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- PDB-4ra8: Structure analysis of the Mip1a P8A mutant -

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Basic information

Entry
Database: PDB / ID: 4ra8
TitleStructure analysis of the Mip1a P8A mutant
ComponentsC-C motif chemokine 3Chemokine
KeywordsCYTOKINE
Function / homology
Function and homology information


granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / signaling / astrocyte cell migration / eosinophil degranulation / CCR5 chemokine receptor binding / negative regulation of bone mineralization ...granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / signaling / astrocyte cell migration / eosinophil degranulation / CCR5 chemokine receptor binding / negative regulation of bone mineralization / regulation of sensory perception of pain / CCR chemokine receptor binding / positive regulation of microglial cell activation / lymphocyte chemotaxis / cell activation / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / phospholipase activator activity / macrophage chemotaxis / positive regulation of calcium ion import / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / Interleukin-10 signaling / monocyte chemotaxis / negative regulation by host of viral transcription / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / cytoskeleton organization / neutrophil chemotaxis / positive regulation of interleukin-1 beta production / calcium-mediated signaling / intracellular calcium ion homeostasis / response to toxic substance / osteoblast differentiation / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of neuron apoptotic process / calcium ion transport / chemotaxis / MAPK cascade / positive regulation of tumor necrosis factor production / cell-cell signaling / cellular response to tumor necrosis factor / kinase activity / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytosol / cytoplasm
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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiang, W.G. / Ren, M. / Guo, 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 9, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionSep 24, 2014ID: 3TN1
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-C motif chemokine 3
B: C-C motif chemokine 3
C: C-C motif chemokine 3
D: C-C motif chemokine 3
E: C-C motif chemokine 3


Theoretical massNumber of molelcules
Total (without water)38,4835
Polymers38,4835
Non-polymers00
Water97354
1
A: C-C motif chemokine 3

A: C-C motif chemokine 3


Theoretical massNumber of molelcules
Total (without water)15,3932
Polymers15,3932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area1030 Å2
ΔGint-8 kcal/mol
Surface area9280 Å2
MethodPISA
2
B: C-C motif chemokine 3
C: C-C motif chemokine 3


Theoretical massNumber of molelcules
Total (without water)15,3932
Polymers15,3932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-9 kcal/mol
Surface area8710 Å2
MethodPISA
3
D: C-C motif chemokine 3
E: C-C motif chemokine 3


Theoretical massNumber of molelcules
Total (without water)15,3932
Polymers15,3932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-9 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.154, 180.154, 77.548
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein
C-C motif chemokine 3 / Chemokine / G0/G1 switch regulatory protein 19-1 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / PAT ...G0/G1 switch regulatory protein 19-1 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / PAT 464.1 / SIS-beta / Small-inducible cytokine A3 / Tonsillar lymphocyte LD78 alpha protein / MIP-1-alpha(4-69) / LD78-alpha(4-69)


Mass: 7696.549 Da / Num. of mol.: 5 / Fragment: UNP residues 23-91 / Mutation: P8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL3, G0S19-1, MIP1A, SCYA3 / Production host: Escherichia coli (E. coli) / References: UniProt: P10147
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 4.72 Å3/Da / Density % sol: 73.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris, pH 5.5, 2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 22020 / Num. obs: 21934 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2x69

2x69


Resolution: 2.6→46.94 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 790 3.05 %RANDOM
Rwork0.2022 ---
obs0.2037 21934 97.3643 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 0 54 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042706
X-RAY DIFFRACTIONf_angle_d0.7443658
X-RAY DIFFRACTIONf_dihedral_angle_d15.22970
X-RAY DIFFRACTIONf_chiral_restr0.03410
X-RAY DIFFRACTIONf_plane_restr0.003472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.7670.2731140.22593677X-RAY DIFFRACTION53
2.767-2.98060.3321150.25073681X-RAY DIFFRACTION53
2.9806-3.28050.28051150.24543680X-RAY DIFFRACTION53
3.2805-3.7550.23641180.21293870X-RAY DIFFRACTION55
3.755-4.73030.2341450.16884599X-RAY DIFFRACTION66
4.7303-46.94710.22781830.19055616X-RAY DIFFRACTION80
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)
16.7605-4.1486-7.76912.00171.99732.0007-0.8310.60743.2709-1.006-0.06210.7181-2.08361.5620.97261.0469-0.0638-0.21490.71650.19351.2386-46.167564.0855-6.0642
24.70130.9332.66310.5852-0.00612.413-0.10860.06550.2556-0.1-0.0130.0205-0.1318-0.2140.1080.2686-0.17460.00720.49870.06190.1922-56.986782.1396-2.1241
31.26750.1310.85191.2371-0.67351.9260.0689-0.10110.0473-0.0411-0.0220.0966-0.1773-0.271-0.01710.2381-0.1779-0.00540.48350.0410.2676-59.591979.595-0.9248
41.57963.1710.35156.36050.70540.0780.0233-0.55440.2520.18730.19660.1929-0.4443-0.436-0.18460.9104-0.1514-0.01740.7171-0.20260.6239-50.776848.9041-12.1519
51.53420.85730.56391.1677-0.02080.7196-0.00380.2415-0.00610.0646-0.0765-0.18510.06890.10870.05480.3338-0.2102-0.03690.47940.05540.2672-52.974262.80253.9509
65.3861-2.3637-0.35139.51831.08765.1879-0.08780.1279-0.2933-0.0525-0.07520.20520.3-0.00730.0510.3485-0.3872-0.06820.6366-0.05910.1094-64.005660.48740.8069
73.052-1.88561.07992.3911-0.88940.4590.14810.29670.0248-0.2197-0.2644-0.07810.28080.04840.15250.3536-0.19540.00140.4370.00720.2117-55.577860.64883.3841
82.30191.0627-0.52663.97770.17430.99380.05390.0128-0.360.0293-0.09590.3880.3057-0.28570.03550.3019-0.3270.02360.5323-0.01660.3118-66.942457.51087.6252
90.7639-3.55831.56432.0001-7.28133.1980.09980.52640.7921-0.2559-0.04990.0881-1.0312-0.22450.00990.60120.2425-0.05950.64930.00980.8003-50.464868.8873-3.14
104.426-4.67822.10028.8834-3.32482.7646-0.1867-0.0714-0.19740.10460.119-0.09480.12660.11710.09870.3648-0.10120.02860.4915-0.00610.2567-42.578956.4453-0.5817
114.33590.16260.90182.00551.44077.3218-0.06780.7188-0.7553-0.92840.3907-1.21160.90160.7731-0.36930.6593-0.05660.15140.6254-0.08050.3968-35.235648.3938-8.9702
127.11450.263-3.3736.18822.83243.0123-0.14250.5713-0.0635-0.85470.1394-0.24010.2340.109-0.03070.9699-0.4050.26660.812-0.21850.4672-35.15153.7018-20.795
137.8762.3512-6.02318.68791.83418.95870.0567-0.0265-0.0757-0.24830.2367-0.3185-0.10860.3103-0.24280.3304-0.19640.04820.65040.01350.339-37.397762.5658-12.2454
141.52670.2072-0.06252.87350.26025.2318-0.0784-0.0501-0.0261-0.27870.16950.09820.4325-0.2746-0.10150.3222-0.20340.01070.578-0.02880.3269-38.756657.0034-8.0307
154.38732.3912-1.53857.1564-2.36356.0135-0.2834-0.0844-0.4709-0.3287-0.2034-1.02840.33620.45480.37230.3893-0.19220.18150.617-0.17720.4664-29.093460.2927-15.0675
160.77521.15121.63951.7022.42453.4502-0.37870.4166-0.2968-0.3784-0.01750.54430.2847-0.51280.32681.218-0.1917-0.06850.736-0.10890.5798-57.369835.2816-16.5021
174.1116-0.1035-2.5020.29110.23063.09810.0151-0.3563-0.2720.2349-0.2077-0.19220.2230.13190.13720.6201-0.2798-0.00460.49930.08380.3594-57.614841.68193.4336
183.4634-0.9742-1.00851.53851.04821.78840.0553-0.21030.14370.4297-0.2444-0.27530.4356-0.14240.16130.6939-0.2868-0.02530.50230.06830.4221-55.524139.57060.7318
195.37243.1287-1.03495.10310.17731.94430.0506-0.4392-0.31970.2648-0.1759-0.0870.27640.12740.1150.9565-0.71140.74330.40140.3772-0.2431-63.41234.96649.3206
207.32343.4779-1.1112.00175.22434.12840.04060.90210.3669-1.0229-0.13060.4526-0.0824-0.33420.07490.9827-0.0087-0.08620.7299-0.04140.3365-53.471351.8842-2.3913
210.8166-0.0245-0.51061.2372-1.65055.092-0.19570.4143-0.3271-0.77860.5084-0.2505-0.3390.1067-0.22140.7687-0.34380.11960.5587-0.05510.4917-48.988540.7852-21.382
221.76720.53981.80422.7215-0.32724.3005-0.05770.0753-0.6817-0.62550.3449-0.43270.00860.0653-0.260.6248-0.2960.16950.457-0.09520.5368-47.875340.7579-18.7009
231.33241.49330.67625.8393-1.93272.1366-0.2840.40070.0824-0.5428-0.0334-0.41630.13910.20150.13771.029-0.49420.08030.8617-0.04780.4232-43.044147.6166-27.8725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:6 )A2 - 6
2X-RAY DIFFRACTION2( CHAIN A AND RESID 7:30 )A7 - 30
3X-RAY DIFFRACTION3( CHAIN A AND RESID 31:69 )A31 - 69
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:5 )B1 - 5
5X-RAY DIFFRACTION5( CHAIN B AND RESID 6:21 )B6 - 21
6X-RAY DIFFRACTION6( CHAIN B AND RESID 22:30 )B22 - 30
7X-RAY DIFFRACTION7( CHAIN B AND RESID 31:56 )B31 - 56
8X-RAY DIFFRACTION8( CHAIN B AND RESID 57:69 )B57 - 69
9X-RAY DIFFRACTION9( CHAIN C AND RESID 4:8 )C4 - 8
10X-RAY DIFFRACTION10( CHAIN C AND RESID 9:13 )C9 - 13
11X-RAY DIFFRACTION11( CHAIN C AND RESID 14:18 )C14 - 18
12X-RAY DIFFRACTION12( CHAIN C AND RESID 19:24 )C19 - 24
13X-RAY DIFFRACTION13( CHAIN C AND RESID 25:30 )C25 - 30
14X-RAY DIFFRACTION14( CHAIN C AND RESID 31:56 )C31 - 56
15X-RAY DIFFRACTION15( CHAIN C AND RESID 57:69 )C57 - 69
16X-RAY DIFFRACTION16( CHAIN D AND RESID 5:8 )D5 - 8
17X-RAY DIFFRACTION17( CHAIN D AND RESID 9:30 )D9 - 30
18X-RAY DIFFRACTION18( CHAIN D AND RESID 31:56 )D31 - 56
19X-RAY DIFFRACTION19( CHAIN D AND RESID 57:69 )D57 - 69
20X-RAY DIFFRACTION20( CHAIN E AND RESID 2:6 )E2 - 6
21X-RAY DIFFRACTION21( CHAIN E AND RESID 7:30 )E7 - 30
22X-RAY DIFFRACTION22( CHAIN E AND RESID 31:56 )E31 - 56
23X-RAY DIFFRACTION23( CHAIN E AND RESID 57:69 )E57 - 69

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