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- PDB-4gbf: Crystal structure of the C-terminal domain of gp131 from bacterio... -

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Basic information

Entry
Database: PDB / ID: 4gbf
TitleCrystal structure of the C-terminal domain of gp131 from bacteriophage phiKZ
ComponentsPHIKZ131
KeywordsVIRAL PROTEIN / 7-bladed beta-propeller / Possibly participates in binding of the phage to the host cell / At the periphery of the baseplate or in the fiber of bacteriophage phiKZ
Function / homologyvirus tail, baseplate / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / PHIKZ131
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.949 Å
AuthorsSycheva, L.V. / Shneider, M.M. / Leiman, P.G.
CitationJournal: Virology / Year: 2012
Title: Crystal structure and location of gp131 in the bacteriophage phiKZ virion.
Authors: Sycheva, L.V. / Shneider, M.M. / Sykilinda, N.N. / Ivanova, M.A. / Miroshnikov, K.A. / Leiman, P.G.
History
DepositionJul 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 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_ref_seq_dif / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: PHIKZ131
B: PHIKZ131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,19311
Polymers87,9292
Non-polymers2639
Water10,971609
1
A: PHIKZ131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1086
Polymers43,9651
Non-polymers1445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHIKZ131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0845
Polymers43,9651
Non-polymers1204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.449, 86.353, 97.362
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: Protein PHIKZ131


Mass: 43964.672 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 375-771)
Source method: isolated from a genetically manipulated source
Details: Modified pET28a / Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Gene: ORF131 / Plasmid: pESL / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8SD31
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 1.9 Å3/Da / Density % sol: 35.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG3350, 0.25M magnesium chloride, 0.1M BisTris, pH 6.0, 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 27, 2011
Details: LN2 cooled fixed-exit Si(111) monochromator and dynamically bendable mirror
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.68 Å / Num. obs: 49414 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 31.824 Å2 / Rsym value: 0.082 / Net I/σ(I): 15.37
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 6863 / Rsym value: 0.546 / % possible all: 97.3

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Processing

Software
NameVersionClassification
RemDAqdata collection
SHELXC/D/Emodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
SHELXC/D/Ephasing
RefinementMethod to determine structure: SAD / Resolution: 1.949→43.18 Å / SU ML: 0.2 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 2470 5 %RANDOM
Rwork0.1606 ---
obs0.1625 49414 99.66 %-
all-49595 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.207 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9538 Å20 Å2-0 Å2
2--0.303 Å2-0 Å2
3----1.2567 Å2
Refinement stepCycle: LAST / Resolution: 1.949→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5748 0 9 609 6366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056043
X-RAY DIFFRACTIONf_angle_d0.8878308
X-RAY DIFFRACTIONf_dihedral_angle_d11.7042121
X-RAY DIFFRACTIONf_chiral_restr0.062894
X-RAY DIFFRACTIONf_plane_restr0.0041084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9489-1.98640.28371290.23052435X-RAY DIFFRACTION94
1.9864-2.02690.26771360.20492582X-RAY DIFFRACTION100
2.0269-2.0710.25961340.18772561X-RAY DIFFRACTION100
2.071-2.11920.2541360.17872574X-RAY DIFFRACTION100
2.1192-2.17220.22021360.1662598X-RAY DIFFRACTION100
2.1722-2.23090.19851360.15952577X-RAY DIFFRACTION100
2.2309-2.29650.23141360.17092589X-RAY DIFFRACTION100
2.2965-2.37060.27161370.17612602X-RAY DIFFRACTION100
2.3706-2.45540.21331360.17252596X-RAY DIFFRACTION100
2.4554-2.55370.25081370.17462604X-RAY DIFFRACTION100
2.5537-2.66990.24731360.1782602X-RAY DIFFRACTION100
2.6699-2.81060.22351360.18142589X-RAY DIFFRACTION100
2.8106-2.98670.19431380.16492624X-RAY DIFFRACTION100
2.9867-3.21720.18111390.14952621X-RAY DIFFRACTION100
3.2172-3.54080.17551390.13962653X-RAY DIFFRACTION100
3.5408-4.05290.15411400.12812657X-RAY DIFFRACTION100
4.0529-5.10490.15311410.12552674X-RAY DIFFRACTION100
5.1049-43.18710.18551480.18872806X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3446-0.1902-0.05972.72240.41762.8925-0.007-0.041-0.0719-0.0116-0.0073-0.0739-0.00510.13810.00940.0836-0.01320.00660.13570.02940.112430.265837.459519.381
20.94910.52960.0470.6690.07131.2778-0.0892-0.1331-0.4882-0.0084-0.015-0.1340.2753-0.0015-0.09780.09030.00030.0412-0.00330.0593-0.007916.225529.626223.4303
31.05170.1963-0.68842.47811.16042.7167-0.12370.2148-0.2301-0.1239-0.08170.17650.4063-0.42260.20920.2244-0.05540.01450.2334-0.02580.1937.869731.97035.4368
41.46550.18050.04860.92770.04951.89090.01740.04810.00210.0289-0.0348-0.0751-0.0761-0.02640.02770.1151-0.00920.01230.13750.00120.126623.855240.04171.859
51.79790.9342-0.86242.6192-0.922.6935-0.03080.0524-0.05960.00510.05720.076-0.0008-0.1737-0.04640.0980.0068-0.0010.1473-0.00540.13358.7219-4.46063.7438
60.8905-0.2898-0.04911.14860.02321.0728-0.0530.0035-0.1906-0.01990.0162-0.0680.21640.0027-0.11340.0757-0.01340.00630.0389-0.00880.095524.665-14.13414.196
71.54-0.23830.17970.78670.36671.9940.002-0.04720.09690.05880.0125-0.0153-0.0159-0.03210.00110.1574-0.0023-0.00010.14550.00210.133116.3375-3.992621.5261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 399:486 )A399 - 486
2X-RAY DIFFRACTION2( CHAIN A AND RESID 487:583 )A487 - 583
3X-RAY DIFFRACTION3( CHAIN A AND RESID 584:641 )A584 - 641
4X-RAY DIFFRACTION4( CHAIN A AND RESID 642:767 )A642 - 767
5X-RAY DIFFRACTION5( CHAIN B AND RESID 398:486 )B398 - 486
6X-RAY DIFFRACTION6( CHAIN B AND RESID 487:618 )B487 - 618
7X-RAY DIFFRACTION7( CHAIN B AND RESID 619:767 )B619 - 767

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