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- PDB-5vh4: Crystal structure of Fab fragment of anti-TNFa antibody inflixima... -

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Basic information

Entry
Database: PDB / ID: 5vh4
TitleCrystal structure of Fab fragment of anti-TNFa antibody infliximab in an I-centered orthorhombic crystal form
Components
  • Infliximab Fab Heavy Chain
  • Infliximab Fab Light Chain
KeywordsIMMUNE SYSTEM / antibody / Fab / biosimilar / infliximab / TNFa / anti-TNFa
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMayclin, S.J. / Edwards, T.E. / Lerch, T.F. / Conlan, H. / Sharpe, P.
CitationJournal: MAbs / Year: 2017
Title: Infliximab crystal structures reveal insights into self-association.
Authors: Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Lee, E. / Conlon, H.D. / Polleck, S. / Rouse, J.C. / Luo, Y. / Zou, Q.
History
DepositionApr 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Infliximab Fab Heavy Chain
L: Infliximab Fab Light Chain
A: Infliximab Fab Heavy Chain
B: Infliximab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,27111
Polymers95,6344
Non-polymers1,6377
Water15,385854
1
H: Infliximab Fab Heavy Chain
L: Infliximab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6676
Polymers47,8172
Non-polymers8504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-22 kcal/mol
Surface area19380 Å2
MethodPISA
2
A: Infliximab Fab Heavy Chain
B: Infliximab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6055
Polymers47,8172
Non-polymers7883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-19 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.850, 93.610, 316.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11H-429-

HOH

21H-472-

HOH

31A-582-

HOH

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Components

#1: Antibody Infliximab Fab Heavy Chain


Mass: 24356.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Infliximab Fab Light Chain


Mass: 23460.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Infliximab Fab at 10 mg/mL against 2.16 M sodium malonate, 10 mM NAD, crystal tracking ID 267666d9, unique puck ID sar8-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 91050 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.007 % / Biso Wilson estimate: 25.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.091 / Χ2: 0.953 / Net I/σ(I): 15.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.055.0120.6542.9366340.8030.7399.9
2.05-2.115.030.5343.5965460.8730.59699.9
2.11-2.175.0380.414.5463340.920.45899.9
2.17-2.245.0350.3385.3961230.9440.378100
2.24-2.315.040.2936.0559640.9450.32799.9
2.31-2.395.0410.2586.7157650.9610.28899.9
2.39-2.485.0460.2267.6255810.9680.25299.8
2.48-2.585.0430.1868.9153760.9770.20899.9
2.58-2.75.0480.14411.2451640.9860.16199.9
2.7-2.835.0350.11213.6349550.9920.12599.9
2.83-2.985.0440.08816.9347000.9940.09899.9
2.98-3.165.0150.06521.8144630.9960.07399.8
3.16-3.385.0040.0526.7441980.9980.05699.9
3.38-3.654.970.04331.0839240.9980.04899.9
3.65-44.9760.03735.136080.9980.04199.8
4-4.474.9420.03140.1332900.9990.03599.8
4.47-5.164.9320.0342.6629110.9990.03399.6
5.16-6.324.9160.0339.924780.9990.03399.4
6.32-8.944.8350.02941.3519390.9990.03398.7
8.94-504.4370.02646.210970.9990.02995.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
Cootmodel building
PHENIXdev_2229refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4g3y
Resolution: 2→50 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.06
RfactorNum. reflection% reflection
Rfree0.1865 4542 4.99 %
Rwork0.1579 --
obs0.1594 91022 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.37 Å2 / Biso mean: 31.5958 Å2 / Biso min: 11.47 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 108 854 7532
Biso mean--72.94 38.89 -
Num. residues----868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066930
X-RAY DIFFRACTIONf_angle_d0.8649469
X-RAY DIFFRACTIONf_chiral_restr0.0551059
X-RAY DIFFRACTIONf_plane_restr0.0051209
X-RAY DIFFRACTIONf_dihedral_angle_d13.4684094
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 (%)
2-2.02280.23141550.216528362991100
2.0228-2.04660.23241410.211428402981100
2.0466-2.07150.25561430.20828813024100
2.0715-2.09780.23841550.204228252980100
2.0978-2.12540.26751410.194228653006100
2.1254-2.15450.20571520.178228503002100
2.1545-2.18530.22441600.176228803040100
2.1853-2.21790.21121360.179328612997100
2.2179-2.25250.19161410.171328893030100
2.2525-2.28950.21131750.170828242999100
2.2895-2.32890.21511530.177628753028100
2.3289-2.37130.18561500.166328492999100
2.3713-2.41690.1791480.173628573005100
2.4169-2.46620.19411370.172828893026100
2.4662-2.51980.24971520.180828643016100
2.5198-2.57840.23291560.178628503006100
2.5784-2.64290.22181550.179228683023100
2.6429-2.71440.22261580.174328773035100
2.7144-2.79420.18571470.173428753022100
2.7942-2.88440.2081550.173128843039100
2.8844-2.98750.2111370.174829003037100
2.9875-3.10710.21011560.172429143070100
3.1071-3.24850.20521520.162728653017100
3.2485-3.41970.21651690.158828813050100
3.4197-3.63390.17461620.139729133075100
3.6339-3.91430.16141450.131128993044100
3.9143-4.3080.11281570.118129283085100
4.308-4.93080.10251260.103229653091100
4.9308-6.20990.15361520.13362963311599
6.2099-46.81780.17281760.16913013318997
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.55930.52710.95361.45480.791.92010.02490.09150.01640.008-0.0361-0.05050.01920.1217-0.00310.1447-0.0044-0.00810.19350.01720.1318-10.89956.193211.0384
22.102-0.03460.75060.75530.78041.1978-0.1051-0.3597-0.22230.31410.1276-0.17230.30160.25150.0140.26540.072-0.00130.3130.06210.2035.6223-0.834935.2923
31.10630.91330.01283.8496-0.76041.1172-0.1480.0369-0.0083-0.07960.1022-0.26390.03330.10550.0490.24210.0470.01340.24910.03170.22836.1347-6.915433.557
42.0801-1.28781.1672.6753-1.2753.43790.0221-0.2597-0.26060.20170.10710.17320.1627-0.2656-0.1290.1682-0.03210.00520.21760.03640.1668-30.1219-2.920826.5441
54.55010.31910.84052.7713-0.19293.39960.1641-0.0746-0.42670.0991-0.0861-0.22670.14650.3698-0.09980.21490.022-0.00880.19930.02120.178-18.9044-6.765820.809
62.0128-1.13270.85094.0607-0.99362.71360.00620.0892-0.5116-0.07070.14050.17630.4819-0.1451-0.15910.2697-0.0649-0.03720.1969-0.02040.2661-29.5016-10.514719.0666
70.5423-0.60920.82010.8403-1.0262.11770.00890.013-0.0836-0.03140.0539-0.0110.22810.0942-0.14020.1820.03620.00690.1578-0.00020.1471-12.9293-6.351632.2991
82.49111.32120.49132.35340.73611.0104-0.12650.05670.16260.08070.05680.03370.04790.18110.06520.23930.0736-0.00740.23850.01590.1884-4.3587-5.507446.9867
93.24091.30090.49842.3296-0.03781.2596-0.0195-0.5549-0.10180.1882-0.2088-0.39080.01790.37090.19820.26780.0823-0.05470.36930.04190.21364.1822-5.443654.0667
101.80260.2614-0.2091.3007-0.91122.0278-0.15110.06240.19930.12320.0382-0.0848-0.11390.00510.07840.1841-0.0209-0.03260.08940.0110.1668-16.011511.742367.8784
111.522-0.5076-1.0622.4967-1.18391.86380.10130.3510.2546-0.2359-0.27690.0625-0.1745-0.12130.16060.25230.0201-0.08070.186-0.01260.3193-23.016428.262543.3844
124.3255-0.63050.61331.8084-0.46621.2773-0.2188-0.25420.48960.33640.0246-0.2482-0.1498-0.04250.18890.21940.0294-0.08380.2138-0.03590.2382-28.673928.860845.308
133.0996-0.33620.82951.9804-0.50552.49820.15330.3331-0.1249-0.245-0.05680.30980.3982-0.0415-0.08240.2315-0.0408-0.02690.1335-0.01150.1679-25.5608-7.380952.6285
142.54750.0240.45264.7861-1.09363.9059-0.02110.12180.2293-0.05260.04130.2579-0.4536-0.09010.00860.2034-0.0284-0.00130.15780.01170.1693-29.12513.88758.3486
153.1094-0.48781.14111.7659-0.80912.67620.1277-0.1386-0.14860.02190.05550.38810.2161-0.4894-0.14190.2003-0.08890.02550.22230.03640.2367-33.2618-6.403960.3346
160.7263-0.82471.27383.4025-2.17295.6252-0.07230.1984-0.10020.02590.19890.5919-0.0406-0.3372-0.07590.1744-0.04150.00580.2076-0.00220.2759-32.36370.855252.9185
170.6957-0.54340.96310.6478-0.61861.74590.03810.03380.1048-0.1109-0.0985-0.02270.06770.00310.06610.14250.02190.0230.18620.00190.2069-27.356915.819838.704
183.55991.7103-1.46542.0816-0.17651.42760.10710.22040.09720.07410.0267-0.0516-0.1591-0.0348-0.09610.18870.0518-0.02990.24990.02440.2032-27.221217.17833.6836
192.80781.43060.49152.70510.10381.1608-0.25260.34250.5216-0.39780.05120.0647-0.22670.12720.15690.22560.0049-0.03480.24620.08540.2588-27.170626.667824.7219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 113 )H1 - 113
2X-RAY DIFFRACTION2chain 'H' and (resid 114 through 141 )H114 - 141
3X-RAY DIFFRACTION3chain 'H' and (resid 142 through 220 )H142 - 220
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 32 )L1 - 32
5X-RAY DIFFRACTION5chain 'L' and (resid 33 through 48 )L33 - 48
6X-RAY DIFFRACTION6chain 'L' and (resid 49 through 75 )L49 - 75
7X-RAY DIFFRACTION7chain 'L' and (resid 76 through 128 )L76 - 128
8X-RAY DIFFRACTION8chain 'L' and (resid 129 through 174 )L129 - 174
9X-RAY DIFFRACTION9chain 'L' and (resid 175 through 213 )L175 - 213
10X-RAY DIFFRACTION10chain 'A' and (resid 1 through 113 )A1 - 113
11X-RAY DIFFRACTION11chain 'A' and (resid 114 through 141 )A114 - 141
12X-RAY DIFFRACTION12chain 'A' and (resid 142 through 220 )A142 - 220
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 32 )B1 - 32
14X-RAY DIFFRACTION14chain 'B' and (resid 33 through 48 )B33 - 48
15X-RAY DIFFRACTION15chain 'B' and (resid 49 through 75 )B49 - 75
16X-RAY DIFFRACTION16chain 'B' and (resid 76 through 90 )B76 - 90
17X-RAY DIFFRACTION17chain 'B' and (resid 91 through 150 )B91 - 150
18X-RAY DIFFRACTION18chain 'B' and (resid 151 through 174 )B151 - 174
19X-RAY DIFFRACTION19chain 'B' and (resid 175 through 213 )B175 - 213

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