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- PDB-5cma: Anti-B7-H3 monoclonal antibody ch8H9 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 5cma
TitleAnti-B7-H3 monoclonal antibody ch8H9 Fab fragment
Components
  • Antibody ch8H9 Fab heavy chain
  • Antibody ch8H9 Fab light chain
KeywordsIMMUNE SYSTEM / B7-H3 8H9 monoclonal antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsAhmed, M. / Goldgur, Y. / Cheng, M. / Cheung, N.K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Humanized Affinity-matured Monoclonal Antibody 8H9 Has Potent Antitumor Activity and Binds to FG Loop of Tumor Antigen B7-H3.
Authors: Ahmed, M. / Cheng, M. / Zhao, Q. / Goldgur, Y. / Cheal, S.M. / Guo, H.F. / Larson, S.M. / Cheung, N.K.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 16, 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
A: Antibody ch8H9 Fab light chain
B: Antibody ch8H9 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)46,8722
Polymers46,8722
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-24 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.576, 207.422, 85.491
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-311-

HOH

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Components

#1: Antibody Antibody ch8H9 Fab light chain


Mass: 23272.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Antibody ch8H9 Fab heavy chain


Mass: 23599.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Lithium sulfate monohydrate; 0.1M BIS-TRIS 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 20058 / % possible obs: 98.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Χ2: 0.494 / Net I/av σ(I): 16.325 / Net I/σ(I): 6 / Num. measured all: 66793
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.30.4469900.8990.2790.5290.43899.4
2.54-2.593.40.39310110.9270.2380.4610.4599.3
2.59-2.643.40.3749700.9170.2280.440.43999.3
2.64-2.693.30.30710100.9330.1860.3610.50299.1
2.69-2.753.40.2599920.960.1580.3050.46398.7
2.75-2.823.10.2289860.9430.1440.2710.47897.2
2.82-2.893.30.1889840.9620.1160.2230.48799.3
2.89-2.963.40.16310180.9820.0970.190.46599.3
2.96-3.053.50.1269930.9880.0770.1480.45899.6
3.05-3.153.40.10310050.9920.0630.1210.48399.2
3.15-3.263.30.08810010.9930.0540.1040.51398.8
3.26-3.393.30.0729990.9940.0440.0850.50598
3.39-3.553.10.0599900.9960.0380.0710.55697.5
3.55-3.733.50.05510100.9960.0330.0640.5699.1
3.73-3.973.40.04810120.9940.0290.0560.55298.9
3.97-4.273.40.049950.9970.0250.0470.54497.5
4.27-4.73.20.0349960.9980.0210.040.54295.8
4.7-5.383.50.03210250.9980.020.0380.52798.3
5.38-6.763.30.03310130.9980.020.0380.46296.1
6.76-303.20.02810580.9980.0170.0330.45794.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation29 Å2.74 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREP11.0.02phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D85

3d85


Resolution: 2.5→29.001 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 977 4.93 %
Rwork0.208 18836 -
obs0.2106 19813 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.64 Å2 / Biso mean: 69.7258 Å2 / Biso min: 35.53 Å2
Refinement stepCycle: final / Resolution: 2.5→29.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 0 49 3303
Biso mean---58.45 -
Num. residues----426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033335
X-RAY DIFFRACTIONf_angle_d0.8694533
X-RAY DIFFRACTIONf_chiral_restr0.033512
X-RAY DIFFRACTIONf_plane_restr0.007579
X-RAY DIFFRACTIONf_dihedral_angle_d14.2851187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.62620.3641100.29832586269694
2.6262-2.79060.33671510.28012627277896
2.7906-3.00590.29071620.26632668283098
3.0059-3.3080.33581560.23892705286199
3.308-3.78580.28061310.2112702283398
3.7858-4.76630.2171270.17062744287197
4.7663-29.00250.22191400.18622804294496
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)
11.2953-0.3543-0.40113.4765-0.44770.1963-0.22770.36960.07870.3405-0.2517-0.4294-0.91191.2250.27760.9207-0.412-0.12680.90480.05480.4987-1.5397-14.487813.1879
22.9234-1.5726-0.53553.65510.9421.5654-0.00940.2453-0.67060.0245-0.2830.1945-1.43140.25610.16781.0735-0.1355-0.11050.50130.13480.6558-13.6626-16.66899.2145
32.75250.8053-0.00391.8736-0.42940.9382-0.5095-0.48990.54190.60970.0156-0.0757-1.52160.44170.3911.2961-0.2745-0.1590.66040.02960.4526-9.792-9.572816.7991
42.0013-0.26551.51222.994-1.6412.7727-0.27160.4435-0.04760.3398-0.1144-0.1174-1.1220.74140.05880.7064-0.221-0.06560.60080.02460.3827-8.5235-21.261413.3861
51.7741-1.0903-0.13592.85350.3583.06380.0106-0.0295-0.0551-0.2147-0.09720.36520.0476-0.16090.11840.3959-0.07430.04230.4289-0.00840.6306-13.7652-51.19598.2348
60.8561-0.9741-0.82833.20892.09391.5222-0.4568-0.697-0.3465-0.0060.4829-0.25920.31620.22580.04670.3821-0.01670.04130.63030.02980.6176-5.3575-53.28285.2055
71.8565-0.2810.37941.68821.06192.73710.0573-0.0554-0.43790.07890.02370.05870.29560.0017-0.11230.4079-0.04460.03860.44410.01780.6508-12.038-52.604310.7522
82.8809-0.84581.04244.699-0.16574.1035-0.49720.23020.4256-0.14150.33380.4088-1.3125-0.87980.14760.90390.1391-0.10510.65920.01880.6102-22.6595-16.5396-8.1688
92.39961.7267-0.80663.41070.20224.6883-0.24580.59560.4922-0.3782-0.2529-0.1327-1.73810.68730.27960.9815-0.1886-0.16310.56540.10410.4855-13.7336-12.9408-9.6537
101.82180.641-0.12354.0016-0.56124.5106-0.09720.25890.215-0.54630.08330.0051-0.97740.26510.09250.5247-0.0631-0.10.50490.07730.5222-14.7676-21.1376-6.2903
110.12690.3334-0.41662.9264-0.60272.8624-0.0622-0.001-0.0086-0.12920.11480.5465-0.0254-0.25450.00280.3621-0.0041-0.0360.485-0.00510.5945-23.4845-43.4123.2946
124.23941.3332-1.02817.5614-4.46597.84830.29210.4396-0.2398-0.43850.4511.12670.7262-0.6904-0.35850.4869-0.0856-0.16180.6224-0.05450.6823-30.591-48.54060.0384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 49 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 75 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 113 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 150 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 163 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 213 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 33 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 34 through 83 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 84 through 124 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 125 through 208 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 209 through 220 )B0

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