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- PDB-3tn2: structure analysis of MIP1-beta P8A -

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Basic information

Entry
Database: PDB / ID: 3tn2
Titlestructure analysis of MIP1-beta P8A
ComponentsC-C motif chemokine 4Chemokine
KeywordsCYTOKINE
Function / homology
Function and homology information


CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR5 chemokine receptor binding / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity ...CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR5 chemokine receptor binding / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / establishment or maintenance of cell polarity / Interleukin-10 signaling / monocyte chemotaxis / negative regulation by host of viral transcription / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / neutrophil chemotaxis / cytokine activity / response to virus / response to toxic substance / cellular response to type II interferon / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / cell adhesion / immune response / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region / identical protein binding
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / 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
C-C motif chemokine 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGuo, Q. / Tang, W.J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structures of human CCL18, CCL3, and CCL4 reveal molecular determinants for quaternary structures and sensitivity to insulin-degrading enzyme.
Authors: Liang, W.G. / Ren, M. / Zhao, F. / Tang, W.J.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Aug 22, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref_seq_dif
Item: _entity.src_method / _entity_name_com.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C motif chemokine 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8814
Polymers7,6851
Non-polymers1963
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: C-C motif chemokine 4
hetero molecules

A: C-C motif chemokine 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7628
Polymers15,3692
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1540 Å2
ΔGint-210 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.062, 36.972, 31.061
Angle α, β, γ (deg.)90.00, 108.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-105-

HOH

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Components

#1: Protein C-C motif chemokine 4 / Chemokine / G-26 T-lymphocyte-secreted protein / HC21 / Lymphocyte activation gene 1 protein / LAG-1 / MIP-1- ...G-26 T-lymphocyte-secreted protein / HC21 / Lymphocyte activation gene 1 protein / LAG-1 / MIP-1-beta(1-69) / Macrophage inflammatory protein 1-beta / MIP-1-beta / PAT 744 / Protein H400 / SIS-gamma / Small-inducible cytokine A4 / T-cell activation protein 2 / ACT-2


Mass: 7684.602 Da / Num. of mol.: 1 / Fragment: MIP-1-beta(3-69) (UNP residues 24-91) / Mutation: P8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL4, LAG1, MIP1B, SCYA4 / Plasmid: pET32 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13236
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.81 Å3/Da / Density % sol: 31.99 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5
Details: 15% v/v ethanol, 0.1 M MES, pH 5.5, 0.2 M zinc acetate, EVAPORATION, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 6944 / Num. obs: 6611 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 1.6 Å / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.45 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.026 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19909 326 4.7 %RANDOM
Rwork0.1572 ---
obs0.15927 6611 95.22 %-
all-6944 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.907 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å20 Å21.23 Å2
2---1.79 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms537 0 3 60 600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022553
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.958755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.269567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8832425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0161585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.65153
X-RAY DIFFRACTIONr_chiral_restr0.1340.282
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021426
X-RAY DIFFRACTIONr_mcbond_it1.3141.5343
X-RAY DIFFRACTIONr_mcangle_it2.0042558
X-RAY DIFFRACTIONr_scbond_it3.1013210
X-RAY DIFFRACTIONr_scangle_it4.8514.5197
LS refinement shellResolution: 1.6→1.646 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 23 -
Rwork0.194 433 -
obs--85.07 %

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