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- PDB-4k70: Crystal Structure of N-terminal half of Pseudorabiesvirus UL37 protein -

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Basic information

Entry
Database: PDB / ID: 4k70
TitleCrystal Structure of N-terminal half of Pseudorabiesvirus UL37 protein
ComponentsUL37
KeywordsVIRAL PROTEIN
Function / homologyHerpesvirus UL37 / Herpesvirus UL37 tegument protein / virion assembly / metal ion binding / NICKEL (II) ION / UL37
Function and homology information
Biological speciesSuid herpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPitts, J.D. / Heldwein, E.E.
CitationJournal: J.Virol. / Year: 2014
Title: Crystal Structure of the Herpesvirus Inner Tegument Protein UL37 Supports Its Essential Role in Control of Viral Trafficking.
Authors: Pitts, J.D. / Klabis, J. / Richards, A.L. / Smith, G.A. / Heldwein, E.E.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Feb 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_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.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_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

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Assembly

Deposited unit
A: UL37
B: UL37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,28837
Polymers107,1452
Non-polymers1,14335
Water10,737596
1
A: UL37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,18620
Polymers53,5721
Non-polymers61319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UL37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,10317
Polymers53,5721
Non-polymers53016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.670, 156.589, 67.381
Angle α, β, γ (deg.)90.00, 91.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UL37 / UL37 protein


Mass: 53572.406 Da / Num. of mol.: 2 / Fragment: UNP residues 1-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid herpesvirus 1 / Strain: Becker / Gene: ul37 / Plasmid: pJP23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q911W0

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Non-polymers , 6 types, 631 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% PEG 1000, 0.3M calcium acetate, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2011
RadiationMonochromator: Synchrotron Radiation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.975→50 Å / Num. all: 72015 / Num. obs: 64382 / % possible obs: 89.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.63
Reflection shellResolution: 1.975→2.03 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2 / % possible all: 53.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAUTOSOLmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD / Resolution: 2→43.117 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 2347 3.65 %
Rwork0.1729 --
obs0.1747 64342 89.37 %
all-73257 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→43.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7304 0 45 596 7945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077502
X-RAY DIFFRACTIONf_angle_d0.93910248
X-RAY DIFFRACTIONf_dihedral_angle_d13.6042694
X-RAY DIFFRACTIONf_chiral_restr0.061184
X-RAY DIFFRACTIONf_plane_restr0.0051364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04080.3415740.22131856X-RAY DIFFRACTION46
2.0408-2.08520.2986960.21392282X-RAY DIFFRACTION56
2.0852-2.13370.26581000.22757X-RAY DIFFRACTION68
2.1337-2.18710.24791260.19573358X-RAY DIFFRACTION82
2.1871-2.24620.25021500.19473652X-RAY DIFFRACTION90
2.2462-2.31230.25161370.18233792X-RAY DIFFRACTION94
2.3123-2.38690.25251610.1813983X-RAY DIFFRACTION97
2.3869-2.47220.2421510.1774017X-RAY DIFFRACTION98
2.4722-2.57120.25621450.17873988X-RAY DIFFRACTION98
2.5712-2.68820.24461470.17584014X-RAY DIFFRACTION98
2.6882-2.82990.22111510.18624014X-RAY DIFFRACTION99
2.8299-3.00720.2131480.18724021X-RAY DIFFRACTION99
3.0072-3.23930.2361530.18814064X-RAY DIFFRACTION99
3.2393-3.56510.21461470.17483929X-RAY DIFFRACTION96
3.5651-4.08070.22321550.15114054X-RAY DIFFRACTION99
4.0807-5.13990.17161520.14564093X-RAY DIFFRACTION100
5.1399-43.12730.18581540.16714121X-RAY DIFFRACTION100

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