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- PDB-5w24: Crystal Structure of 5C4 Fab -

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Basic information

Entry
Database: PDB / ID: 5w24
TitleCrystal Structure of 5C4 Fab
Components
  • 5C4 Fab Heavy Chain
  • 5C4 Fab Light Chain
KeywordsIMMUNE SYSTEM / Fab / Antibody / Neutralizing antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (R,R)-2,3-BUTANEDIOL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
Model detailsThe fusion inhibitor JNJ-2408068 has an occupancy of 0.33 in the asymmetric unit
AuthorsBattles, M.B. / McLellan, J.S. / Taher, N.M.
Citation
Journal: Nat Commun / Year: 2017
Title: Structural basis of respiratory syncytial virus subtype-dependent neutralization by an antibody targeting the fusion glycoprotein.
Authors: Tian, D. / Battles, M.B. / Moin, S.M. / Chen, M. / Modjarrad, K. / Kumar, A. / Kanekiyo, M. / Graepel, K.W. / Taher, N.M. / Hotard, A.L. / Moore, M.L. / Zhao, M. / Zheng, Z.Z. / Xia, N.S. / ...Authors: Tian, D. / Battles, M.B. / Moin, S.M. / Chen, M. / Modjarrad, K. / Kumar, A. / Kanekiyo, M. / Graepel, K.W. / Taher, N.M. / Hotard, A.L. / Moore, M.L. / Zhao, M. / Zheng, Z.Z. / Xia, N.S. / McLellan, J.S. / Graham, B.S.
#1: Journal: To Be Published
Title: Structure of 5C4 Fab
Authors: Battles, M.B. / McLellan, J.S. / Taher, N.M.
History
DepositionJun 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 5C4 Fab Light Chain
H: 5C4 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4993
Polymers53,4092
Non-polymers901
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-26 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.960, 63.010, 56.540
Angle α, β, γ (deg.)90.000, 98.600, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-483-

HOH

21L-548-

HOH

31H-418-

HOH

41H-739-

HOH

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Components

#1: Antibody 5C4 Fab Light Chain


Mass: 26730.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Plasmid: PVRC8400 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody 5C4 Fab Heavy Chain


Mass: 26678.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Plasmid: PVRC8400 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10.1 M sodium acetate trihydrate pH 4.6 and 20% PEG 3350

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→32.883 Å / Num. obs: 60748 / % possible obs: 93.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.026 / Rrim(I) all: 0.051 / Net I/σ(I): 14.9 / Num. measured all: 226910 / Scaling rejects: 657
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.533.50.234785322400.9380.1430.2753.869.7
8.22-37.493.10.0359873200.9950.0230.04325.677.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.3.6data scaling
PDB_EXTRACT3.22data extraction
Aimlessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T3P, 4GAG

3t3p

4gag


Resolution: 1.5→32.883 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.84
RfactorNum. reflection% reflection
Rfree0.2026 3064 5.04 %
Rwork0.1697 --
obs0.1714 60747 93.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.1 Å2 / Biso mean: 22.8928 Å2 / Biso min: 6.62 Å2
Refinement stepCycle: final / Resolution: 1.5→32.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 6 608 3897
Biso mean--25.27 32.18 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063407
X-RAY DIFFRACTIONf_angle_d0.8464659
X-RAY DIFFRACTIONf_chiral_restr0.053538
X-RAY DIFFRACTIONf_plane_restr0.005595
X-RAY DIFFRACTIONf_dihedral_angle_d11.1462046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52340.2519910.21271933202469
1.5234-1.54840.23671070.212255236280
1.5484-1.57510.22911470.20152592273993
1.5751-1.60380.24461290.19942621275094
1.6038-1.63460.25711360.19952657279394
1.6346-1.6680.25641280.19732641276994
1.668-1.70420.21571470.19192651279895
1.7042-1.74390.20381170.19272661277895
1.7439-1.78750.2351350.18882657279295
1.7875-1.83580.22851510.18472638278995
1.8358-1.88980.23661630.18582667283095
1.8898-1.95080.17931550.18052650280595
1.9508-2.02050.1821400.17232708284896
2.0205-2.10140.22591490.17242660280996
2.1014-2.1970.1931440.16922689283396
2.197-2.31280.23911620.16532667282996
2.3128-2.45770.22271320.17362743287596
2.4577-2.64740.19141470.17312709285697
2.6474-2.91370.19791690.16972701287097
2.9137-3.33490.19821440.15692735287997
3.3349-4.20030.17291400.14632762290297
4.2003-32.89070.17021310.15322686281792
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)
13.227-0.15941.37732.5832-0.92522.5377-0.1376-0.08250.2584-0.0763-0.02670.1038-0.0597-0.07660.16690.0848-0.0073-0.01280.0591-0.01260.0697-4.0891-85.7201135.3894
22.8231.2812-0.5092.7014-0.17741.4220.1659-0.1224-0.04810.1416-0.261-0.3192-0.2460.58660.06430.08060.0204-0.0210.12560.0330.144927.2667-88.9721132.1323
32.44580.97450.01033.879-1.24443.56380.00690.04440.0395-0.0594-0.0481-0.0122-0.02060.0110.03860.07040.0019-0.0080.06170.00130.071221.3646-85.7077127.2517
44.20891.7506-0.48293.6084-0.89282.59050.0205-0.05930.36360.2315-0.1402-0.1152-0.38770.40450.11820.1606-0.0601-0.03150.12790.0270.171228.5167-78.1099129.908
53.19480.7457-1.81391.116-1.54065.1088-0.16320.7827-0.0285-0.18120.11560.0090.1874-0.07740.0380.1549-0.0212-0.01950.2936-0.02770.1226-7.5133-93.29114.5069
63.5205-0.9194-0.08820.79860.13211.8396-0.02470.47760.4844-0.0917-0.01720.0315-0.09830.10620.03790.1092-0.001-0.02640.12980.04990.1113-11.7704-84.7555123.3743
72.355-0.8994-0.95290.7995-0.6573.15730.0120.72760.32-0.1123-0.02690.0263-0.0583-0.0040.01070.1246-0.02-0.03680.28590.06350.121-8.9816-87.2343116.7836
86.282-0.3869-2.77333.9582-1.15549.3601-0.13310.2116-0.05550.07080.03590.04670.2034-0.17480.09970.0599-0.0124-0.0170.0517-0.01570.0702-13.5633-94.4923130.3399
90.72480.3108-0.67080.0915-0.23370.5797-0.2981.0779-0.0878-0.30290.22120.02160.1301-0.15490.08520.216-0.0598-0.00890.56250.0150.12668.7265-89.1798108.775
107.0764-0.43642.52152.7696-0.69015.6626-0.2127-0.0266-0.3368-0.07010.105-0.16330.28650.1710.09910.14090.02660.04530.11620.01810.116127.8884-90.3634119.7435
112.0162-5.4593-2.69055.29650.4060.9058-0.190.9127-1.3739-0.6139-0.10180.00360.80750.40210.22990.45730.03630.2170.4165-0.12390.523932.3229-101.6731114.7386
129.1363-4.38473.67094.6754-4.97855.72010.05180.5385-0.2745-0.3468-0.00350.10850.3065-0.0996-0.09020.1529-0.05220.0080.1909-0.0530.089116.6464-91.3242117.1913
135.6257-3.65440.06994.5174-1.36710.7609-0.2945-0.3962-0.6059-0.288-0.1117-0.47660.90530.76130.26430.27190.27350.14940.4480.15910.369835.2925-97.9668125.1023
145.69460.0511.84844.00330.06416.0405-0.16871.4481-0.8475-0.4802-0.0954-0.07790.44590.79130.19880.30190.01570.12620.3945-0.08890.311232.3289-94.9708111.0062
153.969-3.51730.87355.0026-0.84941.1602-0.0825-0.10570.0930.04030.0182-0.0611-0.04550.02880.08710.0829-0.0132-0.01020.0665-0.00910.0577-0.0388-83.2184143.1585
168.1417-3.7054-2.04028.01622.21546.37030.06550.3831-0.6197-0.207-0.31790.28850.39430.08270.13970.1029-0.005-0.04680.08030.00320.0832-2.5361-91.883134.8311
171.9311-0.346-0.63851.39860.21572.7032-0.030.1351-0.08330.1236-0.18360.20080.2477-0.48480.12450.0653-0.031-0.0070.129-0.0230.1171-12.3713-89.3791142.1526
182.3881-0.3818-0.06272.6890.13152.7155-0.0572-0.1534-0.36090.10660.0790.1250.4288-0.03210.14180.1249-0.03380.00260.09010.03390.1089-7.5897-94.823144.9488
192.0522-0.5918-0.16922.3933-0.53061.5815-0.1538-0.1601-0.20470.25210.02460.11410.19730.08750.11210.1083-0.0068-0.00580.07080.030.0791-0.5387-91.005146.0192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 88 through 111 )H88 - 111
2X-RAY DIFFRACTION2chain 'H' and (resid 112 through 134 )H112 - 134
3X-RAY DIFFRACTION3chain 'H' and (resid 135 through 184 )H135 - 184
4X-RAY DIFFRACTION4chain 'H' and (resid 185 through 214 )H185 - 214
5X-RAY DIFFRACTION5chain 'L' and (resid 1 through 25 )L1 - 25
6X-RAY DIFFRACTION6chain 'L' and (resid 26 through 61 )L26 - 61
7X-RAY DIFFRACTION7chain 'L' and (resid 62 through 90 )L62 - 90
8X-RAY DIFFRACTION8chain 'L' and (resid 91 through 101 )L91 - 101
9X-RAY DIFFRACTION9chain 'L' and (resid 102 through 113 )L102 - 113
10X-RAY DIFFRACTION10chain 'L' and (resid 114 through 144 )L114 - 144
11X-RAY DIFFRACTION11chain 'L' and (resid 145 through 155 )L145 - 155
12X-RAY DIFFRACTION12chain 'L' and (resid 156 through 174 )L156 - 174
13X-RAY DIFFRACTION13chain 'L' and (resid 175 through 188 )L175 - 188
14X-RAY DIFFRACTION14chain 'L' and (resid 189 through 211 )L189 - 211
15X-RAY DIFFRACTION15chain 'H' and (resid 1 through 32 )H1 - 32
16X-RAY DIFFRACTION16chain 'H' and (resid 33 through 44 )H33 - 44
17X-RAY DIFFRACTION17chain 'H' and (resid 45 through 59 )H45 - 59
18X-RAY DIFFRACTION18chain 'H' and (resid 60 through 72 )H60 - 72
19X-RAY DIFFRACTION19chain 'H' and (resid 73 through 87 )H73 - 87

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