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- PDB-2ra4: Crystal Structure of Human Monocyte Chemoattractant Protein 4 (MC... -

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Basic information

Entry
Database: PDB / ID: 2ra4
TitleCrystal Structure of Human Monocyte Chemoattractant Protein 4 (MCP-4/CCL13)
ComponentsSmall-inducible cytokine A13
KeywordsCYTOKINE / CCL13 / MCP-4 / CC chemokine family / chemotaxis / monocytes / Inflammatory response / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


CCR chemokine receptor binding / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / cytoskeleton organization / intracellular calcium ion homeostasis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling ...CCR chemokine receptor binding / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / cytoskeleton organization / intracellular calcium ion homeostasis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / regulation of cell shape / G alpha (i) signalling events / killing of cells of another organism / positive regulation of cell migration / inflammatory response / signaling receptor binding / signal transduction / extracellular space / extracellular region
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
trifluoroacetic acid / C-C motif chemokine 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLubkowski, J. / Barinka, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of human monocyte chemoattractant protein 4 (MCP-4/CCL13).
Authors: Barinka, C. / Prahl, A. / Lubkowski, J.
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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: Small-inducible cytokine A13
B: Small-inducible cytokine A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1859
Polymers17,4952
Non-polymers6907
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
MethodPISA
2
A: Small-inducible cytokine A13
B: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
B: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
B: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
B: Small-inducible cytokine A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,74136
Polymers69,9798
Non-polymers2,76228
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area26260 Å2
MethodPISA
3
A: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,14216
Polymers34,9904
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area7040 Å2
MethodPISA
4
B: Small-inducible cytokine A13
hetero molecules

B: Small-inducible cytokine A13
hetero molecules

B: Small-inducible cytokine A13
hetero molecules

B: Small-inducible cytokine A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,59820
Polymers34,9904
Non-polymers1,60916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.673, 74.673, 51.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11B-78-

SO4

21B-78-

SO4

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Components

#1: Protein Small-inducible cytokine A13 / CCL13 / Monocyte chemotactic protein 4 / MCP-4 / Monocyte chemoattractant protein 4 / CK-beta-10 / NCC-1


Mass: 8747.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL13, MCP4, NCC1, SCYA13 / Plasmid: pET-11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)trxB / References: UniProt: Q99616
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, 2 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2004
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. all: 15683 / Num. obs: 15683 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 26.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1dok

1dok


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.106 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21581 783 5 %RANDOM
Rwork0.17974 ---
obs0.18155 14898 99.93 %-
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: 31.722 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 37 72 1147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221153
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9861555
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.3822.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93815239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.215158
X-RAY DIFFRACTIONr_chiral_restr0.1490.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02782
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2483
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2760
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4941.5689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.19821100
X-RAY DIFFRACTIONr_scbond_it3.3833522
X-RAY DIFFRACTIONr_scangle_it4.6874.5455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 54 -
Rwork0.233 1073 -
obs--99.38 %
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)
12.49831.05911.29862.01820.92333.1448-0.03710.01180.01310.17790.0244-0.00230.0480.0740.0127-0.06660.0252-0.0065-0.08180.0068-0.067150.602528.144325.3157
24.89070.04642.14360.8923-0.03863.49430.08570.3958-0.1217-0.14-0.10410.17750.13850.00740.0184-0.04790.0214-0.0053-0.0339-0.0398-0.039739.930121.29124.9028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 674 - 68
2X-RAY DIFFRACTION2BB3 - 674 - 68

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