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- PDB-2w0k: Crystal structure of the recombinant variable domain 6JAL2 -

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Basic information

Entry
Database: PDB / ID: 2w0k
TitleCrystal structure of the recombinant variable domain 6JAL2
ComponentsV1-22 PROTEIN
KeywordsIMMUNE SYSTEM / FIBRILS / GERM LINE / ANTIBODIES / FIBRINOGENIC
Function / homology
Function and homology information


immune response / extracellular space
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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRudino-Pinera, E. / Gonzalezrubio-Garrido, P. / Horjales, E.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A Single Mutation at the Sheet Switch Region Results in Conformational Changes Favoring Lambda6 Light-Chain Fibrillogenesis.
Authors: Hernandez-Santoyo, A. / Del Pozo Yauner, L. / Fuentes-Silva, D. / Ortiz, E. / Rudino-Pinera, E. / Sanchez-Lopez, R. / Horjales, E. / Becerril, B. / Rodriguez-Romero, A.
History
DepositionAug 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V1-22 PROTEIN
B: V1-22 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,9242
Polymers23,9242
Non-polymers00
Water91951
1
A: V1-22 PROTEIN

A: V1-22 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,9242
Polymers23,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_654-x+1,y,-z-11
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area12400 Å2
MethodPISA
2
B: V1-22 PROTEIN

B: V1-22 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,9242
Polymers23,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_553x,-y,-z-3/21
Buried area1490 Å2
ΔGint-9.6 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.267, 71.267, 95.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 1 - 107 / Label seq-ID: 1 - 107

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Antibody V1-22 PROTEIN / VARIABLE DOMAIN 6AJL2


Mass: 11961.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q5NV88
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS ENTRY COMPRISE THE FIRST 98 RESIDUES OF UNIPROT Q5NV88.

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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: 2.85 Å3/Da / Density % sol: 56.8 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: May 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→50.19 Å / Num. obs: 9289 / % possible obs: 87.9 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 48.46 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.5
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CD0

2cd0


Resolution: 2.35→22.63 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / SU B: 17.137 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 441 4.8 %RANDOM
Rwork0.209 ---
obs0.212 8802 86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.35→22.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 0 51 1731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0211716
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.1241.9462334
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3795218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0124.59574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.23615264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.335158
X-RAY DIFFRACTIONr_chiral_restr0.2070.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021318
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3030.2774
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3390.21156
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8591.51125
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17321790
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9643675
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.54.5544
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 840 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.320.05
tight thermal0.380.5
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 39
Rwork0.291 604
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5848-0.56860.22024.003-0.74873.42660.19440.2177-0.0134-0.0719-0.12750.28220.0963-0.414-0.0669-0.1938-0.0086-0.0036-0.17650.0129-0.139126.6923-9.8877-54.7596
25.2397-0.06490.1124.5731-0.22023.6162-0.16220.6288-0.0646-0.53460.2211-0.13750.04750.1424-0.05890.03610.08670.0547-0.0464-0.0363-0.123242.6688-8.9261-78.8037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 107
2X-RAY DIFFRACTION2B1 - 107

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