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- PDB-5n4g: human Fab fragment 12E1 against NHBA from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 5n4g
Titlehuman Fab fragment 12E1 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: 2.75 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 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: HEAVY CHAIN
L: LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4538
Polymers52,0132
Non-polymers4406
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-36 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.880, 82.160, 100.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody HEAVY CHAIN


Mass: 27683.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fab heavy chain. 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)
#2: Antibody LIGHT CHAIN


Mass: 24329.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M potassium sodium tartrate 0.1 M sodium citrate 2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.75→45.71 Å / Num. obs: 14236 / % possible obs: 98.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 68.24 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.091 / Rsym value: 0.151 / Net I/σ(I): 9.9
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.609 / Rpim(I) all: 0.605 / Rsym value: 1.009 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IMK

4imk


Resolution: 2.75→23.99 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.812 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.404 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 3.817 / SU Rfree Blow DPI: 0.362 / SU Rfree Cruickshank DPI: 0.364
RfactorNum. reflection% reflectionSelection details
Rfree0.268 717 5.05 %RANDOM
Rwork0.186 ---
obs0.19 14204 98.2 %-
Displacement parametersBiso mean: 56.44 Å2
Baniso -1Baniso -2Baniso -3
1-25.2435 Å20 Å20 Å2
2--7.8012 Å20 Å2
3----33.0447 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.75→23.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 26 73 3436
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013440HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.294674HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1154SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes497HARMONIC5
X-RAY DIFFRACTIONt_it3440HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion20.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion453SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3723SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.352 153 5.35 %
Rwork0.231 2708 -
all0.237 2861 -
obs--97.75 %

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