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- PDB-1m4r: CRYSTAL STRUCTURE OF RECOMBINANT HUMAN INTERLEUKIN-22 -

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Basic information

Entry
Database: PDB / ID: 1m4r
TitleCRYSTAL STRUCTURE OF RECOMBINANT HUMAN INTERLEUKIN-22
ComponentsInterleukin-22
KeywordsCYTOKINE / interleukin-22 (IL-22) / interleukin-10 (IL-10) / interferon-gamma / cytokines
Function / homology
Function and homology information


interleukin-22 receptor binding / Interleukin-20 family signaling / response to glucocorticoid / acute-phase response / cytokine activity / negative regulation of inflammatory response / Signaling by ALK fusions and activated point mutants / inflammatory response / extracellular space / extracellular region
Similarity search - Function
Interleukin-22 / Interleukin 22 IL-10-related T-cell-derived-inducible factor / Interleukin-10, conserved site / Interleukin-10 family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsNagem, R.A.P. / Colau, D. / Dumoutier, L. / Renauld, J.-C. / Ogata, C. / Polikarpov, I.
Citation
Journal: Structure / Year: 2002
Title: Crystal Structure of Recombinant Human Interleukin-22
Authors: Nagem, R.A.P. / Colau, D. / Dumoutier, L. / Renauld, J.-C. / Ogata, C. / Polikarpov, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and Synchrotron X-ray Diffraction Studies of Human Interleukin-22
Authors: Nagem, R.A.P. / Lucchesi, K.W. / Colau, D. / Dumoutier, L. / Renauld, J.-C. / Polikarpov, I.
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-22
B: Interleukin-22


Theoretical massNumber of molelcules
Total (without water)34,3112
Polymers34,3112
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-7 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.430, 61.610, 73.470
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 Interleukin-22 / IL-22 / IL-10-related T-cell-derived inducible factor / IL-TIF


Mass: 17155.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-codon plus-(DE3)-RIL / References: UniProt: Q9GZX6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.9 sodium tartrate, TRITON X-100 detergent, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.9 Msodium tartrate1reservoir
20.1 MHEPES1reservoirpH7.5
310 mg/mlprotein1drop
420 mMMES1droppH5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2001
RadiationMonochromator: Si (111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→21.72 Å / Num. all: 18125 / Num. obs: 16349 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.8 / % possible all: 82.3
Reflection
*PLUS
Lowest resolution: 21.7 Å / Num. obs: 16382 / % possible obs: 92.7 % / Redundancy: 3.8 % / Num. measured all: 61846
Reflection shell
*PLUS
% possible obs: 82.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.35

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2→21.72 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1118732.49 / Data cutoff high rms absF: 1118732.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 791 5 %RANDOM
Rwork0.188 ---
all0.19 15683 --
obs0.19 15683 89.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.9772 Å2 / ksol: 0.38446 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.58 Å20 Å20 Å2
2---1.25 Å20 Å2
3----3.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→21.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 0 189 2519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 55 4.7 %
Rwork0.219 1845 -
obs-1295 75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 21.7 Å / Num. reflection all: 15684 / Num. reflection obs: 14892 / Num. reflection Rfree: 792 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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