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- PDB-4zsx: Structure of a fusion protein with a helix linker, 2ARH-3-3KAW-2.0 -

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Basic information

Entry
Database: PDB / ID: 4zsx
TitleStructure of a fusion protein with a helix linker, 2ARH-3-3KAW-2.0
ComponentsUncharacterized Fusion Protein
KeywordsUNKNOWN FUNCTION / protein design / bionanotechnology / protein assembly / symmetry / biomaterials
Function / homology
Function and homology information


Uncharacterised conserved protein UCP017998 / Protein of unknown function (DUF1122) / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #360 / Protein of unknown function DUF326 / Copper storage protein / Uncharacterized cysteine-rich protein YhjQ-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase ...Uncharacterised conserved protein UCP017998 / Protein of unknown function (DUF1122) / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #360 / Protein of unknown function DUF326 / Copper storage protein / Uncharacterized cysteine-rich protein YhjQ-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DUF1122 domain-containing protein / Four-helix bundle copper-binding protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 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 1.2Sep 27, 2023Group: 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_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,7726
Polymers68,3922
Non-polymers3804
Water1,36976
1
A: Uncharacterized Fusion Protein
B: Uncharacterized Fusion Protein
hetero molecules

A: Uncharacterized Fusion Protein
B: Uncharacterized Fusion Protein
hetero molecules

A: Uncharacterized Fusion Protein
B: Uncharacterized Fusion Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,31718
Polymers205,1776
Non-polymers1,14012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19200 Å2
ΔGint-200 kcal/mol
Surface area79680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.430, 121.430, 207.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain AAA3 - 2953 - 295
2chain BBB3 - 2963 - 296

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Components

#1: Protein Uncharacterized Fusion Protein


Mass: 34196.195 Da / Num. of mol.: 2
Mutation: Y138F, E158A, K162A, E166A, Q208H, A209H, R212H, E290A, R293A
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
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 4.31 Å3/Da / Density % sol: 71.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.0M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.5
ReflectionResolution: 2.19→93.832 Å / Num. obs: 57982 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.83 % / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.081 / Χ2: 0.985 / Net I/σ(I): 13.81 / Num. measured all: 338449
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
2.19-2.260.8240.651323860429342370.71898.7
2.26-2.320.8730.5063.7322674419141860.56199.9
2.32-2.390.930.434.4924396409940990.471100
2.39-2.460.9450.3435.5623590391439140.375100
2.46-2.540.9590.2786.6422989384538440.304100
2.54-2.630.9740.228.1422003370837070.241100
2.63-2.730.9820.1699.8220724358435820.18699.9
2.73-2.840.9870.13711.2218409343034280.15199.9
2.84-2.970.9920.11114.3320161332133210.122100
2.97-3.110.9930.09316.9419039313631340.10199.9
3.11-3.280.9940.0819.0918173303030300.087100
3.28-3.480.9950.0721.3816597282828260.07799.9
3.48-3.720.9950.06222.814232263426300.06999.8
3.72-4.020.9950.06225.8915274250625040.06899.9
4.02-4.40.9960.05926.8713832227522750.065100
4.4-4.920.9960.05727.312310207720760.063100
4.92-5.680.9940.05826.039840180818040.06599.8
5.68-6.960.9970.05927.449506154015380.06499.9
6.96-9.840.9940.05828.317092119811980.064100
9.840.9930.06528.4337486506490.07199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2arh

3kaw


Resolution: 2.19→93.832 Å / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 28.46 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2492 2958 5.1 %
Rwork0.2277 55008 -
obs0.2294 57982 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.58 Å2 / Biso mean: 53.3913 Å2 / Biso min: 26.93 Å2
Refinement stepCycle: final / Resolution: 2.19→93.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4766 0 20 76 4862
Biso mean--40.14 41.7 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134890
X-RAY DIFFRACTIONf_angle_d1.4436577
X-RAY DIFFRACTIONf_chiral_restr0.062672
X-RAY DIFFRACTIONf_plane_restr0.006863
X-RAY DIFFRACTIONf_dihedral_angle_d15.7291857
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2716X-RAY DIFFRACTION4.034TORSIONAL
12B2716X-RAY DIFFRACTION4.034TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.2380.3811640.39362732289694
2.238-2.27870.37641430.35872742288595
2.2787-2.32250.35931300.3572734286495
2.3225-2.36990.36281530.34632749290295
2.3699-2.42140.31441520.33352789294195
2.4214-2.47780.33581510.31862735288695
2.4778-2.53970.33831590.31272732289194
2.5397-2.60840.30911490.32092750289995
2.6084-2.68520.30411560.29842720287695
2.6852-2.77180.29311540.29622782293695
2.7718-2.87090.29691340.28992744287895
2.8709-2.98590.30941460.28972781292795
2.9859-3.12170.31141450.26722729287495
3.1217-3.28630.27181450.26242770291595
3.2863-3.49220.23091470.22222740288795
3.4922-3.76190.24211470.21232755290295
3.7619-4.14040.22251440.19392752289695
4.1404-4.73940.19691450.15992763290895
4.7394-5.97080.20711460.17652748289495
5.9708-73.95570.19971480.18792761290995

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