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- PDB-3pqh: Crystal structure of the C-terminal fragment of the bacteriophage... -

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Basic information

Entry
Database: PDB / ID: 3pqh
TitleCrystal structure of the C-terminal fragment of the bacteriophage phi92 membrane-piercing protein gp138
Componentsgene product 138
KeywordsVIRAL PROTEIN / Beta-Helix / OB-Fold / Phage Baseplate / Iron-Binding / Cell membrane piercing
Function / homology
Function and homology information


Ubiquitin Ligase Nedd4; Chain: W; - #60 / Glycosyl hydrolase fold - #20 / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Glycosyl hydrolase fold / Vgr protein, OB-fold domain superfamily / Ubiquitin Ligase Nedd4; Chain: W; / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteriophage phi92 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.295 Å
AuthorsBrowning, C. / Shneider, M. / Leiman, P.G.
CitationJournal: Structure / Year: 2012
Title: Phage pierces the host cell membrane with the iron-loaded spike.
Authors: Browning, C. / Shneider, M.M. / Bowman, V.D. / Schwarzer, D. / Leiman, P.G.
History
DepositionNov 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: gene product 138
B: gene product 138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,44111
Polymers26,1692
Non-polymers2739
Water7,548419
1
A: gene product 138
hetero molecules

A: gene product 138
hetero molecules

A: gene product 138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,76621
Polymers39,2533
Non-polymers51218
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area15750 Å2
ΔGint-221 kcal/mol
Surface area13010 Å2
MethodPISA
2
B: gene product 138
hetero molecules

B: gene product 138
hetero molecules

B: gene product 138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,55912
Polymers39,2533
Non-polymers3059
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area14560 Å2
ΔGint-164 kcal/mol
Surface area12950 Å2
MethodPISA
3
A: gene product 138
B: gene product 138
hetero molecules

A: gene product 138
B: gene product 138
hetero molecules

A: gene product 138
B: gene product 138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,32433
Polymers78,5066
Non-polymers81827
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area33110 Å2
ΔGint-394 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.080, 48.080, 553.203
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2-

FE

21B-1-

FE

31A-298-

HOH

41A-444-

HOH

51A-633-

HOH

61B-275-

HOH

71B-426-

HOH

81B-629-

HOH

91B-632-

HOH

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Components

#1: Protein gene product 138


Mass: 13084.402 Da / Num. of mol.: 2 / Fragment: C-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage phi92 (virus) / Production host: Escherichia coli (E. coli) / Strain (production host): 834 (DE3) / References: UniProt: I7HXF9*PLUS
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3547.69
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop6.57mg/ml 34% - 38% PEE 100mM - 400mM KCl 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912vapor diffusion, hanging drop7.57mg/ml 20% -26% PEG 2000 100mM - 400mM CaCl2 100mM Tris pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 7, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→41.52 Å / Num. all: 61805 / Num. obs: 61401 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 16.6 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.082 / Net I/σ(I): 17.6
Reflection shellResolution: 1.29→1.37 Å / Redundancy: 15.6 % / Rmerge(I) obs: 0.811 / Rsym value: 0.759 / % possible all: 98.1

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Processing

Software
NameVersionClassification
RemDAqdata collection
SHELXC/D/Emodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXC/D/Ephasing
RefinementMethod to determine structure: SAD / Resolution: 1.295→41.521 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 13.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1598 3103 5.08 %
Rwork0.1229 --
obs0.1247 61037 96.95 %
all-61805 -
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 95.544 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 21.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.2527 Å20 Å20 Å2
2---0.2527 Å20 Å2
3---0.5053 Å2
Refinement stepCycle: LAST / Resolution: 1.295→41.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 9 419 1976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161731
X-RAY DIFFRACTIONf_angle_d1.7512380
X-RAY DIFFRACTIONf_dihedral_angle_d12.957665
X-RAY DIFFRACTIONf_chiral_restr0.141283
X-RAY DIFFRACTIONf_plane_restr0.01315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.295-1.34130.26242770.20115322X-RAY DIFFRACTION91
1.3413-1.3950.22632920.15935502X-RAY DIFFRACTION94
1.395-1.45850.19663140.13125667X-RAY DIFFRACTION96
1.4585-1.53540.14782690.10395708X-RAY DIFFRACTION97
1.5354-1.63160.14993130.09215779X-RAY DIFFRACTION98
1.6316-1.75750.14043240.08995787X-RAY DIFFRACTION98
1.7575-1.93440.14473230.09475895X-RAY DIFFRACTION99
1.9344-2.21430.1293440.10255912X-RAY DIFFRACTION99
2.2143-2.78970.16123130.11816076X-RAY DIFFRACTION100
2.7897-41.54240.16493340.14376286X-RAY DIFFRACTION99

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