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- PDB-9e6p: Structure of a Mouse KC dimeric mutant -

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Basic information

Entry
Database: PDB / ID: 9e6p
TitleStructure of a Mouse KC dimeric mutant
ComponentsGrowth-regulated alpha protein
KeywordsCYTOKINE / CHEMOKINE(GROWTH FACTOR)
Function / homology
Function and homology information


Chemokine receptors bind chemokines / positive regulation of hematopoietic stem cell proliferation / positive regulation of neutrophil mediated killing of fungus / cellular response to interleukin-17 / G alpha (i) signalling events / chemokine activity / positive regulation of superoxide anion generation / Neutrophil degranulation / growth factor activity / immune response ...Chemokine receptors bind chemokines / positive regulation of hematopoietic stem cell proliferation / positive regulation of neutrophil mediated killing of fungus / cellular response to interleukin-17 / G alpha (i) signalling events / chemokine activity / positive regulation of superoxide anion generation / Neutrophil degranulation / growth factor activity / immune response / 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
Similarity search - Domain/homology
Growth-regulated alpha protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWhite, M.A. / Sepuru, K.M. / Rajarathnam, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI160613 United States
CitationJournal: To Be Published
Title: Structure of a Mouse KC dimeric mutant
Authors: White, M.A. / Sepuru, K.M. / Rajarathnam, K.
History
DepositionOct 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth-regulated alpha protein
B: Growth-regulated alpha protein


Theoretical massNumber of molelcules
Total (without water)15,7152
Polymers15,7152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, NMR and analytical ultracentrufigation have both confirmed that the KC K28C mutation produces a dimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-13 kcal/mol
Surface area7430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.859, 72.184, 42.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 10 through 13 or resid 15...
d_2ens_1(chain "B" and (resid 10 through 13 or resid 15...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11CYSCYSLEULEUAA10 - 1310 - 13
d_12THRTHRVALVALAA15 - 7115 - 71
d_21CYSCYSLEULEUBB10 - 1310 - 13
d_22THRTHRVALVALBB15 - 7115 - 71

NCS oper: (Code: givenMatrix: (-0.826986617907, 0.147746418562, 0.54246117797), (0.184541565209, -0.840062212013, 0.510137129269), (0.531072070922, 0.521983214051, 0.667454852208)Vector: -22. ...NCS oper: (Code: given
Matrix: (-0.826986617907, 0.147746418562, 0.54246117797), (0.184541565209, -0.840062212013, 0.510137129269), (0.531072070922, 0.521983214051, 0.667454852208)
Vector: -22.3730897817, 34.6458211793, -3.30314066403)

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Components

#1: Protein Growth-regulated alpha protein / C-X-C motif chemokine 1 / Platelet-derived growth factor-inducible protein KC / Secretory protein N51


Mass: 7857.354 Da / Num. of mol.: 2 / Mutation: K28C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cxcl1, Gro, Gro1, Mgsa, Scyb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P12850
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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12% PEG-500MME, 6% PEG-20000, 100 mM of Bicine-Tris (base) pH 8.5, with 100 mM of Molecular Dimension's Carboxylic acids mixture II

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 3, 2019
RadiationMonochromator: Confocal Multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 2854 / % possible obs: 99.8 % / Redundancy: 8 % / Biso Wilson estimate: 47.86 Å2 / CC1/2: 0.931 / CC star: 0.982 / Rpim(I) all: 0.121 / Rrim(I) all: 0.351 / Χ2: 0.894 / Net I/σ(I): 7.8
Reflection shellResolution: 3.2→3.35 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 302 / CC1/2: 0.731 / CC star: 0.919 / Rpim(I) all: 0.682 / Rrim(I) all: 0.975 / Χ2: 0.556 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000v722data reduction
HKL-2000v722data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→28.46 Å / SU ML: 0.4259 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 18.4855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 287 10.07 %Random
Rwork0.2312 2563 --
obs0.2365 2850 64.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.26 Å2
Refinement stepCycle: LAST / Resolution: 3.2→28.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms929 0 0 0 929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003939
X-RAY DIFFRACTIONf_angle_d0.73551278
X-RAY DIFFRACTIONf_chiral_restr0.0469163
X-RAY DIFFRACTIONf_plane_restr0.0052166
X-RAY DIFFRACTIONf_dihedral_angle_d4.1822131
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.11312318099 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-4.030.3739900.2939860X-RAY DIFFRACTION43.06
4.03-28.460.24951970.20611703X-RAY DIFFRACTION85.82
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)
10.1902153638330.104597333819-0.05278328235290.151434074114-0.08581653584930.420060880726-0.00607042978544-0.06063527343960.0859521442940.05545190197370.0401699505722-0.01112778618750.114304170213-0.1610398089180.2118792940640.129792579747-0.00921304946466-0.0653287310990.194233437582-0.08544949396270.175712310502-23.058874578710.4462873035-9.74610951876
20.2331370038040.0924247944850.1266042299210.1638660687310.1104328625020.0992054589244-0.0452654929636-0.03948703723360.137751709336-0.1172534289090.001817197654940.06459110009740.0990262559818-0.0673252113097-0.05157746602130.254591910164-0.223687297359-0.02615644029280.139136491309-0.07101095946850.126158009261-19.41355648176.12009309734-9.54458734945
30.2781729910590.0285638152381-0.1142436112110.67764924317-0.4144619033450.2911262387430.0525266029766-0.125561678794-0.1059242360260.07398276894510.17213411425-0.0612506401459-0.3720143184530.07180604499330.07075088304310.5608563628990.073836380407-0.1816503274080.590922736154-0.1900939546010.389596429332-9.6537592923811.3246184463-2.5109120349
40.5637000681870.203438203441-0.006666075255280.07717131323810.01636965377150.1405558332940.0710092826452-0.1181611464260.2061624956960.0703390482327-0.01964497649360.086935432078-0.1038735451810.02571324226920.7753590173860.262581277439-0.356818858681-0.270531920879-0.00872296227288-0.04212709598840.211290699129-7.6111360689116.7456858614-16.4244301651
50.0737819865177-0.153130765315-0.0200546087070.6023100031780.3066963611460.247316249502-0.0002571010142460.06318060083430.08012573217090.1959503839710.07967112918870.1887271181650.0249910390548-0.05731741517050.1033902713820.141860943322-0.001458676045450.06488952521230.07849105081570.005918187807370.414289793022-10.750549906522.3586334354-17.1539948143
60.03223243327340.02015908876660.004532323091970.061658424513-0.03524350951620.05694630031070.1194381042860.0247567782303-0.02198708451820.0816719143927-0.110606015752-0.001322167038130.09249521978430.100766619538-0.07041576258590.282794046465-0.0669939045127-0.04180342363080.581909263228-0.1167902076180.18853748711-13.708097549521.5039215929-4.44426159331
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 39 )AA7 - 391 - 33
22chain 'A' and (resid 40 through 57 )AA40 - 5734 - 51
33chain 'A' and (resid 58 through 71 )AA58 - 7152 - 65
44chain 'B' and (resid 8 through 42 )BB8 - 421 - 35
55chain 'B' and (resid 43 through 57 )BB43 - 5736 - 50
66chain 'B' and (resid 58 through 71 )BB58 - 7151 - 64

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