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- PDB-1zxt: Crystal Structure of A Viral Chemokine -

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Basic information

Entry
Database: PDB / ID: 1zxt
TitleCrystal Structure of A Viral Chemokine
Componentsfunctional macrophage inflammatory protein 1-alpha homolog
KeywordsSIGNALING PROTEIN / chemokine fold / greek key motif
Function / homology
Function and homology information


chemokine activity / immune response / extracellular region
Similarity search - Function
Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Interleukin 8-like CC chemikine / ORF K6
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLuz, J.G. / Yu, M. / Su, Y. / Wu, Z. / Zhou, Z. / Sun, R. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of viral macrophage inflammatory protein I encoded by Kaposi's sarcoma-associated herpesvirus at 1.7A.
Authors: Luz, J.G. / Yu, M. / Su, Y. / Wu, Z. / Zhou, Z. / Sun, R. / Wilson, I.A.
History
DepositionJun 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: functional macrophage inflammatory protein 1-alpha homolog
B: functional macrophage inflammatory protein 1-alpha homolog
C: functional macrophage inflammatory protein 1-alpha homolog
D: functional macrophage inflammatory protein 1-alpha homolog


Theoretical massNumber of molelcules
Total (without water)34,7004
Polymers34,7004
Non-polymers00
Water4,125229
1
A: functional macrophage inflammatory protein 1-alpha homolog


Theoretical massNumber of molelcules
Total (without water)8,6751
Polymers8,6751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: functional macrophage inflammatory protein 1-alpha homolog


Theoretical massNumber of molelcules
Total (without water)8,6751
Polymers8,6751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: functional macrophage inflammatory protein 1-alpha homolog


Theoretical massNumber of molelcules
Total (without water)8,6751
Polymers8,6751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: functional macrophage inflammatory protein 1-alpha homolog


Theoretical massNumber of molelcules
Total (without water)8,6751
Polymers8,6751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.452, 40.636, 55.092
Angle α, β, γ (deg.)83.54, 89.68, 79.19
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
functional macrophage inflammatory protein 1-alpha homolog / ORF K6 / vMIP-I


Mass: 8675.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Genus: Rhadinovirus / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q98158, UniProt: Q76RJ0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 1:1 10mg/ml protein: mother liquor (1.2M NaCl,0.1M NaOAc pH5.5, 22oC), vapor diffusion, sitting drops

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 28953 / % possible obs: 94.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.8
Reflection shellHighest resolution: 1.7 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.4 / % possible all: 89.8

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CM9

1cm9


Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS is also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2914 10.1 %RANDOM
Rwork0.189 ---
obs0.194 26039 90.3 %-
all-28953 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20.13 Å2
2---0.22 Å2-0.06 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 0 229 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222296
X-RAY DIFFRACTIONr_bond_other_d0.0050.022048
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9383148
X-RAY DIFFRACTIONr_angle_other_deg0.98734816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0975272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08522.60992
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34915360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4441516
X-RAY DIFFRACTIONr_chiral_restr0.1340.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02428
X-RAY DIFFRACTIONr_nbd_refined0.2190.2414
X-RAY DIFFRACTIONr_nbd_other0.2080.22022
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0950.21281
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3891.51734
X-RAY DIFFRACTIONr_mcbond_other0.4771.5532
X-RAY DIFFRACTIONr_mcangle_it2.50122316
X-RAY DIFFRACTIONr_scbond_it4.22631053
X-RAY DIFFRACTIONr_scangle_it5.2124.5832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.318 176
Rwork0.256 1660
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)
10.96411.2034-0.01874.8461-0.57155.15840.1337-0.1164-0.02730.5719-0.10840.01470.0729-0.0801-0.0252-0.0832-0.0018-0.0565-0.07140.0106-0.2324-13.2758.03275.903
25.10850.9699-1.43344.0601-0.20561.9792-0.13250.2492-0.3047-0.07880.0507-0.19350.1284-0.09370.0818-0.21860.0217-0.0392-0.0903-0.003-0.19150.2095.92554.81
34.2307-0.5644-0.4975.1103-0.10561.8464-0.08680.07290.0930.04450.04530.2267-0.06560.02040.0416-0.23010.0089-0.0392-0.10640.0278-0.176515.08523.85953.155
41.04390.8120.83716.65574.7488.632-0.15250.019-0.1007-0.41510.2084-0.1268-0.35830.3466-0.0559-0.017-0.0409-0.0412-0.01280.0356-0.21328.05321.18531.633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 734 - 72
2X-RAY DIFFRACTION2BB5 - 734 - 72
3X-RAY DIFFRACTION3CC5 - 734 - 72
4X-RAY DIFFRACTION4DD5 - 734 - 72

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