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- PDB-4zkq: Viral chemokine binding protein R17 encoded by rodent gammaherpes... -

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Basic information

Entry
Database: PDB / ID: 4zkq
TitleViral chemokine binding protein R17 encoded by rodent gammaherpesvirus Peru ( RHVP)
ComponentsPutative uncharacterized protein
KeywordsChemokine binding protein / VIRAL PROTEIN
Function / homologyUncharacterized protein
Function and homology information
Biological speciesCricetid herpesvirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsLubman, O.Y. / Fremont, D.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI019687 United States
Center for Womens Infectious Disease Research United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI057160 United States
CitationJournal: Structure / Year: 2016
Title: Parallel Evolution of Chemokine Binding by Structurally Related Herpesvirus Decoy Receptors.
Authors: Lubman, O.Y. / Fremont, D.H.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Aug 9, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.6Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8972
Polymers47,4731
Non-polymers4241
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint6 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.561, 75.835, 106.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer according to multi-angle static light scaterring

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Components

#1: Protein Putative uncharacterized protein


Mass: 47472.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetid herpesvirus 2 / Gene: RHVP-L.R17, RHVP.R17 / Cell line (production host): 293F / Organ (production host): KIDNEY / Production host: Mammalian expression vector pBGSA (others) / References: UniProt: E9M5R0
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris pH 8.5 20% PEG550 MME / PH range: 8.3-8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 45516 / % possible obs: 93.8 % / Redundancy: 3 % / Rsym value: 0.052 / Net I/σ(I): 20.8
Reflection shellResolution: 1.89→1.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.83 / % possible all: 61.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The 2.7 Angstrom model resolved by SAD experiment

Resolution: 1.898→37.011 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 2024 5.07 %
Rwork0.1844 --
obs0.1862 39897 87.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→37.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 28 355 3449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053230
X-RAY DIFFRACTIONf_angle_d0.9964381
X-RAY DIFFRACTIONf_dihedral_angle_d12.9221195
X-RAY DIFFRACTIONf_chiral_restr0.038496
X-RAY DIFFRACTIONf_plane_restr0.004559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8977-1.94520.3424520.2448779X-RAY DIFFRACTION26
1.9452-1.99780.2476670.22331604X-RAY DIFFRACTION53
1.9978-2.05660.24561140.21142432X-RAY DIFFRACTION79
2.0566-2.12290.23631690.21252732X-RAY DIFFRACTION91
2.1229-2.19880.22261630.19812892X-RAY DIFFRACTION95
2.1988-2.28680.23311610.18852961X-RAY DIFFRACTION97
2.2868-2.39090.22541480.19423044X-RAY DIFFRACTION99
2.3909-2.51690.22011610.19333033X-RAY DIFFRACTION99
2.5169-2.67460.23781630.19863036X-RAY DIFFRACTION99
2.6746-2.8810.25571480.19653068X-RAY DIFFRACTION99
2.881-3.17080.2651740.19353083X-RAY DIFFRACTION99
3.1708-3.62930.18491800.17943072X-RAY DIFFRACTION99
3.6293-4.57120.19791700.15333071X-RAY DIFFRACTION98
4.5712-37.01810.20811540.17393066X-RAY DIFFRACTION93

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