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- PDB-4p5i: Crystal structure of the chemokine binding protein from orf virus -

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Basic information

Entry
Database: PDB / ID: 4p5i
TitleCrystal structure of the chemokine binding protein from orf virus
ComponentsChemokine binding protein
KeywordsVIRAL PROTEIN / HOST CHEMOKINES / SECRETED / CYTOKINE
Function / homologyMajor secreted virus protein, 35kDa / Poxvirus chemokine inhibitor superfamily / Viral chemokine binding protein / identical protein binding / Chemokine binding protein
Function and homology information
Biological speciesOrf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsCounago, R.M. / Krause, K.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
New Zealand Synchrotron Group Limited New Zealand
CitationJournal: Structure / Year: 2015
Title: Structures of Orf Virus Chemokine Binding Protein in Complex with Host Chemokines Reveal Clues to Broad Binding Specificity.
Authors: Counago, R.M. / Knapp, K.M. / Nakatani, Y. / Fleming, S.B. / Corbett, M. / Wise, L.M. / Mercer, A.A. / Krause, K.L.
History
DepositionMar 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jun 13, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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.ptnr1_label_asym_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
Revision 2.1Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemokine binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2253
Polymers29,5801
Non-polymers6462
Water3,135174
1
A: Chemokine binding protein
hetero molecules

A: Chemokine binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4516
Polymers59,1602
Non-polymers1,2914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3890 Å2
ΔGint22 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.250, 76.250, 281.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Chemokine binding protein


Mass: 29579.768 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 17-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orf virus / Strain: NZ2 / Plasmid: PTT5 / Cell line (production host): HEK 293-6E / Production host: HOMO SAPIENS (human) / References: UniProt: Q2F862
#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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4 Å3/Da / Density % sol: 69.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALLIZATION DROPLETS CONSISTED OF 3 UL ORFV CKBP (12 MG ML-1 IN 20 MM HEPES PH 7.0, 1 MM DTT) PLUS 3.0 UL OF A SOLUTION CONTAINING 100 MM L-ARG IN 1.8 M AMMONIUM CITRATE TRIBASIC PH 7.0, ...Details: CRYSTALLIZATION DROPLETS CONSISTED OF 3 UL ORFV CKBP (12 MG ML-1 IN 20 MM HEPES PH 7.0, 1 MM DTT) PLUS 3.0 UL OF A SOLUTION CONTAINING 100 MM L-ARG IN 1.8 M AMMONIUM CITRATE TRIBASIC PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9541, 1.0346, 1.0403, 1.0267
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 2009
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR WITH SAGITTALLY BENT 2ND CRYSTAL
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95411
21.03461
31.04031
41.02671
ReflectionResolution: 2.1→38.286 Å / Num. obs: 29375 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 13.6 % / Biso Wilson estimate: 29.86 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.063 / Net I/σ(I): 26.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.577 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(PHENIX.REFINE: DEV_934)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.25→38.28 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 782 3.25 %
Rwork0.206 --
obs0.207 24048 99.8 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.78 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0654 Å20 Å2-0 Å2
2--1.0654 Å20 Å2
3----2.1309 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 42 174 2068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091948
X-RAY DIFFRACTIONf_angle_d1.2192632
X-RAY DIFFRACTIONf_dihedral_angle_d16.07745
X-RAY DIFFRACTIONf_chiral_restr0.085297
X-RAY DIFFRACTIONf_plane_restr0.007346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.3910.32141290.26583759X-RAY DIFFRACTION99
2.391-2.57550.32211350.2483752X-RAY DIFFRACTION100
2.5755-2.83460.23911230.21913828X-RAY DIFFRACTION100
2.8346-3.24460.24141230.19993847X-RAY DIFFRACTION100
3.2446-4.08720.19461460.17963895X-RAY DIFFRACTION100
4.0872-38.29150.21161260.1994185X-RAY DIFFRACTION99
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)
10.18880.05170.13790.28650.12240.1324-0.1032-0.11510.45950.1479-0.1820.5362-0.0388-0.4937-0.01050.34750.1089-0.07790.4368-0.02570.4649-0.328838.58112.7758
20.32510.00310.40280.12470.05390.59210.21560.174-0.2436-0.05120.1188-0.01670.28710.24040.69120.1980.0684-0.06690.1631-0.00980.156421.126322.110114.7324
30.4649-0.05250.03140.48150.39320.3360.11780.1538-0.16110.0265-0.0630.10980.26450.0386-0.13210.12030.0679-0.04950.14080.00220.105918.017723.42215.499
40.8144-0.0805-0.09780.31060.31310.3004-0.06620.4398-0.02230.0468-0.1076-0.10650.1120.2523-0.43870.1930.0761-0.07640.14250.00840.157517.587622.91976.5144
50.1080.0218-0.07850.1470.06040.101-0.10380.1437-0.0113-0.056-0.1140.25090.16330.0076-0.27370.25120.0876-0.08870.2387-0.0330.214410.906315.36495.702
60.18490.0065-0.49440.5557-0.10241.70620.15940.2433-0.2859-0.07940.01680.40720.3987-0.83350.09980.1591-0.026-0.16760.0826-0.06140.20046.882819.890410.5842
70.40720.18530.22440.09360.10670.12250.1128-0.01760.1604-0.077-0.17930.1038-0.1618-0.0749-0.08630.13610.00940.0080.09760.01590.133214.848232.082621.86
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:26)
2X-RAY DIFFRACTION2chain 'A' and (resseq 27:65)
3X-RAY DIFFRACTION3chain 'A' and (resseq 66:116)
4X-RAY DIFFRACTION4chain 'A' and (resseq 117:159)
5X-RAY DIFFRACTION5chain 'A' and (resseq 160:200)
6X-RAY DIFFRACTION6chain 'A' and (resseq 201:254)
7X-RAY DIFFRACTION7chain 'A' and (resseq 255:270)

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