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- PDB-3wii: Crystal structure of the Fab fragment of B2212A, a murine monoclo... -

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Basic information

Entry
Database: PDB / ID: 3wii
TitleCrystal structure of the Fab fragment of B2212A, a murine monoclonal antibody specific for the third fibronectin domain (Fn3) of human ROBO1.
Components
  • anti-human ROBO1 antibody B2212A Fab heavy chain
  • anti-human ROBO1 antibody B2212A Fab light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin Fab fragment / anti-hepatocellular carcinoma antibody / the third fibronectin type-III domain (Fn3) of human ROBO1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNakayama, T. / Mizohata, E. / Yamashita, T. / Nagatoishi, S. / Nakakido, M. / Iwanari, H. / Mochizuki, Y. / Kado, Y. / Yokota, Y. / Sato, R. ...Nakayama, T. / Mizohata, E. / Yamashita, T. / Nagatoishi, S. / Nakakido, M. / Iwanari, H. / Mochizuki, Y. / Kado, Y. / Yokota, Y. / Sato, R. / Tsumoto, K. / Fujitani, H. / Kodama, T. / Hamakubo, T. / Inoue, T.
CitationJournal: Protein Sci. / Year: 2015
Title: Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses
Authors: Nakayama, T. / Mizohata, E. / Yamashita, T. / Nagatoishi, S. / Nakakido, M. / Iwanari, H. / Mochizuki, Y. / Kado, Y. / Yokota, Y. / Satoh, R. / Tsumoto, K. / Fujitani, H. / Kodama, T. / Hamakubo, T. / Inoue, T.
History
DepositionSep 12, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: anti-human ROBO1 antibody B2212A Fab light chain
H: anti-human ROBO1 antibody B2212A Fab heavy chain
M: anti-human ROBO1 antibody B2212A Fab light chain
I: anti-human ROBO1 antibody B2212A Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)94,7494
Polymers94,7494
Non-polymers00
Water11,944663
1
L: anti-human ROBO1 antibody B2212A Fab light chain
H: anti-human ROBO1 antibody B2212A Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3752
Polymers47,3752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-28 kcal/mol
Surface area19420 Å2
MethodPISA
2
M: anti-human ROBO1 antibody B2212A Fab light chain
I: anti-human ROBO1 antibody B2212A Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3752
Polymers47,3752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-28 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.823, 136.490, 77.512
Angle α, β, γ (deg.)90.00, 91.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody anti-human ROBO1 antibody B2212A Fab light chain


Mass: 23570.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody anti-human ROBO1 antibody B2212A Fab heavy chain


Mass: 23803.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DATABASE OF THE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT ...THE SEQUENCE DATABASE OF THE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3347.29
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop4.625%(w/v) PEG4000, 0.1M Na acetate trihydrate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop5.522%(w/v) PEG3350, 0.1M Na citrate tribasic dehydrate, 0.1%(w/v) n-octyl beta-D-glucopyranoside, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 109771 / % possible obs: 95.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.662.30.249190.4
1.66-1.722.50.209191.6
1.72-1.82.70.18194.4
1.8-1.92.90.157196
1.9-2.023.20.136197.3
2.02-2.173.50.123198.5
2.17-2.393.70.111199
2.39-2.743.80.11199.2
2.74-3.454.10.098199.6
3.45-503.90.105192.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
BBSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→14.907 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / SU ML: 0.2 / σ(F): 0.73 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 5363 5.01 %
Rwork0.1851 --
obs0.1873 107141 94.07 %
all-109771 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.869 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→14.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 0 663 7321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086843
X-RAY DIFFRACTIONf_angle_d1.2299313
X-RAY DIFFRACTIONf_dihedral_angle_d12.3392443
X-RAY DIFFRACTIONf_chiral_restr0.0551065
X-RAY DIFFRACTIONf_plane_restr0.0061183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.30751640.26723187X-RAY DIFFRACTION89
1.6182-1.63720.30291800.25313351X-RAY DIFFRACTION94
1.6372-1.65710.29481890.24813373X-RAY DIFFRACTION94
1.6571-1.67810.281880.22933395X-RAY DIFFRACTION94
1.6781-1.70010.27771860.22653338X-RAY DIFFRACTION93
1.7001-1.72340.26611800.22093385X-RAY DIFFRACTION94
1.7234-1.7480.2711780.21643418X-RAY DIFFRACTION94
1.748-1.7740.23942030.21233336X-RAY DIFFRACTION95
1.774-1.80170.27871650.20373421X-RAY DIFFRACTION94
1.8017-1.83120.25292010.20043398X-RAY DIFFRACTION95
1.8312-1.86270.28811810.20073367X-RAY DIFFRACTION94
1.8627-1.89650.27312080.20093443X-RAY DIFFRACTION94
1.8965-1.93290.25391640.19883389X-RAY DIFFRACTION95
1.9329-1.97230.25981870.19323403X-RAY DIFFRACTION94
1.9723-2.01510.25591680.18263431X-RAY DIFFRACTION95
2.0151-2.06180.24541870.183389X-RAY DIFFRACTION95
2.0618-2.11320.2191590.18193448X-RAY DIFFRACTION95
2.1132-2.17020.22871740.17563452X-RAY DIFFRACTION95
2.1702-2.23390.23671560.18273446X-RAY DIFFRACTION95
2.2339-2.30570.26621730.18753458X-RAY DIFFRACTION95
2.3057-2.38780.23881760.1923414X-RAY DIFFRACTION95
2.3878-2.4830.24931600.20223518X-RAY DIFFRACTION96
2.483-2.59540.26141970.19873450X-RAY DIFFRACTION96
2.5954-2.73150.21511940.19313403X-RAY DIFFRACTION95
2.7315-2.90140.23911680.18893489X-RAY DIFFRACTION96
2.9014-3.12360.19651770.18363480X-RAY DIFFRACTION96
3.1236-3.43440.20231980.17183488X-RAY DIFFRACTION97
3.4344-3.92350.18691950.15713450X-RAY DIFFRACTION96
3.9235-4.91360.19071630.15533233X-RAY DIFFRACTION89
4.9136-14.90810.26431440.19883025X-RAY DIFFRACTION82
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)
10.1320.0978-0.27470.406-0.1950.54860.01120.05040.02150.11820.02890.0496-0.0008-0.049-0.04010.0183-0.0035-0.00040.06690.00830.032110.16323.726942.9187
20.0217-0.0406-0.03950.54260.06330.1015-0.0048-0.0080.0067-0.00460.01510.00170.01190.0187-0.01030.0112-0.0044-0.00610.05270.00230.029519.8413-1.189929.1356
30.10390.1714-0.00050.4141-0.02890.0719-0.01480.015-0.0071-0.01970.0092-0.00560.0043-0.01190.00560.00840.0001-0.00140.0464-0.00170.036541.061928.8156-7.7911
40.09420.075-0.02480.5088-0.09250.0903-0.00420.0046-0.0102-0.00110.00030.0051-0.00240.00050.0040.0058-0.0011-0.00340.0456-0.00340.031435.249233.72878.2541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND ( RESID 1:213 OR RESID 301:422 ) )L1 - 213
2X-RAY DIFFRACTION1( CHAIN L AND ( RESID 1:213 OR RESID 301:422 ) )L301 - 422
3X-RAY DIFFRACTION2( CHAIN H AND ( RESID 1:220 OR RESID 301:474 ) )H1 - 220
4X-RAY DIFFRACTION2( CHAIN H AND ( RESID 1:220 OR RESID 301:474 ) )H301 - 474
5X-RAY DIFFRACTION3( CHAIN M AND ( RESID 1:213 OR RESID 301:449 ) )M1 - 213
6X-RAY DIFFRACTION3( CHAIN M AND ( RESID 1:213 OR RESID 301:449 ) )M301 - 449
7X-RAY DIFFRACTION4( CHAIN I AND ( RESID 1:220 OR RESID 301:518 ) )I1 - 220
8X-RAY DIFFRACTION4( CHAIN I AND ( RESID 1:220 OR RESID 301:518 ) )I301 - 518

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