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- PDB-6xmi: Structure of Fab4 bound to P22 TerL(1-33) -

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Basic information

Entry
Database: PDB / ID: 6xmi
TitleStructure of Fab4 bound to P22 TerL(1-33)
Components
  • Fab Heavy chainFragment antigen-binding
  • Fab Light chainFragment antigen-binding
  • Terminase, large subunit
KeywordsVIRAL PROTEIN / IMMUNE SYSTEM / Synthetic fab / large terminase / genome-packaging / crystallization chaperone
Function / homology
Function and homology information


viral terminase complex / viral terminase, large subunit / viral DNA genome packaging / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Terminase, large subunit BPP22-like / Terminase, large subunit gp17-like, C-terminal / Terminase RNaseH-like domain / Terminase large subunit, T4likevirus-type, N-terminal / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Terminase, large subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Salmonella phage P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 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
DepositionJun 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 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 18, 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
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
A: Fab Light chain
B: Fab Heavy chain
D: Fab Light chain
E: Fab Heavy chain
F: Terminase, large subunit
C: Terminase, large subunit


Theoretical massNumber of molelcules
Total (without water)106,5766
Polymers106,5766
Non-polymers00
Water14,538807
1
A: Fab Light chain
B: Fab Heavy chain
C: Terminase, large subunit


Theoretical massNumber of molelcules
Total (without water)53,2883
Polymers53,2883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-35 kcal/mol
Surface area21410 Å2
MethodPISA
2
D: Fab Light chain
E: Fab Heavy chain
F: Terminase, large subunit


Theoretical massNumber of molelcules
Total (without water)53,2883
Polymers53,2883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-36 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.180, 86.395, 86.151
Angle α, β, γ (deg.)90.000, 97.720, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain B
22(chain E and resid 220 through 450)
13(chain C and (resid 1 through 30 or resid 32))
23(chain F and (resid 1 through 30 or resid 32))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 214
211chain DD1 - 214
112chain BB220 - 450
212(chain E and resid 220 through 450)E220 - 450
113(chain C and (resid 1 through 30 or resid 32))C0
213(chain F and (resid 1 through 30 or resid 32))F0

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Fab Light chain / Fragment antigen-binding


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 Fab Heavy chain / Fragment antigen-binding


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: Protein/peptide Terminase, large subunit / DNA-packaging protein gp2 / Gene product 2 / gp2


Mass: 3976.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Salmonella phage P22 (virus)
References: UniProt: P26745, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate ...References: UniProt: P26745, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 807 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Succinic acid pH 7.0 and 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.51→15 Å / Num. obs: 161937 / % possible obs: 96 % / Redundancy: 2.9 % / Biso Wilson estimate: 20.4 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.042 / Rsym value: 0.06 / Net I/σ(I): 32.7
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 15816 / CC1/2: 0.456 / Rpim(I) all: 0.573 / Rsym value: 0.713 / % possible all: 94.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VHM

6vhm
PDB Unreleased entry


Resolution: 1.51→14.985 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 1966 1.24 %
Rwork0.1672 157170 -
obs0.1677 159136 94.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.2 Å2 / Biso mean: 37.3203 Å2 / Biso min: 14.14 Å2
Refinement stepCycle: final / Resolution: 1.51→14.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7262 0 0 807 8069
Biso mean---43.83 -
Num. residues----954
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1968X-RAY DIFFRACTION8.316TORSIONAL
12D1968X-RAY DIFFRACTION8.316TORSIONAL
21B2040X-RAY DIFFRACTION8.316TORSIONAL
22E2040X-RAY DIFFRACTION8.316TORSIONAL
31C286X-RAY DIFFRACTION8.316TORSIONAL
32F286X-RAY DIFFRACTION8.316TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.51-1.54770.29111300.26231047889
1.5477-1.58950.33361340.26231054389
1.5895-1.63620.29221430.24121139196
1.6362-1.6890.2591420.22891146897
1.689-1.74930.2631420.21551138496
1.7493-1.81920.23631420.19211133896
1.8192-1.90180.24671370.18421099093
1.9018-2.00190.18741470.16181163498
2.0019-2.1270.18871440.15421161998
2.127-2.29070.19451450.1521155197
2.2907-2.52020.21691420.15951134095
2.5202-2.88260.18821460.15991171998
2.8826-3.62330.18691370.16011091291
3.6233-14.980.18961350.15661080389

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