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- PDB-1t2j: Crystal structure of a Human VH domain -

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Basic information

Entry
Database: PDB / ID: 1t2j
TitleCrystal structure of a Human VH domain
ComponentsM12-Variable Heavy domain
KeywordsIMMUNE SYSTEM / beta-sandwich / Immunoglobulin fold
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / 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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Single chain Fv
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGaur, R.K. / Fischer, R. / Hoffmann, K.M.V.
CitationJournal: To be Published
Title: Crystal structure of a human VH domain at 1.5 angstrom
Authors: Gaur, R.K. / Fischer, R. / Hoffmann, K.M.V.
History
DepositionApr 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE AUTHORS STATE THIS SEQUENCE HAS NOT BEEN DEPOSITED TO A SEQUENCE DATABASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M12-Variable Heavy domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4762
Polymers12,3701
Non-polymers1061
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.336, 37.965, 37.187
Angle α, β, γ (deg.)90.00, 109.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-225-

HOH

21A-273-

HOH

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Components

#1: Antibody M12-Variable Heavy domain


Mass: 12369.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSyn / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: Q9HCC1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.92 Å3/Da / Density % sol: 35.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystals grew from 3 microlitre hangingdrop formed by mixing 1.5 microlitre of protein:subtilisin mixture (250:1 M ratio) at protein conc. 13.5 mg/ml with 1.5 microlitre of reservoir ...Details: Crystals grew from 3 microlitre hangingdrop formed by mixing 1.5 microlitre of protein:subtilisin mixture (250:1 M ratio) at protein conc. 13.5 mg/ml with 1.5 microlitre of reservoir solution 100mM MES, pH6.5, 10mM ZnSO4, 25% v/v PEG550MME, 4mM DTT and 0.04% v/v NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.802 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 5, 2003 / Details: Rh coated mirror
RadiationMonochromator: Triangular Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 1.5→34.922 Å / Num. obs: 15017 / % possible obs: 90.7 % / Redundancy: 4.29 % / Biso Wilson estimate: 16.67 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.69
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 7.26 / Num. unique all: 696 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HOU

1hou


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.218 / SU ML: 0.046 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: used weighted full matrix least square procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.19652 762 5 %RANDOM
Rwork0.15787 ---
all0.1763 15144 --
obs0.15979 14358 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.603 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0.54 Å2
2--1.87 Å20 Å2
3----1.48 Å2
Refine analyzeLuzzati coordinate error obs: 0.153 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms877 0 0 146 1023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021889
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9221198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6515115
X-RAY DIFFRACTIONr_chiral_restr0.110.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02668
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021
X-RAY DIFFRACTIONr_nbd_refined0.2410.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.230
X-RAY DIFFRACTIONr_mcbond_it1.9243564
X-RAY DIFFRACTIONr_mcangle_it3.2294901
X-RAY DIFFRACTIONr_scbond_it3.5044325
X-RAY DIFFRACTIONr_scangle_it3.8974297
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 56 -
Rwork0.197 1022 -
obs-762 92.9 %

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