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- PDB-1qac: CHANGE IN DIMERIZATION MODE BY REMOVAL OF A SINGLE UNSATISFIED PO... -

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Basic information

Entry
Database: PDB / ID: 1qac
TitleCHANGE IN DIMERIZATION MODE BY REMOVAL OF A SINGLE UNSATISFIED POLAR RESIDUE
ComponentsIMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN
KeywordsIMMUNE SYSTEM / BETA BARREL IMMUNOGLOBULIN VL DOMAIN DIMER / FLIPPED DOMAIN DIMER
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / 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 / blood microparticle / adaptive immune response / Potential therapeutics for SARS / 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 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPokkuluri, P.R. / Cai, X. / Johnson, G. / Stevens, F.J. / Schiffer, M.
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. / Wilkins Stevens, P. / Stevens, F.J. / Schiffer, M.
History
DepositionFeb 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 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
A: IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN
B: IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN


Theoretical massNumber of molelcules
Total (without water)25,2702
Polymers25,2702
Non-polymers00
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-10 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.300, 83.600, 42.800
Angle α, β, γ (deg.)90.00, 109.00, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Antibody IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN


Mass: 12635.041 Da / Num. of mol.: 2 / Fragment: VARIABLE DOMAIN / Mutation: Q89L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06312*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 18% PEG 8000, 0.2M AMMONIUM SULPHATE AT 4 DEG C, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG80001reservoir
20.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 29, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 22265 / Num. obs: 21776 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 8.6 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
CNS0.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LVE with GLU-38 and GLN-89 changed to ALA

3lve


Resolution: 1.8→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
Details: CONJUGATE-GRADIENT MINIMIZATION. MAXIMUM LIKELIHOOD BASED ON AMPLITUDES TARGET USED
RfactorNum. reflection% reflection
Rfree0.226 1925 10 %
Rwork0.193 --
all-19236 -
obs-19236 89.3 %
Solvent computationSolvent model: FLAT / Bsol: 65.1 Å2 / ksol: 0.46 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.42 Å20 Å21.26 Å2
2--1.04 Å20 Å2
3---4.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 0 305 2068
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.691.5
X-RAY DIFFRACTIONx_mcangle_it1.162
X-RAY DIFFRACTIONx_scbond_it1.042
X-RAY DIFFRACTIONx_scangle_it1.522.5
LS refinement shellResolution: 1.8→1.83 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.258 86 10.3 %
Rwork0.202 748 -
obs--69.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 19237
Solvent computation
*PLUS
Displacement parameters
*PLUS
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
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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