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- PDB-1mco: THREE-DIMENSIONAL STRUCTURE OF A HUMAN IMMUNOGLOBULIN WITH A HING... -

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Basic information

Entry
Database: PDB / ID: 1mco
TitleTHREE-DIMENSIONAL STRUCTURE OF A HUMAN IMMUNOGLOBULIN WITH A HINGE DELETION
Components
  • IGG1 MCG INTACT ANTIBODY (HEAVY CHAIN)
  • IGG1 MCG INTACT ANTIBODY (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsGuddat, L.W. / Edmundson, A.B.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 1993
Title: Three-dimensional structure of a human immunoglobulin with a hinge deletion.
Authors: Guddat, L.W. / Herron, J.N. / Edmundson, A.B.
#1: Journal: Mol.Immunol. / Year: 1983
Title: Three-Dimensional Structure of the Mcg Igg1 Immunoglobulin
Authors: Rajan, S.S. / Ely, K.R. / Abola, E.E. / Wood, M.K. / Colman, P.M. / Athay, R.J. / Edmundson, A.B.
#2: Journal: Contemp.Top.Mol.Immunol. / Year: 1978
Title: Conformational Flexibility in Immunoglobulins
Authors: Edmundson, A.B. / Ely, K.R. / Abola, E.E.
#3: Journal: J.Biol.Chem. / Year: 1970
Title: A Crystallographic Investigation of a Human Igg Immunoglobulin
Authors: Edmundson, A.B. / Wood, M.K. / Schiffer, M. / Hardman, K.D. / Ainsworth, C.F. / Ely, K.R.
History
DepositionFeb 25, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1 MCG INTACT ANTIBODY (LIGHT CHAIN)
H: IGG1 MCG INTACT ANTIBODY (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6513
Polymers69,7342
Non-polymers1,9171
Water0
1
L: IGG1 MCG INTACT ANTIBODY (LIGHT CHAIN)
H: IGG1 MCG INTACT ANTIBODY (HEAVY CHAIN)
hetero molecules

L: IGG1 MCG INTACT ANTIBODY (LIGHT CHAIN)
H: IGG1 MCG INTACT ANTIBODY (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,3016
Polymers139,4684
Non-polymers3,8332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area19280 Å2
ΔGint1 kcal/mol
Surface area64440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.400, 110.000, 186.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: TYR L 144 - PRO L 145 OMEGA ANGLE = 90.421 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: PHE H 150 - PRO H 151 OMEGA ANGLE = 235.747 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: GLN H 152 - PRO H 153 OMEGA ANGLE = 247.018 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: TYR H 358 - PRO H 359 OMEGA ANGLE = 278.722 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: PRO H 380 - PRO H 381 OMEGA ANGLE = 221.018 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Antibody IGG1 MCG INTACT ANTIBODY (LIGHT CHAIN)


Mass: 22835.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: PIR: S14675
#2: Antibody IGG1 MCG INTACT ANTIBODY (HEAVY CHAIN)


Mass: 46898.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 243866
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-gulopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1916.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2LGulpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/7,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1121h-1a_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1b_1-5]/1-1-2-3-1-4-1-5-6-7/a4-b1_a6-j1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1_h3-i2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Manp]{[(2+?)][]{[(?+2)][b-D-Manp]{}}}}LINUCSPDB-CARE
Sequence detailsTHE FOLLOWING TABLE MAY BE USED TO RELATE THE ENTRIES SEQUENCE NUMBERING TO THE NUMBERING SYSTEM OF ...THE FOLLOWING TABLE MAY BE USED TO RELATE THE ENTRIES SEQUENCE NUMBERING TO THE NUMBERING SYSTEM OF E.KABAT (E.A.KABAT,T.T.WU,M.REID-MILLER,H.M.PERRY,K.S.GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 4TH ED., (1987), NATIONAL INSTITUTE OF HEALTH,BETHESDA,MD.). LIGHT CHAIN HEAVY CHAIN COMPUTER KABAT COMPUTER KABAT FILE NUMBER FILE NUMBER NUMBER NUMBER 1-9 1-9 1-35 1-35 10-26 11-27 36 35A 27 27A 37 35B 28 27B 38-84 36-82 29 27C 85 82A 30-97 28-95 86 82B 110 106A 87 82C 111-172 107-168 88-103 83-98 173-203 170-200 104 100K 204 203-215 105-134 101-130 135-156 133-154 157-158 158-159 159-166 162-169 167-177 171-181 178-191 183-196 192-194 198-200 195-199 202-206 200-216 208-224 217-222 231-237 (EU NUMBERING) 223-428 238-443 (EU NUMBERING)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: unknown / Details: Edmundson, A.B., (1970) J.Biol.Chem., 245, 2763.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl11
230-60 mg/mlprotein11
3deionized water12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 9999 Å / Num. all: 15365 / Num. obs: 14525 / % possible obs: 94.5 % / Num. measured all: 43520 / Rmerge(I) obs: 0.1479

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.232 / Rfactor obs: 0.232 / Highest resolution: 3.2 Å
Refinement stepCycle: LAST / Highest resolution: 3.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4911 0 130 0 5041
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
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_deg
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
Highest resolution: 3.2 Å / Rfactor obs: 0.232 / Lowest resolution: 6 Å / Num. reflection obs: 11875
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 0.027

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