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- PDB-5lve: STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGH... -

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Basic information

Entry
Database: PDB / ID: 5lve
TitleSTRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGHT CHAIN LEN
ComponentsBENCE-JONES PROTEIN LENBence Jones protein
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / BENCE-JONES PROTEIN
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / antigen binding / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa variable 4-1 / Immunoglobulin kappa variable 4-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchiffer, M. / Huang, D.-B. / Chang, C.-H.
Citation
Journal: Protein Sci. / Year: 2000
Title: Change in dimerization mode by removal of a single unsatisfied polar residue located at the interface.
Authors: Pokkuluri, P.R. / Cai, X. / Johnson, G. / Stevens, F.J. / Schiffer, M.
#1: Journal: Structure / Year: 1998
Title: A domain flip as a result of a single amino-acid substitution.
Authors: Pokkuluri, P.R. / Huang, D.B. / Raffen, R. / Cai, X. / Johnson, G. / Stevens, P.W. / Stevens, F.J. / Schiffer, M.
History
DepositionFeb 24, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: BENCE-JONES PROTEIN LEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6582
Polymers12,5931
Non-polymers651
Water2,810156
1
A: BENCE-JONES PROTEIN LEN
hetero molecules

A: BENCE-JONES PROTEIN LEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3174
Polymers25,1862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area1700 Å2
ΔGint-11 kcal/mol
Surface area10640 Å2
MethodPISA, PQS
2
A: BENCE-JONES PROTEIN LEN
hetero molecules

A: BENCE-JONES PROTEIN LEN
hetero molecules

A: BENCE-JONES PROTEIN LEN
hetero molecules

A: BENCE-JONES PROTEIN LEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6338
Polymers50,3724
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area4280 Å2
ΔGint-133 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.300, 106.300, 45.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-200-

ZN

21A-214-

HOH

31A-274-

HOH

41A-353-

HOH

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Components

#1: Antibody BENCE-JONES PROTEIN LEN / Bence Jones protein


Mass: 12592.961 Da / Num. of mol.: 1 / Fragment: G KAPPA CHAIN V-IV, VARIABLE DOMAIN, LIGHT CHAIN / Mutation: Q89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P01625, UniProt: P06312*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsA ZN+2 ION (RESIDUE 200) AND THREE WATERS (RESIDUES 214, 274 AND 353) ARE LOCATED ON SYMMETRY AXES ...A ZN+2 ION (RESIDUE 200) AND THREE WATERS (RESIDUES 214, 274 AND 353) ARE LOCATED ON SYMMETRY AXES AND THEIR OCCUPANCY IS SET TO 0.5
Sequence detailsQ89A MUTANT

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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: 3 Å3/Da / Density % sol: 59 %
Crystal growpH: 7.5
Details: 2.0 M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, 1MM ZINC ACETATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.8 Mammonium sulfate1reservoir
30.1 Msodium HEPES1reservoir
40.001 Mzinc acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 7471 / % possible obs: 97 % / Redundancy: 10 % / Biso Wilson estimate: 6.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 25
Reflection shellResolution: 2→2.07 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 6.8 / % possible all: 88.3
Reflection shell
*PLUS
% possible obs: 88.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LVE WITH GLN89 CHANGED TO ALA

1lve


Resolution: 2→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 388280.78 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
Details: BULK SOLVENT MODEL USED THE LAST TWO RESIDUES (LYS-107 AND ARG-108) ARE NOT WELL DEFINED IN THE DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 949 10.4 %RANDOM
Rwork0.186 ---
obs-9087 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.8 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å2-3.57 Å20 Å2
2---1.32 Å20 Å2
3---2.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 1 156 1040
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.77
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.721.5
X-RAY DIFFRACTIONx_mcangle_it1.22
X-RAY DIFFRACTIONx_scbond_it1.182
X-RAY DIFFRACTIONx_scangle_it1.812.5
LS refinement shellResolution: 2→2.04 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.186 36 10.5 %
Rwork0.166 308 -
obs--60.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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