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- PDB-7km6: APOBEC3B antibody 5G7 Fv-clasp -

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Open data


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Basic information

Entry
Database: PDB / ID: 7km6
TitleAPOBEC3B antibody 5G7 Fv-clasp
Components(5G7 human monoclonal FAB ...) x 2
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsTang, H. / Shi, K. / Aihara, H.
Funding support United States, China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Natural Science Foundation of China (NSFC)31470160 China
CitationJournal: Viruses / Year: 2021
Title: Structural Characterization of a Minimal Antibody against Human APOBEC3B.
Authors: Tang, H. / Demir, O. / Kurniawan, F. / Brown, W.L. / Shi, K. / Moeller, N.H. / Carpenter, M.A. / Belica, C. / Orellana, K. / Du, G. / LeBeau, A.M. / Amaro, R.E. / Harris, R.S. / Aihara, H.
History
DepositionNov 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 5G7 human monoclonal FAB light chain
H: 5G7 human monoclonal FAB heavy chain
l: 5G7 human monoclonal FAB light chain
h: 5G7 human monoclonal FAB heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,30619
Polymers77,5334
Non-polymers77315
Water7,494416
1
L: 5G7 human monoclonal FAB light chain
H: 5G7 human monoclonal FAB heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,19710
Polymers38,7672
Non-polymers4318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-48 kcal/mol
Surface area17270 Å2
MethodPISA
2
l: 5G7 human monoclonal FAB light chain
h: 5G7 human monoclonal FAB heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1099
Polymers38,7672
Non-polymers3427
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-61 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.074, 68.823, 88.759
Angle α, β, γ (deg.)90.000, 107.050, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain H and (resid 1 through 21 or resid 23...
21(chain h and (resid 1 through 21 or resid 23...
12(chain L and (resid 1 through 13 or resid 15...
22(chain l and (resid 1 through 13 or resid 15...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUSERSER(chain H and (resid 1 through 21 or resid 23...HB1 - 212 - 22
121ALAALASERSER(chain H and (resid 1 through 21 or resid 23...HB23 - 3024 - 31
131TYRTYRALAALA(chain H and (resid 1 through 21 or resid 23...HB32 - 9233 - 93
141GLUGLUHISHIS(chain H and (resid 1 through 21 or resid 23...HB1 - 1702 - 171
151TRPTRPILEILE(chain H and (resid 1 through 21 or resid 23...HB128 - 148129 - 149
161GLUGLUHISHIS(chain H and (resid 1 through 21 or resid 23...HB1 - 1702 - 171
171GLNGLNLYSLYS(chain H and (resid 1 through 21 or resid 23...HB156 - 158157 - 159
181GLNGLNHISHIS(chain H and (resid 1 through 21 or resid 23...HB160 - 170161 - 171
211GLUGLUSERSER(chain h and (resid 1 through 21 or resid 23...hD1 - 212 - 22
221ALAALASERSER(chain h and (resid 1 through 21 or resid 23...hD23 - 3024 - 31
231TYRTYRALAALA(chain h and (resid 1 through 21 or resid 23...hD32 - 9233 - 93
241METMETHISHIS(chain h and (resid 1 through 21 or resid 23...hD0 - 1701 - 171
251TRPTRPILEILE(chain h and (resid 1 through 21 or resid 23...hD128 - 148129 - 149
261METMETHISHIS(chain h and (resid 1 through 21 or resid 23...hD0 - 1701 - 171
271GLNGLNLYSLYS(chain h and (resid 1 through 21 or resid 23...hD156 - 158157 - 159
281GLNGLNHISHIS(chain h and (resid 1 through 21 or resid 23...hD160 - 170161 - 171
112ASPASPVALVAL(chain L and (resid 1 through 13 or resid 15...LA1 - 132 - 14
122VALVALTHRTHR(chain L and (resid 1 through 13 or resid 15...LA15 - 2016 - 21
132METMETALAALA(chain L and (resid 1 through 13 or resid 15...LA0 - 1641 - 165
142METMETALAALA(chain L and (resid 1 through 13 or resid 15...LA0 - 1641 - 165
152LEULEUTYRTYR(chain L and (resid 1 through 13 or resid 15...LA89 - 9390 - 94
162GLNGLNTYRTYR(chain L and (resid 1 through 13 or resid 15...LA95 - 9896 - 99
172METMETMETMET(chain L and (resid 1 through 13 or resid 15...LA01
182ARGARGTYRTYR(chain L and (resid 1 through 13 or resid 15...LA148 - 151149 - 152
192ARGARGTYRTYR(chain L and (resid 1 through 13 or resid 15...LA148 - 151149 - 152
1102SERSERPROPRO(chain L and (resid 1 through 13 or resid 15...LA153 - 157154 - 158
212ASPASPVALVAL(chain l and (resid 1 through 13 or resid 15...lC1 - 132 - 14
222VALVALTHRTHR(chain l and (resid 1 through 13 or resid 15...lC15 - 2016 - 21
232SERSERSERSER(chain l and (resid 1 through 13 or resid 15...lC2223
242ILEILEILEILE(chain l and (resid 1 through 13 or resid 15...lC23
252SERSERLEULEU(chain l and (resid 1 through 13 or resid 15...lC28 - 8929 - 90
262LEULEUTYRTYR(chain l and (resid 1 through 13 or resid 15...lC89 - 9890 - 99
272SERSERSERSER(chain l and (resid 1 through 13 or resid 15...lC910
282METMETLYSLYS(chain l and (resid 1 through 13 or resid 15...lC0 - 1651 - 166
292METMETLYSLYS(chain l and (resid 1 through 13 or resid 15...lC0 - 1651 - 166
2102ARGARGTYRTYR(chain l and (resid 1 through 13 or resid 15...lC148 - 151149 - 152
2112SERSERPROPRO(chain l and (resid 1 through 13 or resid 15...lC153 - 157154 - 158

NCS ensembles :
ID
1
2

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Components

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Antibody , 2 types, 4 molecules LlHh

#1: Antibody 5G7 human monoclonal FAB light chain


Mass: 18769.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody 5G7 human monoclonal FAB heavy chain


Mass: 19997.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 431 molecules

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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM Bis-Tris/Hydrochloric acid pH 6.5, 400 mM sodium chloride, 30% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.65→84.86 Å / Num. obs: 71357 / % possible obs: 97.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.053 / Rrim(I) all: 0.104 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.682.70.833731027240.60.5370.9980.974.1
9.05-84.863.50.0516574790.9970.0310.05920.899

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XCQ

5xcq


Resolution: 1.67→84.86 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 6391 4.68 %
Rwork0.1887 130094 -
obs0.1909 71268 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.51 Å2 / Biso mean: 33.5936 Å2 / Biso min: 17.26 Å2
Refinement stepCycle: final / Resolution: 1.67→84.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 45 417 5785
Biso mean--49.94 43.55 -
Num. residues----672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095657
X-RAY DIFFRACTIONf_angle_d0.997649
X-RAY DIFFRACTIONf_chiral_restr0.061806
X-RAY DIFFRACTIONf_plane_restr0.007983
X-RAY DIFFRACTIONf_dihedral_angle_d12.6262123
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11H1500X-RAY DIFFRACTION4.461TORSIONAL
12h1500X-RAY DIFFRACTION4.461TORSIONAL
21L1334X-RAY DIFFRACTION4.461TORSIONAL
22l1334X-RAY DIFFRACTION4.461TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.67-1.690.38552140.37484124433890
1.69-1.710.34152050.35694307451296
1.71-1.730.37562050.34224281448696
1.73-1.750.32522340.32434354458896
1.75-1.770.31882300.31794285451596
1.77-1.80.32672290.31644316454596
1.8-1.820.33362230.29744260448395
1.82-1.850.34352420.29744311455396
1.85-1.880.30852080.29694357456596
1.88-1.910.31822280.28964364459296
1.91-1.940.32571900.26854332452296
1.94-1.980.26692560.25594226448295
1.98-2.020.29251540.23284298445295
2.02-2.060.27512320.2254119435193
2.06-2.10.23522030.21624308451195
2.1-2.150.22872500.20954439468998
2.15-2.210.26462340.20134419465398
2.21-2.270.23182100.1964403461398
2.27-2.330.25172340.19464424465898
2.33-2.410.23282090.18734424463398
2.41-2.490.24692070.18524404461198
2.49-2.590.2341750.18514432460797
2.59-2.710.22372210.17614353457497
2.71-2.860.20511870.17174347453496
2.86-3.030.22381770.17224238441593
3.03-3.270.23372020.17224413461598
3.27-3.60.20752160.15184442465898
3.6-4.120.20951380.13974450458897
4.12-5.190.16892020.13564379458197
5.19-84.860.23032760.17294285456196
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)
11.59561.03720.58522.39850.79761.4914-0.02610.03580.0838-0.0756-0.040.1864-0.106-0.10280.06330.20980.01680.01580.2170.01260.23977.0539-9.2591-35.4234
25.40241.1772.0266.82495.93969.49930.39860.26080.38810.0103-0.8090.88720.3603-0.96710.42460.29030.08360.0280.4310.00660.4663-11.1404-26.9717-42.2711
37.1627-7.00987.54356.8527-7.43578.0123-0.18140.25050.24180.2229-0.21-0.088-0.22420.06860.21790.318-0.01930.00770.2612-0.0110.239510.0802-37.9939-33.3935
41.998-0.26180.20871.9164-0.28923.15990.04550.03420.0398-0.02290.0277-0.12790.04990.1767-0.06630.15030.0169-0.00920.1907-0.01060.191224.5942-21.0922-31.917
50.0413-0.25430.3796.863-7.38518.2812-0.0505-0.1078-0.0030.60470.11940.0853-0.57940.0577-0.06530.32590.037-0.02420.33190.03950.284120.4044-43.7933-15.2049
64.4397-4.8075.10475.2628-5.62055.99330.35480.2146-0.2563-0.2029-0.07730.40230.53-0.1772-0.40560.4138-0.0329-0.0050.3163-0.0590.29783.1772-45.0142-34.7095
73.7325-3.3854-3.73248.71543.68646.8498-0.06021.146-0.0198-0.4515-0.37020.6614-0.0004-0.32310.23320.2783-0.05650.03290.31650.02910.29692.4903-4.6481-19.0553
87.1395-5.81997.50925.4634-5.40559.8444-0.1636-0.10170.55360.28440.0027-0.3762-0.45060.38150.18190.2337-0.02270.04340.3759-0.01320.349415.652-8.9395-9.0961
96.3042-2.2071-4.20227.36083.43547.41680.3779-0.32960.8106-0.0940.1225-0.4113-0.7787-0.3606-0.44820.26250.02770.0250.1694-0.0030.315-1.80385.882-9.5129
102.1713-0.05330.45885.486-0.38421.30290.0663-0.1365-0.20880.0054-0.1141-0.0620.11740.08710.01770.1690.02540.00760.2233-0.00770.2843.7627-13.943-3.9386
112.7453-1.65991.31183.6189-1.46953.5205-0.0258-0.090.20440.18890.0523-0.1944-0.11310.1613-0.01910.2271-0.0064-0.00440.2908-0.0460.33067.4592-3.296-1.4955
124.2495-1.41491.17123.6196-0.46931.853-0.0527-0.30760.04730.20.1937-0.2236-0.10820.0239-0.15940.20970.00880.01960.2256-0.00960.25379.9499-12.463-4.3145
135.6214-0.17591.89672.96670.23063.4995-0.15850.3378-0.18920.0337-0.00930.405-0.0865-0.18340.12410.22890.00470.02080.20950.01810.213-2.5725-6.0581-13.5327
144.9101-6.50095.48288.6072-7.25966.1240.46940.35550.0121-0.5071-0.634-0.24420.6340.54680.03810.36040.0215-0.00340.42420.05710.420722.8249-23.1133-5.3462
159.0361-1.8262-5.09235.91842.30663.1642-0.0188-1.10840.81140.25070.2216-0.7018-0.0180.8107-0.20.362-0.0466-0.07080.53230.02060.512725.4842-24.10246.0821
167.37095.95627.1525.90456.91378.6143-0.0087-0.19160.2369-0.0391-0.35340.24740.0535-0.2690.41020.290.03410.00110.22770.0150.31372.0518-35.6376-9.2148
172.0078-1.1924-1.27316.58835.50356.4190.0555-0.1994-0.02690.11320.015-0.04030.2175-0.1377-0.07750.1445-0.03610.00310.17530.0140.2372-12.6004-25.1244-7.9318
181.97880.01360.32021.6440.41742.53550.01310.068-0.0411-0.0697-0.0026-0.00190.0228-0.034200.15960.00680.00360.1972-0.02040.2112-11.2476-17.6518-12.0629
192.28350.47052.89031.9804-2.19027.77830.55080.1024-0.0121-0.1955-0.12030.5532-0.8712-0.3623-0.32570.5650.07930.11260.4955-0.23910.5451-9.6819-49.567-30.5428
204.56655.65674.95296.99326.1495.38450.2355-0.1175-0.20790.2191-0.0195-0.32950.3690.1637-0.3780.33730.0162-0.00790.33590.02660.34129.8852-41.7105-7.0487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 0 through 108 )L0 - 108
2X-RAY DIFFRACTION2chain 'L' and (resid 109 through 125 )L109 - 125
3X-RAY DIFFRACTION3chain 'L' and (resid 126 through 164 )L126 - 164
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 111 )H1 - 111
5X-RAY DIFFRACTION5chain 'H' and (resid 112 through 129 )H112 - 129
6X-RAY DIFFRACTION6chain 'H' and (resid 130 through 170 )H130 - 170
7X-RAY DIFFRACTION7chain 'l' and (resid 0 through 7 )l0 - 7
8X-RAY DIFFRACTION8chain 'l' and (resid 8 through 25 )l8 - 25
9X-RAY DIFFRACTION9chain 'l' and (resid 26 through 38 )l26 - 38
10X-RAY DIFFRACTION10chain 'l' and (resid 39 through 54 )l39 - 54
11X-RAY DIFFRACTION11chain 'l' and (resid 55 through 81 )l55 - 81
12X-RAY DIFFRACTION12chain 'l' and (resid 82 through 96 )l82 - 96
13X-RAY DIFFRACTION13chain 'l' and (resid 97 through 108 )l97 - 108
14X-RAY DIFFRACTION14chain 'l' and (resid 109 through 118 )l109 - 118
15X-RAY DIFFRACTION15chain 'l' and (resid 119 through 125 )l119 - 125
16X-RAY DIFFRACTION16chain 'l' and (resid 126 through 165 )l126 - 165
17X-RAY DIFFRACTION17chain 'h' and (resid 0 through 25 )h0 - 25
18X-RAY DIFFRACTION18chain 'h' and (resid 26 through 122 )h26 - 122
19X-RAY DIFFRACTION19chain 'h' and (resid 123 through 129 )h123 - 129
20X-RAY DIFFRACTION20chain 'h' and (resid 130 through 170 )h130 - 170

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