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- PDB-5t93: Immunoglobulin light chain variable domain AL-T05 -

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Basic information

Entry
Database: PDB / ID: 5t93
TitleImmunoglobulin light chain variable domain AL-T05
ComponentsALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient
KeywordsIMMUNE SYSTEM / immunoglobulin light chain / amyloid / light chain amyloidosis / variable domain / antibodies
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRamirez-Alvarado, M. / Blancas-Mejia, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM 071514 United States
CitationJournal: Biochemistry / Year: 2017
Title: Differences in Protein Concentration Dependence for Nucleation and Elongation in Light Chain Amyloid Formation.
Authors: Blancas-Mejia, L.M. / Misra, P. / Ramirez-Alvarado, M.
History
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.value
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient
B: ALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient
C: ALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient
D: ALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,95121
Polymers45,9034
Non-polymers1,04817
Water8,683482
1
A: ALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient
C: ALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,44310
Polymers22,9512
Non-polymers4918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-115 kcal/mol
Surface area9990 Å2
MethodPISA
2
B: ALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient
D: ALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,50811
Polymers22,9512
Non-polymers5579
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-153 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.459, 42.118, 64.995
Angle α, β, γ (deg.)80.66, 86.24, 63.02
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
ALT-05 immunoglobulin light chain variable domain from light chain amyloidosis patient


Mass: 11475.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: last residue was not visible on electron density / Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV / Plasmid: pET12a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium acetate 0.1 M sodium cacodylate 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5241 Å
DetectorType: RIGAKU / Detector: DIFFRACTOMETER / Date: Jan 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5241 Å / Relative weight: 1
ReflectionResolution: 1.9→37.1 Å / Num. obs: 24891 / % possible obs: 88.05 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.0731 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 0.0731 / Num. unique all: 1447 / % possible all: 51.49

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q20

2q20


Resolution: 1.9→34.426 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 553 2.22 %
Rwork0.1709 --
obs0.1721 24891 88.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→34.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 47 482 3765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113442
X-RAY DIFFRACTIONf_angle_d1.1034721
X-RAY DIFFRACTIONf_dihedral_angle_d9.3442030
X-RAY DIFFRACTIONf_chiral_restr0.064530
X-RAY DIFFRACTIONf_plane_restr0.007620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.09120.23931030.16924907X-RAY DIFFRACTION71
2.0912-2.39370.25481400.15786444X-RAY DIFFRACTION93
2.3937-3.01560.20871600.18566506X-RAY DIFFRACTION94
3.0156-34.43130.21851500.16846481X-RAY DIFFRACTION94

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