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- PDB-1mrf: PREPARATION, CHARACTERIZATION AND CRYSTALLIZATION OF AN ANTIBODY ... -

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Basic information

Entry
Database: PDB / ID: 1mrf
TitlePREPARATION, CHARACTERIZATION AND CRYSTALLIZATION OF AN ANTIBODY FAB FRAGMENT THAT RECOGNIZES RNA. CRYSTAL STRUCTURES OF NATIVE FAB AND THREE FAB-MONONUCLEOTIDE COMPLEXES
Components(IGG2B-KAPPA JEL103 FAB ...) x 2
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 2'-DEOXYINOSINE-5'-MONOPHOSPHATE / IMIDAZOLE / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsPokkuluri, P.R. / Cygler, M.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes.
Authors: Pokkuluri, P.R. / Bouthillier, F. / Li, Y. / Kuderova, A. / Lee, J. / Cygler, M.
History
DepositionJun 13, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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: IGG2B-KAPPA JEL103 FAB (LIGHT CHAIN)
H: IGG2B-KAPPA JEL103 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6685
Polymers47,2012
Non-polymers4673
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-29 kcal/mol
Surface area18940 Å2
MethodPISA
2
L: IGG2B-KAPPA JEL103 FAB (LIGHT CHAIN)
hetero molecules

H: IGG2B-KAPPA JEL103 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,6685
Polymers47,2012
Non-polymers4673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area970 Å2
ΔGint-33 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.200, 75.500, 104.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141 / 4: CIS PROLINE - PRO H 149 / 5: CIS PROLINE - PRO H 200

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody IGG2B-KAPPA JEL103 FAB (LIGHT CHAIN)


Mass: 24180.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: PIR: PC4203
#2: Antibody IGG2B-KAPPA JEL103 FAB (HEAVY CHAIN)


Mass: 23020.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 387221

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Non-polymers , 4 types, 85 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-DI / 2'-DEOXYINOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 332.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O7P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal grow
*PLUS
pH: 8.8 / Method: unknown
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1PEG800011
2Tris-HCl11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / Num. obs: 18146 / % possible obs: 88.8 % / Num. measured all: 74014 / Rmerge(I) obs: 0.068

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.184 / Rfactor obs: 0.184 / Highest resolution: 2.4 Å / Details: RESIDUES ARG 24 AND ARG 77 WERE REFINED AS LYS.
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 28 82 3302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
σ(I): 1.5
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.6 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.8

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