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- PDB-5n4j: human Fab fragment 10C3 against NHBA from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 5n4j
Titlehuman Fab fragment 10C3 against NHBA from Neisseria meningitidis
Components
  • HEAVY CHAIN
  • LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Fab fragment / antibody / human
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.503 Å
AuthorsMaritan, M. / Malito, E.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structures of human Fabs targeting the Bexsero meningococcal vaccine antigen NHBA.
Authors: Maritan, M. / Cozzi, R. / Lo Surdo, P. / Veggi, D. / Bottomley, M.J. / Malito, E.
History
DepositionFeb 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: LIGHT CHAIN
H: HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)50,0852
Polymers50,0852
Non-polymers00
Water12,629701
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-21 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.910, 79.830, 82.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody LIGHT CHAIN


Mass: 22766.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRS5a / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody HEAVY CHAIN


Mass: 27319.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: the sequence provided include the cleavable tag / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRS5a / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.17 M ammonium sulfate, 15% v/v glycerol, 25.5% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979788 Å / Relative weight: 1
ReflectionResolution: 1.503→32.19 Å / Num. obs: 73404 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05052 / Rpim(I) all: 0.03079 / Rrim(I) all: 0.059 / Net I/σ(I): 14.88
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.35 / CC1/2: 0.521 / Rrim(I) all: 1.16 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H8W

4h8w


Resolution: 1.503→32.19 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.07
RfactorNum. reflection% reflection
Rfree0.2115 3669 5 %
Rwork0.1788 --
obs0.1805 73375 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.503→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3130 0 0 701 3831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013241
X-RAY DIFFRACTIONf_angle_d1.2724427
X-RAY DIFFRACTIONf_dihedral_angle_d12.5791144
X-RAY DIFFRACTIONf_chiral_restr0.057506
X-RAY DIFFRACTIONf_plane_restr0.007566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5031-1.52290.34191300.33392455X-RAY DIFFRACTION92
1.5229-1.54380.35371390.29352641X-RAY DIFFRACTION100
1.5438-1.56580.28971400.28182674X-RAY DIFFRACTION99
1.5658-1.58920.28511410.26882678X-RAY DIFFRACTION100
1.5892-1.6140.27791410.25562662X-RAY DIFFRACTION100
1.614-1.64050.29951390.24232648X-RAY DIFFRACTION100
1.6405-1.66880.28121410.2342675X-RAY DIFFRACTION100
1.6688-1.69910.26191410.2212690X-RAY DIFFRACTION100
1.6991-1.73180.28121410.21262664X-RAY DIFFRACTION100
1.7318-1.76710.22221420.20792700X-RAY DIFFRACTION100
1.7671-1.80550.23031390.19672648X-RAY DIFFRACTION100
1.8055-1.84750.2631420.19592690X-RAY DIFFRACTION100
1.8475-1.89370.22651410.18532696X-RAY DIFFRACTION100
1.8937-1.94490.19051410.17862676X-RAY DIFFRACTION100
1.9449-2.00220.22181410.18172683X-RAY DIFFRACTION100
2.0022-2.06680.22241410.16912679X-RAY DIFFRACTION100
2.0668-2.14060.20731410.17272661X-RAY DIFFRACTION100
2.1406-2.22630.221420.17482702X-RAY DIFFRACTION99
2.2263-2.32760.21531420.18092697X-RAY DIFFRACTION99
2.3276-2.45030.25371420.17822708X-RAY DIFFRACTION100
2.4503-2.60370.24231420.18582695X-RAY DIFFRACTION99
2.6037-2.80470.19761430.18032714X-RAY DIFFRACTION99
2.8047-3.08670.21821420.17372698X-RAY DIFFRACTION99
3.0867-3.53290.18691440.16122733X-RAY DIFFRACTION99
3.5329-4.44920.16011450.14392751X-RAY DIFFRACTION98
4.4492-32.19740.1681460.15292788X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 17.0932 Å / Origin y: -17.7426 Å / Origin z: 5.101 Å
111213212223313233
T0.1235 Å20.0041 Å20.0076 Å2-0.1607 Å20.0033 Å2--0.1389 Å2
L0.2623 °20.1026 °20.1285 °2-0.6177 °2-0.06 °2--0.3595 °2
S-0.027 Å °-0.0089 Å °0.0231 Å °-0.037 Å °0.0132 Å °0.0161 Å °-0.044 Å °-0.0404 Å °0.0122 Å °
Refinement TLS groupSelection details: all

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