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- PDB-5nyx: human Fab fragment 5H2 against NHBA from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 5nyx
Titlehuman Fab fragment 5H2 against NHBA from Neisseria meningitidis
Components
  • HEAVY CHAIN
  • LIGHT CHAIN
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMalito, E. / Maritan, M.
CitationJournal: PLoS ONE / Year: 2018
Title: Structures of NHBA elucidate a broadly conserved epitope identified by a vaccine induced antibody.
Authors: Maritan, M. / Veggi, D. / Cozzi, R. / Dello Iacono, L. / Bartolini, E. / Lo Surdo, P. / Maruggi, G. / Spraggon, G. / Bottomley, M.J. / Malito, E.
History
DepositionMay 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Jan 17, 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: HEAVY CHAIN
L: LIGHT CHAIN
M: HEAVY CHAIN
N: LIGHT CHAIN
O: HEAVY CHAIN
P: LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,47020
Polymers153,1736
Non-polymers1,29714
Water13,079726
1
H: HEAVY CHAIN
L: LIGHT CHAIN
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, the complete protein is composed by two chains named heavy and light chain that assemble to form a heterodimer in solution. The elution profile of the protein correspond to ...Evidence: gel filtration, the complete protein is composed by two chains named heavy and light chain that assemble to form a heterodimer in solution. The elution profile of the protein correspond to the dimer. This assembly has further been demonstrated by SDS-PAGE analysis of the eluted fractions, which were showing the presence of two chains
  • 51.4 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)51,4306
Polymers51,0582
Non-polymers3724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-52 kcal/mol
Surface area18800 Å2
MethodPISA
2
M: HEAVY CHAIN
N: LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5187
Polymers51,0582
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-26 kcal/mol
Surface area19010 Å2
MethodPISA
3
O: HEAVY CHAIN
P: LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5227
Polymers51,0582
Non-polymers4645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-23 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.025, 105.749, 86.259
Angle α, β, γ (deg.)90.00, 112.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody HEAVY CHAIN


Mass: 27962.980 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: CHAIN H AND O ARE TWO SEPARATE POLYPEPTIDE CHAINS. fab heavy chains. The sequence provided contains the cleavable strep tag that has been removed prior to crystallisation
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody LIGHT CHAIN


Mass: 23094.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: fab light chain / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M (NH4)2SO4, 0.1 M Na-Cacodilate pH 6.5, 30 %w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97721 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97721 Å / Relative weight: 1
ReflectionResolution: 1.88→47.02 Å / Num. obs: 109382 / % possible obs: 98.8 % / Redundancy: 3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.056 / Rrim(I) all: 0.1 / Net I/σ(I): 6.6
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 10764 / CC1/2: 0.474 / Rpim(I) all: 0.563 / Rrim(I) all: 1.008 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2356: ???)refinement
XDSdata reduction
Aimlessdata scaling
MoRDa1.2.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TNM and 3HI6

3tnm

3hi6


Resolution: 1.88→47.017 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2264 5540 5.07 %
Rwork0.1864 --
obs0.1884 109345 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→47.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9718 0 82 726 10526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710120
X-RAY DIFFRACTIONf_angle_d0.93413779
X-RAY DIFFRACTIONf_dihedral_angle_d12.7486078
X-RAY DIFFRACTIONf_chiral_restr0.0551572
X-RAY DIFFRACTIONf_plane_restr0.0051741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90140.34141780.29093462X-RAY DIFFRACTION99
1.9014-1.92370.33591960.29063474X-RAY DIFFRACTION99
1.9237-1.94720.35091600.28033482X-RAY DIFFRACTION99
1.9472-1.97190.30842020.26223435X-RAY DIFFRACTION99
1.9719-1.99780.27241760.24833482X-RAY DIFFRACTION99
1.9978-2.02520.28471920.23933446X-RAY DIFFRACTION99
2.0252-2.05410.28562170.22863453X-RAY DIFFRACTION99
2.0541-2.08480.24791800.22473395X-RAY DIFFRACTION98
2.0848-2.11730.27641760.21783455X-RAY DIFFRACTION98
2.1173-2.1520.27881590.22283442X-RAY DIFFRACTION98
2.152-2.18920.29611760.21773458X-RAY DIFFRACTION99
2.1892-2.2290.26811650.21263501X-RAY DIFFRACTION99
2.229-2.27180.26941850.2063496X-RAY DIFFRACTION99
2.2718-2.31820.26792070.20853417X-RAY DIFFRACTION99
2.3182-2.36860.29241920.20623452X-RAY DIFFRACTION99
2.3686-2.42370.251950.20283447X-RAY DIFFRACTION99
2.4237-2.48430.24631880.19333489X-RAY DIFFRACTION99
2.4843-2.55150.26131890.1923441X-RAY DIFFRACTION99
2.5515-2.62660.25041930.20183464X-RAY DIFFRACTION98
2.6266-2.71130.24391600.20493477X-RAY DIFFRACTION99
2.7113-2.80820.27171920.19813439X-RAY DIFFRACTION99
2.8082-2.92060.24862000.19123480X-RAY DIFFRACTION99
2.9206-3.05350.21961860.18713457X-RAY DIFFRACTION99
3.0535-3.21450.22531450.18293500X-RAY DIFFRACTION98
3.2145-3.41580.22351700.17783466X-RAY DIFFRACTION98
3.4158-3.67950.18061740.16183483X-RAY DIFFRACTION99
3.6795-4.04960.18191710.15923470X-RAY DIFFRACTION98
4.0496-4.63510.16841840.13863429X-RAY DIFFRACTION97
4.6351-5.8380.18452130.15523448X-RAY DIFFRACTION98
5.838-47.03160.19732190.18353465X-RAY DIFFRACTION97

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