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- PDB-4zsz: Structure of a fusion protein with a helix linker, 2ARH-3-3KAW-3.0 -

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Basic information

Entry
Database: PDB / ID: 4zsz
TitleStructure of a fusion protein with a helix linker, 2ARH-3-3KAW-3.0
ComponentsUncharacterized Fusion 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 / Copper storage protein / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.251 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 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Apr 25, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.5Sep 27, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Uncharacterized Fusion Protein
B: Uncharacterized Fusion Protein


Theoretical massNumber of molelcules
Total (without water)68,6792
Polymers68,6792
Non-polymers00
Water00
1
A: Uncharacterized Fusion Protein
B: Uncharacterized Fusion Protein

A: Uncharacterized Fusion Protein
B: Uncharacterized Fusion Protein


Theoretical massNumber of molelcules
Total (without water)137,3584
Polymers137,3584
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area7970 Å2
ΔGint-35 kcal/mol
Surface area54050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.930, 112.930, 150.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 2 - 295 / Label seq-ID: 2 - 295

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Uncharacterized Fusion Protein


Mass: 34339.402 Da / Num. of mol.: 2
Mutation: Y138F, E158A, K162A, E166A, Q208H, A209H, R212H, E124A, R293H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria), (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: VF5, ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
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: 4.02 Å3/Da / Density % sol: 69.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris (pH=5.5) and 1.5M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 4.25→81.927 Å / Num. obs: 8061 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.38 % / Biso Wilson estimate: 163.84 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.128 / Χ2: 0.903 / Net I/σ(I): 12.66 / Num. measured all: 43354
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
4.25-4.360.6510.8082.0327375885560.90594.6
4.36-4.480.7830.5723.0731135715690.63499.6
4.48-4.610.8530.583.1530245505490.64299.8
4.61-4.750.890.4733.7430685565540.52399.6
4.75-4.910.9170.4014.3729295295290.444100
4.91-5.080.9130.4034.4427715065060.446100
5.08-5.270.9380.3055.4926844924910.33899.8
5.27-5.490.9480.2746.1926764844840.303100
5.49-5.730.9530.2955.8825384644620.32699.6
5.73-6.010.9480.2576.7223964414410.285100
6.01-6.340.9720.1759.4522964184170.19499.8
6.34-6.720.9910.12612.321493993990.14100
6.72-7.190.9940.09516.0719993763730.10599.2
7.19-7.760.9960.07819.5219003513500.08699.7
7.76-8.50.9980.04729.3718213383340.05298.8
8.5-9.510.9990.03338.6815522962940.03799.3
9.51-10.980.9990.02646.8613852652610.02998.5
10.98-13.4410.02350.0111452262220.02698.2
13.44-19.010.9990.02652.719211931880.02997.4
19.010.9990.02340.89250111820.02873.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ARH, 3KAW

2arh

3kaw


Resolution: 4.251→46.492 Å / SU ML: 0.76 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2862 402 4.99 %
Rwork0.2645 7654 -
obs0.2658 8056 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50 Å2 / Biso mean: 49.2866 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 4.251→46.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 0 0 4794
Num. residues----588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054906
X-RAY DIFFRACTIONf_angle_d0.8596598
X-RAY DIFFRACTIONf_chiral_restr0.033676
X-RAY DIFFRACTIONf_plane_restr0.005866
X-RAY DIFFRACTIONf_dihedral_angle_d16.0681866
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2793X-RAY DIFFRACTION10.023TORSIONAL
12B2793X-RAY DIFFRACTION10.023TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.251-4.8660.4011300.35792485261599
4.866-6.12840.37481340.343125442678100
6.1284-46.4950.221380.20372625276398

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