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- PDB-2x6g: X-ray Structure of Macrophage Inflammatory Protein-1 alpha (D27A) -

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Basic information

Entry
Database: PDB / ID: 2x6g
TitleX-ray Structure of Macrophage Inflammatory Protein-1 alpha (D27A)
ComponentsC-C MOTIF CHEMOKINE 3
KeywordsIMMUNE SYSTEM / INFLAMMATORY RESPONSE / SECRETED / CYTOKINE / CHEMOTAXIS
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 / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain ...granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain / negative regulation of bone mineralization / 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 / positive regulation of calcium ion import / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / macrophage chemotaxis / 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 / response to toxic substance / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of inflammatory response / osteoblast differentiation / calcium ion transport / chemotaxis / positive regulation of tumor necrosis factor production / MAPK cascade / positive regulation of neuron apoptotic process / cell-cell signaling / kinase activity / cellular response to tumor necrosis factor / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / 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 / cytoplasm / cytosol
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: 2.18 Å
AuthorsGuo, Q. / Ren, M. / Tang, W.
CitationJournal: Embo J. / Year: 2010
Title: Polymerization of Mip-1 Chemokine (Ccl3 and Ccl4) and Clearance of Mip-1 by Insulin-Degrading Enzyme.
Authors: Ren, M. / Guo, Q. / Guo, L. / Lenz, M. / Qian, F. / Koenen, R.R. / Xu, H. / Schilling, A.B. / Weber, C. / Ye, R.D. / Dinner, A.R. / Tang, W.
History
DepositionFeb 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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
F: C-C MOTIF CHEMOKINE 3
G: C-C MOTIF CHEMOKINE 3
H: C-C MOTIF CHEMOKINE 3
I: C-C MOTIF CHEMOKINE 3
J: C-C MOTIF CHEMOKINE 3
K: C-C MOTIF CHEMOKINE 3
L: C-C MOTIF CHEMOKINE 3
M: C-C MOTIF CHEMOKINE 3
N: C-C MOTIF CHEMOKINE 3
O: C-C MOTIF CHEMOKINE 3
P: C-C MOTIF CHEMOKINE 3
Q: C-C MOTIF CHEMOKINE 3
R: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)139,49418
Polymers139,49418
Non-polymers00
Water8,089449
1
Q: C-C MOTIF CHEMOKINE 3
R: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,4992
Polymers15,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-11.4 kcal/mol
Surface area7840 Å2
MethodPISA
2
E: C-C MOTIF CHEMOKINE 3
F: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,4992
Polymers15,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-10.8 kcal/mol
Surface area8350 Å2
MethodPISA
3
O: C-C MOTIF CHEMOKINE 3
P: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,4992
Polymers15,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-9.5 kcal/mol
Surface area8370 Å2
MethodPISA
4
C: C-C MOTIF CHEMOKINE 3
D: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,4992
Polymers15,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10.6 kcal/mol
Surface area8190 Å2
MethodPISA
5
I: C-C MOTIF CHEMOKINE 3
J: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,4992
Polymers15,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-10.2 kcal/mol
Surface area8410 Å2
MethodPISA
6
A: C-C MOTIF CHEMOKINE 3
B: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,4992
Polymers15,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-10.4 kcal/mol
Surface area8120 Å2
MethodPISA
7
G: C-C MOTIF CHEMOKINE 3
H: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,4992
Polymers15,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-9.7 kcal/mol
Surface area8360 Å2
MethodPISA
8
M: C-C MOTIF CHEMOKINE 3
N: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,4992
Polymers15,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-9.9 kcal/mol
Surface area8160 Å2
MethodPISA
9
K: C-C MOTIF CHEMOKINE 3
L: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,4992
Polymers15,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8.4 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.211, 113.527, 173.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
C-C MOTIF CHEMOKINE 3 / MACROPHAGE INFLAMMATORY PROTEIN 1-ALPHA / SMALL-INDUCIBLE CYTOKINE A3 / MIP-1-ALPHA / TONSILLAR ...MACROPHAGE INFLAMMATORY PROTEIN 1-ALPHA / SMALL-INDUCIBLE CYTOKINE A3 / MIP-1-ALPHA / TONSILLAR LYMPHOCYTE LD78 ALPHA PROTEIN / G0/G1 SWITCH REGULATORY PROTEIN 19-1 / SIS-BETA / PAT 464.1


Mass: 7749.654 Da / Num. of mol.: 18 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P10147
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 49 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN C, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN D, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN E, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN F, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN G, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN H, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN I, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN J, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN K, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN L, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN M, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN N, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN O, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN P, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN Q, ASP 49 TO ALA ENGINEERED RESIDUE IN CHAIN R, ASP 49 TO ALA
Sequence detailsD49A MUTATION REDUCES SELF-ASSOCIATION; IN BB-10010: IMPROVED PHARMACEUTICAL PROPERTIES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.12 % / Description: NONE
Crystal growDetails: 0.2M NH4AC, 0.1M HEPES (PH7.8), 26% PEG3350

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 61457 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.6
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→49.012 Å / SU ML: 0.32 / σ(F): 0.1 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2857 3027 5.1 %
Rwork0.2105 --
obs0.2143 59783 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.442 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.8955 Å2-0 Å20 Å2
2---10.0695 Å2-0 Å2
3---3.174 Å2
Refinement stepCycle: LAST / Resolution: 2.18→49.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9142 0 0 449 9591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089392
X-RAY DIFFRACTIONf_angle_d1.11212704
X-RAY DIFFRACTIONf_dihedral_angle_d18.6283345
X-RAY DIFFRACTIONf_chiral_restr0.0771407
X-RAY DIFFRACTIONf_plane_restr0.0051637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1494-2.22620.32082330.23524537X-RAY DIFFRACTION77
2.2262-2.31540.32092690.22765497X-RAY DIFFRACTION94
2.3154-2.42070.32742820.22665558X-RAY DIFFRACTION95
2.4207-2.54840.31123260.22125644X-RAY DIFFRACTION97
2.5484-2.7080.31372980.24045760X-RAY DIFFRACTION98
2.708-2.91710.33693480.24335733X-RAY DIFFRACTION98
2.9171-3.21060.30853230.2225884X-RAY DIFFRACTION99
3.2106-3.6750.28063180.19415913X-RAY DIFFRACTION100
3.675-4.62960.24873180.17875994X-RAY DIFFRACTION100
4.6296-49.02450.25063120.20466236X-RAY DIFFRACTION99

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