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- PDB-4r90: Anti CD70 Llama glama Fab 27B3 -

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Basic information

Entry
Database: PDB / ID: 4r90
TitleAnti CD70 Llama glama Fab 27B3
Components
  • Anti CD70 Llama glama Fab 27B3 Heavy chain
  • Anti CD70 Llama glama Fab 27B3 Light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold / human CD70
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLlama glama (llama)
Llama Glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.746 Å
AuthorsKlarenbeek, A. / El Mazouari, K. / Desmyter, A. / Blanchetot, C. / Hultberg, A. / Roovers, R.C. / Cambillau, C. / Spinelli, S. / Del-Favero, J. / Verrips, T. ...Klarenbeek, A. / El Mazouari, K. / Desmyter, A. / Blanchetot, C. / Hultberg, A. / Roovers, R.C. / Cambillau, C. / Spinelli, S. / Del-Favero, J. / Verrips, T. / de Haard, H. / Achour, I.
CitationJournal: MAbs / Year: 2015
Title: Camelid Ig V genes reveal significant human homology not seen in therapeutic target genes, providing for a powerful therapeutic antibody platform.
Authors: Klarenbeek, A. / Mazouari, K.E. / Desmyter, A. / Blanchetot, C. / Hultberg, A. / de Jonge, N. / Roovers, R.C. / Cambillau, C. / Spinelli, S. / Del-Favero, J. / Verrips, T. / de Haard, H.J. / Achour, I.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Anti CD70 Llama glama Fab 27B3 Light chain
H: Anti CD70 Llama glama Fab 27B3 Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3814
Polymers47,2492
Non-polymers1322
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-38 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.570, 66.880, 125.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Anti CD70 Llama glama Fab 27B3 Light chain


Mass: 22905.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Llama glama (llama) / Cell (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Anti CD70 Llama glama Fab 27B3 Heavy chain


Mass: 24343.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Llama Glama (llama) / Cell (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2M Ammonium sulphate (Sigma-Aldrich, A4418) and 0.15 M Na citrate pH 5.5 (Sigma-Aldrich, PHR1416). , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.931 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2011
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.746→65 Å / Num. all: 55037 / Num. obs: 55037 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.4
Reflection shellResolution: 1.746→1.85 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3 / Num. unique all: 8761 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VXS

2vxs


Resolution: 1.746→62.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.335 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18499 2753 5 %RANDOM
Rwork0.16278 ---
all0.16391 52290 --
obs0.16391 52290 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.206 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å2-0 Å2-0 Å2
2---0.6 Å20 Å2
3----0.53 Å2
Refine analyzeLuzzati coordinate error obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.746→62.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 7 567 3809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023502
X-RAY DIFFRACTIONr_bond_other_d0.0010.022274
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9544821
X-RAY DIFFRACTIONr_angle_other_deg0.79735624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6065474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79124.882127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78815532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7961510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
LS refinement shellResolution: 1.746→1.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 190 -
Rwork0.217 3535 -
obs--99.84 %
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)
11.7087-0.1443-1.25681.69090.53385.6164-0.2467-0.19030.14060.02090.1605-0.3182-0.51240.59260.08620.1649-0.0625-0.0720.1023-0.00370.116-7.42512.252-59.533
21.5788-0.12080.48842.24511.28782.9648-0.1068-0.11380.06240.1353-0.03560.1159-0.1309-0.0670.14240.0444-0.0093-0.0220.02370.01280.0372-16.8314.773-63.576
34.7299-0.3133-0.01542.26670.20533.9227-0.1930.00340.2422-0.21030.04830.0088-0.5777-0.14620.14480.1694-0.003-0.06760.01850.01420.0495-17.17613.3-67.381
41.0616-1.1071-0.89422.34052.23824.7116-0.2044-0.0895-0.0310.00950.06910.0307-0.20310.07710.13520.0975-0.0003-0.02490.04680.01870.0725-13.4396.897-59.928
51.9867-2.13860.54453.1339-0.90170.8432-0.091-0.119-0.02530.02340.0638-0.0006-0.0308-0.07680.02720.02660.0095-0.00520.0315-0.01350.0405-0.34-0.046-36.017
61.7609-0.89390.05493.06780.04120.6344-0.02510.06550.0503-0.1434-0.0537-0.1909-0.05820.00130.07880.03670.00950.01070.02170.0040.0263.9790.615-40.698
72.2632-0.3050.57670.6836-0.17150.4441-0.0389-0.1262-0.12660.02320.06040.0640.0422-0.0793-0.02150.0196-0.00620.00920.05020.00030.0428-20.706-17.176-60.875
81.84630.12010.30551.8847-0.71041.1146-0.0516-0.03950.02410.08430.0142-0.16-0.09670.05690.03740.0364-0.0073-0.00760.0504-0.00510.0531-13.212-8.107-63.813
93.34390.44121.50630.70620.01621.3228-0.05950.1592-0.0903-0.07690.0272-0.0190.02470.1250.03230.0223-0.01210.01340.069-0.01740.0406-12.997-16.481-71.998
100.9959-0.25210.40250.5896-0.08380.6788-0.0912-0.05270.023-0.04920.0564-0.0101-0.0428-0.00270.03480.0222-0.0082-0.00370.0421-0.0040.0358-15.994-10.524-64.277
110.3560.17090.18270.70120.8461.49710.0840.0070.0189-0.0236-0.0112-0.05140.0147-0.0447-0.07280.0573-0.00420.01190.0253-0.01280.041-3.464-10.303-32.574
120.60740.36360.05950.98710.51111.53990.0759-0.0259-0.0160.0966-0.08020.04740.0344-0.03220.00430.0321-0.00190.01370.0233-0.01930.0352-6.032-9.641-26.542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L2 - 30
2X-RAY DIFFRACTION2L31 - 50
3X-RAY DIFFRACTION3L51 - 75
4X-RAY DIFFRACTION4L76 - 110
5X-RAY DIFFRACTION5L111 - 150
6X-RAY DIFFRACTION6L151 - 212
7X-RAY DIFFRACTION7H1 - 30
8X-RAY DIFFRACTION8H31 - 50
9X-RAY DIFFRACTION9H51 - 75
10X-RAY DIFFRACTION10H76 - 118
11X-RAY DIFFRACTION11H119 - 160
12X-RAY DIFFRACTION12H161 - 224

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