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- PDB-1d6v: CONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-CO... -

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Basic information

Entry
Database: PDB / ID: 1d6v
TitleCONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-COPE ANTIBODY MATURATION
Components
  • CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (HEAVY CHAIN)
  • CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin ...: / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
: / Chem-HOP / IgM heavy chain variable region / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1 / Immunoglobulin gamma-1 heavy chain / Anti-colorectal carcinoma light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsMundorff, E.C. / Hanson, M.A. / Schultz, P.G. / Stevens, R.C.
CitationJournal: Biochemistry / Year: 2000
Title: Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement.
Authors: Mundorff, E.C. / Hanson, M.A. / Varvak, A. / Ulrich, H. / Schultz, P.G. / Stevens, R.C.
History
DepositionOct 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: diffrn_radiation_wavelength / entity ...diffrn_radiation_wavelength / entity / entity_src_gen / exptl_crystal_grow / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _exptl_crystal_grow.temp ..._entity.pdbx_fragment / _exptl_crystal_grow.temp / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

Downloads & links

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Assembly

Deposited unit
L: CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (LIGHT CHAIN)
H: CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9567
Polymers47,1242
Non-polymers8315
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-39 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.718, 64.446, 73.870
Angle α, β, γ (deg.)90.00, 99.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (LIGHT CHAIN)


Mass: 23506.186 Da / Num. of mol.: 1
Fragment: chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS PRODUCED AS A CHIMERIC FAB FRAGMENT. THE VARIABLE DOMAINS (CHAINS A,L 1-107, CHAINS B,H 1-113) ARE MURINE. THE CONSTANT DOMAINS (CHAINS A, L 108-211 AND CHAINS B,H 113-214) ARE HUMAN.
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Genus: Mus, Homo / Species: , / Gene: IGKC / Production host: Escherichia coli (E. coli) / References: UniProt: Q7TS98, UniProt: P01834
#2: Antibody CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (HEAVY CHAIN)


Mass: 23618.234 Da / Num. of mol.: 1
Fragment: chimeric fab fragment (UNP K7T9I5 residues 1-112, P0DOX5 residues 120-220)
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS PRODUCED AS A CHIMERIC FAB FRAGMENT. THE VARIABLE DOMAINS (CHAINS A,L 1-107, CHAINS B,H 1-113) ARE MURINE. THE CONSTANT DOMAINS (CHAINS A, L 108-211 AND CHAINS B,H 113-214) ARE HUMAN.
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Genus: Mus, Homo / Species: , / Production host: Escherichia coli (E. coli)
References: UniProt: K7T9I5, UniProt: P0DOX5, UniProt: P01857*PLUS
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-HOP / (1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL / OXY-COPE-HAPTEN


Mass: 381.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 9% polyethylene glycol 4000 250mM ammonium sulfate 80mM Cadmium Chloride 75mM Hepes 20% 1,4 butanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 19K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2100 mM1dropNaCl
310 mMTris-HCl1drop
41 mMmethionine1drop
580 mMcadmium chloride1reservoir
675 mMHEPES1reservoir
7250 mMammonium sulfate1reservoir
820 %1,4-butanediol1reservoir
99 %PEG40001reservoir
102 mMTSA11reservoir

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 78215 / Num. obs: 66483 / % possible obs: 85.2 % / Observed criterion σ(I): 12 / Redundancy: 2.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12
Reflection
*PLUS
Num. obs: 28062 / Num. measured all: 66483
Reflection shell
*PLUS
% possible obs: 83 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementResolution: 2→9.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1265132.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2726 10 %RANDOM
Rwork0.224 ---
obs0.224 27361 83.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.28 Å2 / ksol: 0.459 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å23.7 Å2
2--0.44 Å20 Å2
3---0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.03 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 2→9.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 32 138 3486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d28.1
X-RAY DIFFRACTIONc_improper_angle_d1.38
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 442 10.4 %
Rwork0.212 3824 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CPH.PARCPH.TOP
X-RAY DIFFRACTION3PAR.LIBWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMTOP.LIB
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.265
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.38

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