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- PDB-3mli: 2ouf-ds, a disulfide-linked dimer of Helicobacter pylori protein ... -

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Basic information

Entry
Database: PDB / ID: 3mli
Title2ouf-ds, a disulfide-linked dimer of Helicobacter pylori protein HP0242
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / unknotted control
Function / homologyHP0242-like domain / HP0242-like fold / Protein of unknown function DUF2018 / HP0242-like superfamily / Domain of unknown function (DUF2018) / Orthogonal Bundle / Mainly Alpha / metal ion binding / DUF2018 family protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7586
Polymers47,6784
Non-polymers802
Water19811
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)23,8392
Polymers23,8392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-47 kcal/mol
Surface area9720 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9194
Polymers23,8392
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-50 kcal/mol
Surface area10740 Å2
MethodPISA
3
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)47,7586
Polymers47,6784
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area9760 Å2
ΔGint-119 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.318, 75.648, 134.029
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
Putative uncharacterized protein


Mass: 11919.561 Da / Num. of mol.: 4 / Mutation: CYS44LEU, LEU93ASN
Source method: isolated from a genetically manipulated source
Details: The designed gene is a mutant of the Helicobacter pylori gene HP0242
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_0242 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25025
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8.3% 2-propanol, 0.1 M MES pH 6.0, 0.32 M calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→80 Å / Num. all: 11588 / Num. obs: 11588 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rmerge(I) obs: 0.096 / Χ2: 1.077 / Net I/σ(I): 17.6
Reflection shellResolution: 2.9→3.02 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.537 / Num. unique all: 1136 / Χ2: 1.355 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å65.88 Å
Translation3.5 Å65.88 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
TNTrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OUF

2ouf
PDB Unreleased entry


Resolution: 2.9→50.16 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 487 4.71 %RANDOM
Rwork0.237 ---
all0.239 10345 --
obs0.239 10345 --
Displacement parametersBiso max: 205.4 Å2 / Biso mean: 109.992 Å2 / Biso min: 45.39 Å2
Baniso -1Baniso -2Baniso -3
1-3.127 Å20 Å20 Å2
2--12.106 Å20 Å2
3----15.233 Å2
Refine analyzeLuzzati coordinate error obs: 0.683 Å
Refinement stepCycle: LAST / Resolution: 2.9→50.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 2 11 2749
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d978SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes397HARMONIC5
X-RAY DIFFRACTIONt_it2776HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion382SEMIHARMONIC5
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_contact3257SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2776HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3748HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion2.05
X-RAY DIFFRACTIONt_other_torsion24.53
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.311 145 5.04 %
Rwork0.257 2730 -
all0.26 2875 -
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)
13.2619-0.63320.89173.0705-3.149413.3815-0.32760.23580.1761-0.0489-0.0209-0.2329-0.73351.08850.3485-0.0147-0.1117-0.09840.20920.0101-0.3618-4.2162.4523-4.117
25.2329-0.95-0.54942.6851-2.619715.5507-0.2065-0.2374-0.3564-0.04880.1982-0.10060.50791.04210.0083-0.12670.0248-0.07770.0148-0.0451-0.3976-6.5782-2.93474.4915
32.69330.77040.19786.51150.611414.22950.3718-0.07280.3457-0.4947-0.14980.286-1.0867-0.1917-0.2220.0720.03480.0677-0.02020.0129-0.3761-9.72964.789428.0378
45.01121.7644-0.84115.9778-0.918315.31880.1201-0.1728-0.1233-0.15520.2353-0.3041-0.72660.7491-0.35550.0472-0.09080.04750.1512-0.0668-0.4509-5.46242.131137.778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 93
2X-RAY DIFFRACTION2{ B|* }B13 - 97
3X-RAY DIFFRACTION3{ C|* }C11 - 99
4X-RAY DIFFRACTION4{ D|* }D3 - 96

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