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- PDB-4nwt: Crystal structure of the anti-human NGF Fab APE1531 -

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Basic information

Entry
Database: PDB / ID: 4nwt
TitleCrystal structure of the anti-human NGF Fab APE1531
Components(APE1531 Ab Fab ...) x 2
KeywordsIMMUNE SYSTEM / beta sandwich / human beta nerve growth factor
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / Classical antibody-mediated complement activation / immunoglobulin complex, circulating / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / Classical antibody-mediated complement activation / immunoglobulin complex, circulating / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Immunoglobulin heavy constant gamma 1 / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVerdino, P. / Stanfield, R.L. / Wilson, I.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Nucleotide insertions and deletions complement point mutations to massively expand the diversity created by somatic hypermutation of antibodies.
Authors: Bowers, P.M. / Verdino, P. / Wang, Z. / da Silva Correia, J. / Chhoa, M. / Macondray, G. / Do, M. / Neben, T.Y. / Horlick, R.A. / Stanfield, R.L. / Wilson, I.A. / King, D.J.
History
DepositionDec 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Jun 2, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / software ...entity_src_gen / software / struct_ref_seq / struct_site
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _software.name / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 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
L: APE1531 Ab Fab light chain
H: APE1531 Ab Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0719
Polymers49,2942
Non-polymers7777
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-24 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.720, 64.360, 63.810
Angle α, β, γ (deg.)90.00, 108.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-498-

HOH

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody APE1531 Ab Fab light chain


Mass: 24342.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#2: Antibody APE1531 Ab Fab heavy chain


Mass: 24950.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: P01857

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Non-polymers , 4 types, 380 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG 20000, 0.1M NaCl, 0.1M MES pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9783 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 1.75→38.64 Å / Num. obs: 48714 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.3
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.9 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Web-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QOT for VHVL, 3SOB for CH1CL

3qot
PDB Unreleased entry

3sob


Resolution: 1.75→38.64 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.164 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18121 2452 5 %RANDOM
Rwork0.1504 ---
obs0.15194 46262 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.289 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.53 Å2
2--1.46 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 50 373 3883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023715
X-RAY DIFFRACTIONr_bond_other_d0.0010.023391
X-RAY DIFFRACTIONr_angle_refined_deg1.9881.9595086
X-RAY DIFFRACTIONr_angle_other_deg0.8783.0037867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24224.575153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16715587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2911514
X-RAY DIFFRACTIONr_chiral_restr0.1210.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02844
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 165 -
Rwork0.246 3407 -
obs--97.28 %
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)
14.07950.1265-2.64181.7248-0.46053.8761-0.06050.3052-0.0741-0.08260.08070.07940.1682-0.3407-0.02030.1304-0.022-0.02490.05050.00180.082815.528318.059729.4874
21.82570.93460.33112.99481.65893.39270.03560.027-0.2310.1018-0.085-0.00540.32610.04170.04940.10980.02620.00190.07060.01170.081237.09918.119828.6697
32.90151.17411.95732.30250.98643.1063-0.0836-0.14770.1835-0.11240.03470.033-0.0757-0.27150.04890.056-0.0035-0.00840.04180.00450.061219.795836.766962.5172
43.46970.3081-1.77830.7531-0.05264.2645-0.0852-0.0665-0.06170.01670.03390.06510.16520.07760.05140.0731-0.0114-0.0170.00930.00270.047131.622425.924460.7261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2H1 - 113
3X-RAY DIFFRACTION3L109 - 214
4X-RAY DIFFRACTION4H114 - 231

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