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- PDB-1ol0: Crystal structure of a camelised human VH -

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Basic information

Entry
Database: PDB / ID: 1ol0
TitleCrystal structure of a camelised human VH
ComponentsIMMUNOGLOBULIN G
KeywordsIMMUNOGLOBULIN / CAMELISED VARIABLE HEAVY DOMAIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDottorini, T. / Vaughan, C.K. / Walsh, M.A. / Losurdo, P. / Sollazzo, M.
Citation
Journal: Biochemistry / Year: 2004
Title: Crystal Structure of a Human Vh: Requirements for Maintaining a Monomeric Fragment
Authors: Dottorini, T. / Vaughan, C.K. / Walsh, M.A. / Losurdo, P. / Sollazzo, M.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Inhibition of the Hepatitis C Virus Ns3/4A Protease. The Crystal Structures of Two Protease-Inhibitor Complexes
Authors: Dimarco, S. / Rizzi, M. / Volpari, C. / Walsh, M.A. / Narjes, F. / Colarusso, S. / Defrancesco, R. / Matassa, V.G. / Sollazzo, M.
#2: Journal: Protein Eng. / Year: 1997
Title: Affinity Selection of a Camelized V(H) Domain Antibody Inhibitor of Hepatitis C Virus Ns3 Protease
Authors: Martin, F. / Volpari, C. / Steinkuhler, C. / Dimasibrunetti, M. / Biasiol, G. / Altamura, S. / Cortese, R. / Defrancesco, R. / Sollazzo, M.
#3: Journal: J.Mol.Biol. / Year: 1996
Title: Rearrangement of the Former Vl Interface in the Solution Structure of a Camelised, Single Antibody Vh Domain
Authors: Riechmann, L.
History
DepositionAug 2, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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: IMMUNOGLOBULIN G
B: IMMUNOGLOBULIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,45012
Polymers26,5092
Non-polymers94110
Water6,990388
1
A: IMMUNOGLOBULIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7196
Polymers13,2541
Non-polymers4645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: IMMUNOGLOBULIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7316
Polymers13,2541
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.300, 75.300, 101.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999943, -0.009568, -0.00477), (0.001752, -0.586769, 0.809753), (-0.010547, 0.809698, 0.586752)
Vector: 95.6402, 37.7088, -18.9345)

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Components

#1: Antibody IMMUNOGLOBULIN G


Mass: 13254.387 Da / Num. of mol.: 2 / Fragment: VARIABLE HEAVY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 59.5 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALS GREW FROM 4 MICROLITRE HANGING DROPS FORMED BY MIXING 2 MICROLITERS OF PROTEIN AT A CONCENTRATION OF 5MG/ML WITH 2 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 15-20% (W/V) PEG ...Details: CRYSTALS GREW FROM 4 MICROLITRE HANGING DROPS FORMED BY MIXING 2 MICROLITERS OF PROTEIN AT A CONCENTRATION OF 5MG/ML WITH 2 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 15-20% (W/V) PEG 8000, 0.4 M AMMONIUM SULPHATE AND 0.1M HEPES AT PH 7.5.
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
215-20 %(w/v)PEG80001reservoir
30.4 Mammonium sulfate1reservoir
40.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2000 / Details: TOROIDAL
RadiationMonochromator: DIAMON 100/GE 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 29910 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 1.5 / % possible all: 71.5
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 25.2 Å / Num. measured all: 69437 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Lowest resolution: 1.84 Å / % possible obs: 71.5 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HCV

1hcv


Resolution: 1.8→25.24 Å / SU B: 1.401 / SU ML: 0.044 / Cross valid method: THROUGHOUT EXCEPT IN LAST RO / ESU R: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.18015 1506 5 %RANDOM
Rwork0.15449 ---
obs0.15576 29892 94.95 %-
Displacement parametersBiso mean: 17.342 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 55 388 2293
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 25.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.1802 / Rfactor Rwork: 0.1558
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.017
X-RAY DIFFRACTIONangle_d0.038
X-RAY DIFFRACTIONplane_restr0.044
X-RAY DIFFRACTIONchiral_restr0.096

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