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- PDB-2cgr: LOCAL AND TRANSMITTED CONFORMATIONAL CHANGES ON COMPLEXATION OF A... -

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Basic information

Entry
Database: PDB / ID: 2cgr
TitleLOCAL AND TRANSMITTED CONFORMATIONAL CHANGES ON COMPLEXATION OF AN ANTI-SWEETENER FAB
Components
  • IGG2B-KAPPA NC6.8 FAB (HEAVY CHAIN)
  • IGG2B-KAPPA NC6.8 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


: / 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 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-GAS / : / : / Kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsGuddat, L.W. / Shan, L. / Edmundson, A.B.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Local and transmitted conformational changes on complexation of an anti-sweetener Fab.
Authors: Guddat, L.W. / Shan, L. / Anchin, J.M. / Linthicum, D.S. / Edmundson, A.B.
History
DepositionNov 23, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: IGG2B-KAPPA NC6.8 FAB (LIGHT CHAIN)
H: IGG2B-KAPPA NC6.8 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4123
Polymers47,0272
Non-polymers3841
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-25 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.000, 114.100, 37.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 100 / 3: CIS PROLINE - PRO L 146 / 4: CIS PROLINE - PRO H 150 / 5: CIS PROLINE - PRO H 192

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Components

#1: Antibody IGG2B-KAPPA NC6.8 FAB (LIGHT CHAIN)


Mass: 24123.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: PIR: S16112, UniProt: A2P1G9*PLUS
#2: Antibody IGG2B-KAPPA NC6.8 FAB (HEAVY CHAIN)


Mass: 22903.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 1613777
#3: Chemical ChemComp-GAS / N-(P-CYANOPHENYL)-N'-DIPHENYLMETHYL-GUANIDINE-ACETIC ACID


Mass: 384.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN WAS SEQUENCED BY J.M. ANCHIN AND D.S.LINTHICUM. TEXAS A & M UNIVERSITY, COLLEGE STATION, TX.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal grow
*PLUS
Method: other / Details: Shan, L., (1993) J. Crystal Growth, 126, 229.

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. all: 29286 / Num. obs: 24544 / % possible obs: 83.8 % / Observed criterion σ(I): 1 / Num. measured all: 126541 / Rmerge(I) obs: 0.0719
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 58.8 % / Num. possible: 3524 / Num. unique obs: 2072 / Num. measured obs: 8432 / Rmerge(I) obs: 0.1794

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.214 -
obs0.214 24227
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 29 175 3508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.05
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.214 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.55
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Num. reflection Rfree: 2072 / Total num. of bins used: 8 / Rfactor obs: 0.214

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