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- PDB-4hsv: Crystal Structure of CXCL4L1 -

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Basic information

Entry
Database: PDB / ID: 4hsv
TitleCrystal Structure of CXCL4L1
ComponentsPlatelet factor 4 variant
KeywordsANTITUMOR PROTEIN / ANTI-ANGIOGENESIS / HEPARIN / EXTRACELLULAR
Function / homology
Function and homology information


CXCR chemokine receptor binding / chemokine activity / Common Pathway of Fibrin Clot Formation / neutrophil chemotaxis / Cell surface interactions at the vascular wall / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / cellular response to lipopolysaccharide / inflammatory response / extracellular space
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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 ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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
Platelet factor 4 variant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.083 Å
AuthorsKuo, J.H. / Liu, J.S. / Wu, W.G. / Sue, S.C.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Alternative C-terminal helix orientation alters chemokine function: structure of the anti-angiogenic chemokine, CXCL4L1
Authors: Kuo, J.H. / Chen, Y.P. / Liu, J.S. / Dubrac, A. / Quemener, C. / Prats, H. / Bikfalvi, A. / Wu, W.G. / Sue, S.C.
History
DepositionOct 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Platelet factor 4 variant
B: Platelet factor 4 variant
C: Platelet factor 4 variant
D: Platelet factor 4 variant


Theoretical massNumber of molelcules
Total (without water)31,8174
Polymers31,8174
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.672, 55.180, 68.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Platelet factor 4 variant / C-X-C motif chemokine 4 variant / CXCL4L1 / PF4alt / PF4var1 / Platelet factor 4 variant(5-74)


Mass: 7954.357 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PF4V1, CXCL4V1, SCYB4V1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10720
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 291 K / Method: vapor batch / pH: 8
Details: 0.1M Tris, 0.2M Sodium citrate, 20% PEG 400, 26% Isopropanol, pH 8.0, Vapor batch, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2012
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.08→30 Å / Num. obs: 17842 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible all
2.08-2.157.2189.9
2.15-2.247.9199.9
2.24-2.3481100
2.34-2.478199.9
2.47-2.6281100
2.62-2.8281100
2.82-3.117.91100
3.11-3.567.91100
3.56-4.487.7199.2
4.48-307.1197.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.083→25.921 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7261 / SU ML: 0.26 / σ(F): 1.35 / Phase error: 32.62 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 889 5.07 %RANDOM
Rwork0.2363 ---
all0.2725 17658 --
obs0.2384 17533 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.57 Å2 / Biso mean: 79.756 Å2 / Biso min: 41.93 Å2
Refinement stepCycle: LAST / Resolution: 2.083→25.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 0 38 1967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011961
X-RAY DIFFRACTIONf_angle_d1.3372631
X-RAY DIFFRACTIONf_dihedral_angle_d15.209763
X-RAY DIFFRACTIONf_chiral_restr0.074331
X-RAY DIFFRACTIONf_plane_restr0.007319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0833-2.21380.33961660.2593269399
2.2138-2.38460.33061470.26062725100
2.3846-2.62430.31551480.25472766100
2.6243-3.00360.30391430.25062767100
3.0036-3.78230.26491380.23552816100
3.7823-25.92290.25561470.2236287798
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)
16.63110.91621.84492.1534-1.58426.831-0.09540.2842-0.2218-0.63130.17450.02220.0529-0.3054-0.11750.4934-0.039-0.03670.4108-0.00880.355320.952914.01351.943
27.30231.7154-0.14642.1554-1.11953.3002-0.64-0.77622.5391-0.5639-0.94431.3102-3.8364-0.08840.10231.2070.0858-0.25870.5988-0.18741.04520.187934.558211.1409
37.1449-0.5019-0.57466.27590.82644.1511-0.0871-0.2276-0.10250.08280.07520.0416-0.30770.37910.05890.4913-0.0736-0.04630.41320.06110.406324.746418.68879.9988
42.7179-6.6345-7.15886.23841.91162.5915-0.3555-0.08340.51150.002-0.15521.1147-0.7076-0.36610.30070.5789-0.0052-0.0860.5886-0.050.888814.752625.984110.5477
52.58232.18295.28351.8611-0.84687.0285-0.0446-0.6382-0.2089-0.5975-0.7366-1.2404-1.02850.00351.10250.7544-0.1360.07970.7434-0.05630.99134.717733.97299.2912
62.9069-6.6012-0.0510.1742-1.77441.9089-0.6674-0.0786-0.99741.64420.18220.22961.396-0.815-0.18690.7715-0.2143-0.03140.8536-0.03120.693530.441413.642826.7263
74.5232-1.52221.48714.68060.89284.0277-0.1828-1.275-0.14591.02940.25280.7476-0.1745-0.32770.06770.7729-0.0860.03110.67370.03460.515522.298720.456823.4092
88.91643.50577.15868.43892.92228.54620.59-0.2835-0.7457-0.4299-0.3201-0.84361.06210.2399-0.18750.60050.0011-0.02180.59070.0990.421736.393117.726425.5515
92.111-3.26122.3287.1594-3.41282.2871-1.9181-1.81371.70412.28681.0172-0.5329-1.32220.19620.26020.8141-0.1130.23881.0713-0.11320.713513.307311.631530.6242
106.0251-2.22131.22168.7224-2.71364.2319-0.0423-0.71590.30330.2046-0.3261-0.0470.66350.09970.2190.6975-0.11740.13290.5886-0.01210.507614.84597.498622.5908
118.77444.37-5.96228.4544-5.00574.6870.2681-0.27470.7647-0.03070.2490.5564-0.3005-0.6403-0.58060.5573-0.04240.10550.7032-0.06740.39425.302610.343625.1546
126.66751.9193-0.17192.28952.67698.08730.06430.21010.5977-1.29880.22820.1454-0.15110.2231-0.0240.5937-0.12350.00620.4279-0.02990.459316.826412.55721.9588
135.24772.58181.77772.06450.1348.4190.2208-0.3928-0.2128-0.4147-0.26-0.21181.6776-0.1716-0.05190.6519-0.06840.07520.3783-0.0290.413215.43982.81810.8231
142.7217-4.5714.75729.2944-5.20289.34510.23760.5873-0.26890.1274-0.787-0.14570.65280.52250.46450.4974-0.06370.10780.4871-0.00230.542221.31061.856310.9712
158.77982.871-2.81522.10872.89412.0678-0.2425-0.6741-0.124-0.4832-0.4874-1.2643-0.3055-0.66010.3110.7802-0.14380.13110.74210.05891.1786.0926-3.95899.0252
165.78350.7873-1.86736.67412.19162.04790.4138-0.762-1.86310.5455-0.0981-2.3010.78861.58230.86910.8118-0.24460.0051.0081-0.0081.2784-0.7158-9.728711.7972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 15 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 23 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 45 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 54 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 55 through 70 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 23 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 45 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 46 through 68 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 9 through 20 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 21 through 39 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 40 through 67 )C0
12X-RAY DIFFRACTION12chain 'D' and (resid 6 through 15 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 16 through 39 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 40 through 54 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 55 through 63 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 64 through 70 )D0

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