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- PDB-5dtf: context-independent anti-hypusine antibody FabHpu98.61 in complex... -

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Basic information

Entry
Database: PDB / ID: 5dtf
Titlecontext-independent anti-hypusine antibody FabHpu98.61 in complex with hypusine
Components
  • (Fab Hpu98.61 ...) x 2
  • Peptide: GLY-5CT-GLY-ALA
KeywordsIMMUNE SYSTEM / hypusine / antibody / FabHpu98.61 / eIF5A
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hypusine / Ig gamma chain C region
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhai, Q. / Carter, P.J.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Analysis and Optimization of Context-Independent Anti-Hypusine Antibodies.
Authors: Zhai, Q. / He, M. / Song, A. / Deshayes, K. / Dixit, V.M. / Carter, P.J.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2May 4, 2016Group: Non-polymer description
Revision 1.3Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab Hpu98.61 Heavy Chain
L: Fab Hpu98.61 Light Chain
A: Fab Hpu98.61 Heavy Chain
B: Fab Hpu98.61 Light Chain
P: Peptide: GLY-5CT-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4848
Polymers94,1275
Non-polymers3573
Water5,801322
1
H: Fab Hpu98.61 Heavy Chain
L: Fab Hpu98.61 Light Chain
P: Peptide: GLY-5CT-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3354
Polymers47,2733
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fab Hpu98.61 Heavy Chain
B: Fab Hpu98.61 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1494
Polymers46,8542
Non-polymers2952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.120, 75.770, 120.610
Angle α, β, γ (deg.)90.000, 120.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide Peptide: GLY-5CT-GLY-ALA


Mass: 418.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 2 types, 4 molecules HALB

#1: Antibody Fab Hpu98.61 Heavy Chain


Mass: 24230.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01870*PLUS
#2: Antibody Fab Hpu98.61 Light Chain


Mass: 22624.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 325 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-5CT / Hypusine / N~6~-[(2S)-4-amino-2-hydroxybutyl]-L-lysine


Type: peptide linking / Mass: 233.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H23N3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 24% PEG 1000 0.1M HEPES 7.6 10mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→37.2 Å / Num. obs: 77821 / % possible obs: 97.9 % / Redundancy: 3.4 % / Rsym value: 0.09 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.2 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DS8

5ds8


Resolution: 1.9→37.216 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 2007 2.58 %
Rwork0.2123 75814 -
obs0.2134 77821 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.56 Å2 / Biso mean: 28.0266 Å2 / Biso min: 12.71 Å2
Refinement stepCycle: final / Resolution: 1.9→37.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 23 322 6617
Biso mean--33.32 29.37 -
Num. residues----843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056453
X-RAY DIFFRACTIONf_angle_d0.8438839
X-RAY DIFFRACTIONf_chiral_restr0.051053
X-RAY DIFFRACTIONf_plane_restr0.0051112
X-RAY DIFFRACTIONf_dihedral_angle_d10.8273830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9003-1.94780.27921380.25195197533594
1.9478-2.00050.26221420.24015346548897
2.0005-2.05930.24591400.23255347548797
2.0593-2.12580.31341390.22555447558699
2.1258-2.20170.26481430.22435427557098
2.2017-2.28990.2671500.22475415556598
2.2899-2.39410.2721380.22385399553798
2.3941-2.52030.28761400.22625412555297
2.5203-2.67810.28561510.22155412556399
2.6781-2.88490.25051470.21885462560998
2.8849-3.1750.28241420.22665424556698
3.175-3.63410.23831470.21155505565299
3.6341-4.57730.23231470.1855461560898
4.5773-37.22330.21721430.19115560570398
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)
11.1351-0.17610.62010.1063-0.1540.3606-0.30290.17690.2470.09070.07940.20390.0144-0.41180.17970.31240.00960.04270.2764-0.01970.3277-52.4867-4.5602119.0582
22.53770.31160.61240.77720.74921.52510.13450.01810.3120.2775-0.05810.1961-0.08130.0126-0.07010.2296-0.03290.05330.2097-0.04350.1989-38.61723.5381126.2156
31.35760.0848-0.27931.7543-0.19851.8012-0.0596-0.006-0.076-0.06410.0440.09660.26060.25780.02380.20550.00620.05070.1801-0.00530.2099-34.1077-2.9362120.7368
41.36051.2229-0.79492.20970.28921.4873-0.1350.0393-0.1253-0.1075-0.15480.00710.1472-0.01720.2050.2567-0.04460.03570.2239-0.03040.2886-44.1657-5.7634119.2645
51.23490.2684-0.56411.39210.18741.48320.13560.07190.18620.1554-0.0344-0.01560.00050.18210.06040.2121-0.06380.03220.2314-0.02770.2337-35.28067.0966129.7448
60.0097-0.07050.04920.2848-0.20240.1367-0.0102-0.15580.1642-0.2590.115-0.4277-0.13740.072-0.11150.2578-0.03210.03170.2808-0.06820.3058-56.8553-7.9041124.8741
72.4815-0.1166-0.81123.53160.94622.62940.0268-0.32510.2530.49690.00410.20430.1545-0.3150.03690.21460.0395-0.00520.23390.0140.1836-73.0289-5.0437141.794
81.1675-0.09980.39280.8824-0.50051.14290.0719-0.02630.1363-0.06890.01-0.0987-0.3412-0.1526-0.09830.26110.02250.03050.19270.00630.198-65.0982-1.9918137.4614
91.10730.57590.46741.346-0.12731.7852-0.0517-0.2330.27920.36880.080.3426-0.3626-0.6452-0.03770.33830.15550.01080.41650.02460.2679-73.62862.2659135.2946
102.2315-0.2646-1.73991.68410.45165.0431-0.11590.01720.1204-0.0846-0.1494-0.0460.0395-0.01240.15380.27350.0902-0.09010.54650.05140.3563-75.496-0.8074132.4747
110.53520.1017-1.02580.63570.35563.4453-0.0935-0.2025-0.10360.02990.0167-0.12790.16160.54050.06460.19910.00710.00090.2982-0.00960.2173-33.80082.8576142.595
121.08090.92250.02871.08110.06820.7077-0.0140.0358-0.041-0.08810.0382-0.02350.00040.0025-0.02390.2034-0.0003-0.01810.1829-0.00890.1818-64.62-11.7446150.0752
130.77460.2070.01750.1297-0.08950.07440.17470.2234-0.4168-0.1998-0.07120.18190.1492-0.1748-0.17350.32320.0328-0.02080.2498-0.03970.2816-58.0257-34.0391127.6618
142.245-0.36090.20061.5254-0.4642.50020.0391-0.0159-0.0228-0.2569-0.1946-0.08730.34650.07020.1760.28030.07640.04430.2393-0.00310.2094-44.726-41.2026137.4441
151.12540.5168-0.08382.5284-0.57371.871-0.0847-0.14270.06090.03610.17560.2111-0.0442-0.1026-0.05740.23630.02150.01660.1756-0.0050.1694-48.8802-35.2674143.6344
161.5741-1.0929-0.65170.74050.26162.04170.05330.0125-0.1257-0.1519-0.14650.07460.16780.08190.07250.24650.04580.00340.2150.04920.2209-45.7577-40.9007135.794
170.43210.50360.18970.59250.43571.5607-0.1345-0.1715-0.18630.40840.18630.10660.05470.08110.00930.31690.11620.00010.22370.03540.1985-56.2099-28.1118120.0182
181.57980.42530.58482.08340.13051.97290.03970.2794-0.0977-0.33650.0819-0.1767-0.03650.14850.02360.1859-0.02090.01810.1857-0.04050.2252-47.5972-33.888298.555
191.47850.14920.39491.21850.18261.3012-0.060.0138-0.1568-0.04890.0793-0.1190.09510.20110.0240.19840.03010.01820.15250.03030.2055-47.4721-37.0696107.6994
203.0515-0.3573-0.31142.18310.47423.6424-0.01070.4665-0.1781-0.2880.1273-0.05240.1614-0.0785-0.13040.1952-0.0214-0.0090.2334-0.01110.2217-55.1042-39.9629101.3127
211.8015-0.4374-2.11340.58330.58262.2541-0.0941-0.5428-0.08370.06420.0677-0.0713-0.05390.64930.04060.20520.0694-0.01240.36210.02610.2137-28.2695-41.8625132.658
220.9941-0.29640.17990.5254-0.35290.5323-0.03390.02290.07020.04210.00080.06250.00920.10120.02360.14820.01060.00710.1463-0.00590.2064-35.8744-30.0189103.0404
231.4881-0.9770.25771.7788-0.51380.5572-0.0363-0.01690.04110.06420.04330.019-0.06120.0415-0.01240.15890.0041-0.00870.1685-0.01330.1838-36.8894-25.033100.5812
244.08881.62290.32211.56460.26220.04290.099-0.0502-0.0040.0334-0.1265-0.334-0.20180.55160.03650.0989-0.2057-0.03840.5737-0.0140.2849-20.80887.0416129.5402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 5 through 21 )H5 - 21
2X-RAY DIFFRACTION2chain 'H' and (resid 22 through 45 )H22 - 45
3X-RAY DIFFRACTION3chain 'H' and (resid 46 through 72 )H46 - 72
4X-RAY DIFFRACTION4chain 'H' and (resid 73 through 87 )H73 - 87
5X-RAY DIFFRACTION5chain 'H' and (resid 88 through 103 )H88 - 103
6X-RAY DIFFRACTION6chain 'H' and (resid 104 through 119 )H104 - 119
7X-RAY DIFFRACTION7chain 'H' and (resid 120 through 145 )H120 - 145
8X-RAY DIFFRACTION8chain 'H' and (resid 146 through 185 )H146 - 185
9X-RAY DIFFRACTION9chain 'H' and (resid 186 through 200 )H186 - 200
10X-RAY DIFFRACTION10chain 'H' and (resid 201 through 210 )H201 - 210
11X-RAY DIFFRACTION11chain 'L' and (resid 1 through 101 )L1 - 101
12X-RAY DIFFRACTION12chain 'L' and (resid 102 through 208 )L102 - 208
13X-RAY DIFFRACTION13chain 'A' and (resid 5 through 21 )A5 - 21
14X-RAY DIFFRACTION14chain 'A' and (resid 22 through 52 )A22 - 52
15X-RAY DIFFRACTION15chain 'A' and (resid 53 through 72 )A53 - 72
16X-RAY DIFFRACTION16chain 'A' and (resid 73 through 106 )A73 - 106
17X-RAY DIFFRACTION17chain 'A' and (resid 107 through 119 )A107 - 119
18X-RAY DIFFRACTION18chain 'A' and (resid 120 through 145 )A120 - 145
19X-RAY DIFFRACTION19chain 'A' and (resid 146 through 185 )A146 - 185
20X-RAY DIFFRACTION20chain 'A' and (resid 186 through 210 )A186 - 210
21X-RAY DIFFRACTION21chain 'B' and (resid 1 through 101 )B1 - 101
22X-RAY DIFFRACTION22chain 'B' and (resid 102 through 149 )B102 - 149
23X-RAY DIFFRACTION23chain 'B' and (resid 150 through 211 )B150 - 211
24X-RAY DIFFRACTION24chain 'P' and (resid 3 through 6 )P3 - 6

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