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- PDB-7obf: Crystal structure of the human VH antibody domain HEL4 -

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Basic information

Entry
Database: PDB / ID: 7obf
TitleCrystal structure of the human VH antibody domain HEL4
ComponentsHEL4
KeywordsHYDROLASE / lysozyme / human VH antibody domain / HEL4 / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsBelviso, B.D. / Caliandro, R. / Carrozzini, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission712965European Union
CitationJournal: To Be Published
Title: Crystal structure of the human VH antibody domain HEL4
Authors: Belviso, B.D. / Caliandro, R. / Carrozzini, B.
History
DepositionApr 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEL4
B: HEL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5489
Polymers26,7462
Non-polymers8037
Water1,78399
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-39 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.080, 76.080, 187.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-500-

SO4

21A-346-

HOH

31B-626-

HOH

41B-646-

HOH

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Components

#1: Antibody HEL4


Mass: 13372.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: MgSO4, Hepes, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07234 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07234 Å / Relative weight: 1
ReflectionResolution: 2.699→48.25 Å / Num. obs: 7840 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 0.968 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.099 / Rrim(I) all: 0.255 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.834.40.84440710090.7110.4320.9492.997.5
8.95-48.255.60.15413612420.9490.0720.1721496

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
Sir2014phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ohq

1ohq


Resolution: 2.699→48.25 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 384 4.9 %
Rwork0.214 7454 -
obs0.2166 7838 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.06 Å2 / Biso mean: 15.4485 Å2 / Biso min: 0.04 Å2
Refinement stepCycle: final / Resolution: 2.699→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 48 99 1960
Biso mean--45.12 15.74 -
Num. residues----245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.699-3.08910.34511070.2642243499
3.0891-3.89160.26741180.1999248299
3.8916-48.250.22931590.1978253898

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