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- PDB-4zsv: Structure of a fusion protein with a helix linker, 2ARH-3-3KAW-1.0 -

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Basic information

Entry
Database: PDB / ID: 4zsv
TitleStructure of a fusion protein with a helix linker, 2ARH-3-3KAW-1.0
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / protein design / bionanotechnology / protein assembly / symmetry / biomaterials
Function / homologyUncharacterised conserved protein UCP017998 / Protein of unknown function (DUF1122) / Protein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / Acyl-CoA N-acyltransferase / DUF1122 domain-containing protein / Four-helix bundle copper-binding protein
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2 Å
AuthorsLai, Y.-T. / Yeates, T.O.
CitationJournal: Protein Eng.Des.Sel. / Year: 2015
Title: On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker.
Authors: Lai, Y.T. / Jiang, L. / Chen, W. / Yeates, T.O.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)70,5692
Polymers70,5692
Non-polymers00
Water00
1
A: Uncharacterized protein
B: Uncharacterized protein

A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)141,1384
Polymers141,1384
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area7900 Å2
ΔGint-43 kcal/mol
Surface area56340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.610, 191.610, 114.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 296 / Label seq-ID: 12 - 305

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Uncharacterized protein


Mass: 35284.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria), (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: VF5, ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: aq_1966, PA2107 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67778, UniProt: Q9I208

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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: 4.31 Å3/Da / Density % sol: 71.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.9M ammonium tartrate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.2→95.81 Å / Num. obs: 9491 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 19.3 % / Biso Wilson estimate: 158.244 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.065 / Χ2: 0.943 / Net I/σ(I): 35.75 / Num. measured all: 183546
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
4.2-4.310.9660.517.55135096756690.52399.1
4.31-4.430.9820.3969.57137236716710.406100
4.43-4.560.9860.32211.94133656576570.33100
4.56-4.70.990.25414.21123656186180.261100
4.7-4.850.9930.22616.11121826156150.232100
4.85-5.020.9940.21216.67111935935930.218100
5.02-5.210.9960.18118.67105355785780.186100
5.21-5.420.9960.16521.29112865535530.169100
5.42-5.660.9970.16620.88107615325320.171100
5.66-5.940.9960.15821.97101105095080.16299.8
5.94-6.260.9980.12725.5896004924920.131100
6.26-6.640.9990.08935.1586704674670.091100
6.64-7.10.9990.06543.4980674364360.067100
7.1-7.670.9990.05356.5483904224220.054100
7.67-8.410.03873.2673213773760.03999.7
8.4-9.3910.02797.8865063503500.028100
9.39-10.8510.022109.4552913143140.023100
10.85-13.2810.021121.1650372732730.022100
13.28-18.7910.021121.7437112262260.022100
18.7910.017127.4919241421410.01899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→95.81 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.3453 / WRfactor Rwork: 0.2938 / FOM work R set: 0.5353 / SU B: 138.785 / SU ML: 1.515 / SU Rfree: 1.2231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3762 949 10 %RANDOM
Rwork0.333 ---
obs0.3374 8541 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50 Å2 / Biso mean: 49.581 Å2 / Biso min: 50 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.45 Å20 Å2
2--0.91 Å20 Å2
3----2.94 Å2
Refinement stepCycle: final / Resolution: 4.2→95.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4764 0 0 0 4764
Num. residues----588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194866
X-RAY DIFFRACTIONr_bond_other_d0.0030.024642
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.9766540
X-RAY DIFFRACTIONr_angle_other_deg0.822310696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23123.175252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.68915884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7461550
X-RAY DIFFRACTIONr_chiral_restr0.0560.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215496
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021162
Refine LS restraints NCS

Ens-ID: 1 / Number: 17956 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 4.2→4.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 66 -
Rwork0.529 598 -
all-664 -
obs--99.1 %

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