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- PDB-6vi2: Structure of the unaligned Fab4 -

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Basic information

Entry
Database: PDB / ID: 6vi2
TitleStructure of the unaligned Fab4
Components
  • FAB4 heavy chain
  • FAB4 light chain
KeywordsIMMUNE SYSTEM / Synthetic fab / large terminase / genome-packaging / crystallization chaperone
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsCingolani, G. / Lokareddy, R. / Ko, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD017987 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA56036 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Recognition of an alpha-helical hairpin in P22 large terminase by a synthetic antibody fragment.
Authors: Lokareddy, R.K. / Ko, Y.H. / Hong, N. / Doll, S.G. / Paduch, M. / Niederweis, M. / Kossiakoff, A.A. / Cingolani, G.
History
DepositionJan 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Oct 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAB4 light chain
B: FAB4 heavy chain
C: FAB4 light chain
D: FAB4 heavy chain


Theoretical massNumber of molelcules
Total (without water)98,6244
Polymers98,6244
Non-polymers00
Water21,4201189
1
A: FAB4 light chain
B: FAB4 heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3122
Polymers49,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-29 kcal/mol
Surface area20130 Å2
MethodPISA
2
C: FAB4 light chain
D: FAB4 heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3122
Polymers49,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-29 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.765, 65.843, 107.419
Angle α, β, γ (deg.)90.000, 99.830, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22(chain D and resid 221 through 451)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLYchain AAA0 - 2141 - 215
21SERSERGLYGLYchain CCC0 - 2141 - 215
12VALVALSERSERchain BBB221 - 4517 - 237
22VALVALSERSER(chain D and resid 221 through 451)DD221 - 4517 - 237

NCS ensembles :
ID
1
2

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Components

#1: Antibody FAB4 light chain


Mass: 23286.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody FAB4 heavy chain


Mass: 26025.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1189 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 292 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.15→15 Å / Num. obs: 293620 / % possible obs: 93.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 15.9 Å2 / Rpim(I) all: 0.027 / Rsym value: 0.054 / Net I/σ(I): 50.4
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 18649 / CC1/2: 0.511 / Rpim(I) all: 0.559 / Rsym value: 0.779 / % possible all: 59.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EU7

5eu7


Resolution: 1.15→14.99 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.49
RfactorNum. reflection% reflection
Rfree0.1709 1996 0.68 %
Rwork0.1575 --
obs0.1576 293445 93.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.69 Å2 / Biso mean: 26.3855 Å2 / Biso min: 10.92 Å2
Refinement stepCycle: final / Resolution: 1.15→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6785 0 0 1189 7974
Biso mean---33.99 -
Num. residues----897
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1296X-RAY DIFFRACTION5.373TORSIONAL
12C1296X-RAY DIFFRACTION5.373TORSIONAL
21B1390X-RAY DIFFRACTION5.373TORSIONAL
22D1390X-RAY DIFFRACTION5.373TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.180.2774800.2838116781175852
1.18-1.210.30141170.2628172791739678
1.21-1.250.23581450.2277211722131795
1.25-1.290.22661480.2041216522180098
1.29-1.330.23791490.1949217652191498
1.33-1.390.19981490.1736218202196998
1.39-1.450.20151500.1605218612201198
1.45-1.530.18861500.1519218292197998
1.53-1.620.16591490.1428217852193498
1.62-1.750.18091510.1453218832203498
1.75-1.920.15751510.1431220522220399
1.92-2.20.14361510.1441220712222299
2.2-2.770.18911520.1614222482240099
2.77-14.990.15581540.1548223542250899

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