HEADER IMMUNE SYSTEM 09-JAN-20 6VHI TITLE CRYSTAL STRUCTURE OF THE HUMAN ILRUN FW DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ILRUN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: INFLAMMATION AND LIPID REGULATOR WITH UBA-LIKE AND NBR1-LIKE COMPND 5 DOMAINS PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ILRUN, C6ORF106; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET43 KEYWDS FW DOMAIN, INNATE IMMUNE SYSTEM, IMMUNOGLOBULIN FOLD, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.T.CAPUTO,T.E.ADAMS REVDAT 2 11-OCT-23 6VHI 1 JRNL REMARK REVDAT 1 01-JUL-20 6VHI 0 JRNL AUTH R.L.AMBROSE,A.M.BRICE,A.T.CAPUTO,M.R.ALEXANDER,L.TRIBOLET, JRNL AUTH 2 Y.C.LIU,T.E.ADAMS,A.G.D.BEAN,C.R.STEWART JRNL TITL MOLECULAR CHARACTERISATION OF ILRUN, A NOVEL INHIBITOR OF JRNL TITL 2 PROINFLAMMATORY AND ANTIMICROBIAL CYTOKINES. JRNL REF HELIYON V. 6 04115 2020 JRNL REFN ESSN 2405-8440 JRNL PMID 32518853 JRNL DOI 10.1016/J.HELIYON.2020.E04115 REMARK 2 REMARK 2 RESOLUTION. 2.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4775 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 233 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.46 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2057 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 21 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 834 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -24.30810 REMARK 3 B22 (A**2) : 15.61180 REMARK 3 B33 (A**2) : 8.69640 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -11.98230 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.380 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.352 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.223 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1657 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2988 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 486 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 254 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 854 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 109 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1174 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.11 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.47 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.32 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 23.6769 14.4436 5.7397 REMARK 3 T TENSOR REMARK 3 T11: 0.2483 T22: -0.1838 REMARK 3 T33: -0.2501 T12: 0.0086 REMARK 3 T13: -0.0348 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 4.3979 L22: 2.1781 REMARK 3 L33: 3.8925 L12: 0.9865 REMARK 3 L13: 0.5197 L23: 0.1335 REMARK 3 S TENSOR REMARK 3 S11: 0.0186 S12: -0.0675 S13: 0.0054 REMARK 3 S21: -0.0675 S22: -0.043 S23: -0.3831 REMARK 3 S31: 0.0054 S32: -0.3831 S33: 0.0244 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED LSSR RESTRAINTS GENERATED FROM PDB REMARK 3 ENTRY 4OLE REMARK 4 REMARK 4 6VHI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246406. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.45865 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4775 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.460 REMARK 200 RESOLUTION RANGE LOW (A) : 67.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MRBUMP REMARK 200 STARTING MODEL: 4OLE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M AMMONIUM SULFATE AND 0.15 M REMARK 280 TRISODIUM CITRATE-CITRIC ACID, PH 5.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 67.96550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.48850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.96550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.48850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 64 REMARK 465 PHE A 65 REMARK 465 GLU A 66 REMARK 465 SER A 67 REMARK 465 PRO A 68 REMARK 465 ASN A 69 REMARK 465 ILE A 70 REMARK 465 GLY A 124 REMARK 465 HIS A 125 REMARK 465 VAL A 181 REMARK 465 GLY A 182 REMARK 465 GLY A 183 REMARK 465 LEU A 184 REMARK 465 LEU A 185 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 85 CB CG CD OE1 OE2 REMARK 480 GLU A 87 CB CG CD OE1 OE2 REMARK 480 GLU A 180 CB CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH TYR A 117 O GLY A 120 1.50 REMARK 500 OE2 GLU A 79 HH11 ARG A 100 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 83 72.05 52.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 6VHI A 64 185 UNP Q9H6K1 ILRUN_HUMAN 64 185 SEQRES 1 A 122 ASP PHE GLU SER PRO ASN ILE SER VAL PRO SER MET SER SEQRES 2 A 122 PHE VAL GLU ASP VAL THR ILE GLY GLU GLY GLU SER ILE SEQRES 3 A 122 PRO PRO ASP THR GLN PHE VAL LYS THR TRP ARG ILE GLN SEQRES 4 A 122 ASN SER GLY ALA GLU ALA TRP PRO PRO GLY VAL CYS LEU SEQRES 5 A 122 LYS TYR VAL GLY GLY ASP GLN PHE GLY HIS VAL ASN MET SEQRES 6 A 122 VAL MET VAL ARG SER LEU GLU PRO GLN GLU ILE ALA ASP SEQRES 7 A 122 VAL SER VAL GLN MET CYS SER PRO SER ARG ALA GLY MET SEQRES 8 A 122 TYR GLN GLY GLN TRP ARG MET CYS THR ALA THR GLY LEU SEQRES 9 A 122 TYR TYR GLY ASP VAL ILE TRP VAL ILE LEU SER VAL GLU SEQRES 10 A 122 VAL GLY GLY LEU LEU FORMUL 2 HOH *6(H2 O) SHEET 1 AA1 3 SER A 76 ASP A 80 0 SHEET 2 AA1 3 GLN A 94 GLN A 102 -1 O ARG A 100 N VAL A 78 SHEET 3 AA1 3 ILE A 139 CYS A 147 -1 O MET A 146 N PHE A 95 SHEET 1 AA2 5 SER A 88 ILE A 89 0 SHEET 2 AA2 5 TYR A 168 VAL A 179 1 O SER A 178 N ILE A 89 SHEET 3 AA2 5 GLY A 153 CYS A 162 -1 N GLY A 153 O VAL A 179 SHEET 4 AA2 5 CYS A 114 GLY A 120 -1 N GLY A 119 O GLN A 158 SHEET 5 AA2 5 MET A 128 MET A 130 -1 O VAL A 129 N LEU A 115 CRYST1 135.931 40.977 23.291 90.00 91.43 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007357 0.000000 0.000184 0.00000 SCALE2 0.000000 0.024404 0.000000 0.00000 SCALE3 0.000000 0.000000 0.042948 0.00000