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- PDB-5x4g: Crystal structure of Fab fragment of anti-CD147 monoclonal antibo... -

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Basic information

Entry
Database: PDB / ID: 5x4g
TitleCrystal structure of Fab fragment of anti-CD147 monoclonal antibody 6H8
Components
  • 6H8 Fab heavy chain
  • 6H8 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / CD147
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLin, P. / Zhang, M.-Y. / Chen, X. / Ye, S. / Yu, X.-L. / Zhang, R.-G. / Zhu, P. / Chen, Z.-N.
Funding support China, 2items
OrganizationGrant numberCountry
National Science and Technology Major Project2013ZX09301301 China
National Basic Research Program of China2015CB553701 China
CitationJournal: To Be Published
Title: Crystal structure of CD147 C2 domain in complex with Fab of its monoclonal antibody
Authors: Zhang, M.-Y. / Lin, P. / Zhu, P. / Chen, Z.-N.
History
DepositionFeb 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6H8 Fab heavy chain
B: 6H8 Fab light chain


Theoretical massNumber of molelcules
Total (without water)52,2452
Polymers52,2452
Non-polymers00
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-19 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.104, 100.448, 108.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody 6H8 Fab heavy chain


Mass: 26331.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody 6H8 Fab light chain


Mass: 25913.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 289 K / Method: evaporation / Details: 0.16M NaSCN, 26% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.45→31.34 Å / Num. obs: 77443 / % possible obs: 98.5 % / Redundancy: 1 % / Net I/σ(I): 10.9
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 1 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 3 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→31.339 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.88
RfactorNum. reflection% reflection
Rfree0.226 3890 5.02 %
Rwork0.2064 --
obs0.2074 77438 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→31.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 0 503 3800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063382
X-RAY DIFFRACTIONf_angle_d0.9884607
X-RAY DIFFRACTIONf_dihedral_angle_d18.281221
X-RAY DIFFRACTIONf_chiral_restr0.096514
X-RAY DIFFRACTIONf_plane_restr0.005586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4474-1.46510.32281370.25962489X-RAY DIFFRACTION95
1.4651-1.48360.27721270.25942606X-RAY DIFFRACTION98
1.4836-1.50320.28061310.24352559X-RAY DIFFRACTION98
1.5032-1.52370.23271240.23482594X-RAY DIFFRACTION98
1.5237-1.54550.27921280.23282624X-RAY DIFFRACTION98
1.5455-1.56860.23131500.21952556X-RAY DIFFRACTION98
1.5686-1.59310.27451520.23072596X-RAY DIFFRACTION98
1.5931-1.61920.22191290.21392589X-RAY DIFFRACTION98
1.6192-1.64710.22951450.23042584X-RAY DIFFRACTION98
1.6471-1.67710.25221380.21212632X-RAY DIFFRACTION99
1.6771-1.70930.23311280.21692579X-RAY DIFFRACTION99
1.7093-1.74420.24241470.22192667X-RAY DIFFRACTION99
1.7442-1.78210.24031440.21822585X-RAY DIFFRACTION99
1.7821-1.82360.22761420.2162643X-RAY DIFFRACTION99
1.8236-1.86920.20771170.2072636X-RAY DIFFRACTION99
1.8692-1.91970.23981540.21012622X-RAY DIFFRACTION99
1.9197-1.97620.23361300.2032632X-RAY DIFFRACTION99
1.9762-2.040.22071260.20692686X-RAY DIFFRACTION100
2.04-2.11290.21771320.20242663X-RAY DIFFRACTION99
2.1129-2.19750.25441310.20572634X-RAY DIFFRACTION99
2.1975-2.29740.25691400.21352675X-RAY DIFFRACTION100
2.2974-2.41850.24571580.21332663X-RAY DIFFRACTION100
2.4185-2.570.27081340.22312701X-RAY DIFFRACTION100
2.57-2.76830.22791300.21372691X-RAY DIFFRACTION100
2.7683-3.04670.24491640.20132698X-RAY DIFFRACTION100
3.0467-3.4870.19181430.19052722X-RAY DIFFRACTION100
3.487-4.39140.18991410.1772680X-RAY DIFFRACTION97
4.3914-31.34620.20571680.20862542X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: -7.4795 Å / Origin y: -30.3007 Å / Origin z: 11.6731 Å
111213212223313233
T0.1015 Å2-0.0157 Å20.0234 Å2-0.1269 Å20.0071 Å2--0.1185 Å2
L0.0432 °2-0.208 °20.0356 °2-1.0198 °2-0.2348 °2--0.2098 °2
S-0.0049 Å °-0.0243 Å °0.0142 Å °0.0601 Å °0.0253 Å °0.0531 Å °-0.0765 Å °0.0107 Å °-0.0154 Å °
Refinement TLS groupSelection details: all

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