170.4 Å2 / Biso mean: 51.514 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.263 Å20 Å20 Å2
2--4.695 Å20 Å2
3----6.958 Å2
Refine analyzeLuzzati coordinate error obs: 0.482 Å
Refinement stepCycle: LAST / Resolution: 2.29→21.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 0 50 2570
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d943SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes350HARMONIC5
X-RAY DIFFRACTIONt_it2548HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion352SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3128SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2548HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3425HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion20.88
LS refinement shellResolution: 2.29→2.43 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.268 85 5.21 %
Rwork0.241 1545 -
all0.242 1630 -
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)
15.4759-1.6133-0.62455.7519-2.69548.68760.12020.2502-0.17770.3040.0092-0.00730.38450.0956-0.1294-0.14640.03910.0066-0.1554-0.0042-0.3132-3.6624-7.231111.489
25.26231.51891.61345.7137-1.07617.78670.06330.00890.275-0.5520.00130.0045-0.32760.6878-0.0646-0.1686-0.0936-0.0164-0.12420.0228-0.3142-3.89917.1421-18.0769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|13 - A|181 }A13 - 181
2X-RAY DIFFRACTION2{ B|13 - B|181 }B13 - 181

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