PDB Short entry for 1ILR HEADER BINDING PROTEIN 20-JUN-94 1ILR TITLE CRYSTAL STRUCTURE OF THE INTERLEUKIN-1 RECEPTOR ANTAGONIST COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 RECEPTOR ANTAGONIST PROTEIN; COMPND 3 CHAIN: 1, 2; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.A.SCHREUDER,J.-M.RONDEAU,C.TARDIF REVDAT 3 29-NOV-17 1ILR 1 HELIX REVDAT 2 24-FEB-09 1ILR 1 VERSN REVDAT 1 07-FEB-95 1ILR 0 JRNL AUTH H.A.SCHREUDER,J.M.RONDEAU,C.TARDIF,A.SOFFIENTINI,E.SARUBBI, JRNL AUTH 2 A.AKESON,T.L.BOWLIN,S.YANOFSKY,R.W.BARRETT JRNL TITL REFINED CRYSTAL STRUCTURE OF THE INTERLEUKIN-1 RECEPTOR JRNL TITL 2 ANTAGONIST. PRESENCE OF A DISULFIDE LINK AND A CIS-PROLINE. JRNL REF EUR.J.BIOCHEM. V. 227 838 1995 JRNL REFN ISSN 0014-2956 JRNL PMID 7867645 JRNL DOI 10.1111/J.1432-1033.1995.TB20209.X REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 15610 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 2285 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ILR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 58.65000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.65000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.97500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.65000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.65000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.32500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.65000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.65000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 87.97500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.65000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.65000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.32500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.65000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, 2 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 ARG 1 1 REMARK 465 PRO 1 2 REMARK 465 SER 1 3 REMARK 465 GLY 1 4 REMARK 465 ARG 1 5 REMARK 465 LYS 1 6 REMARK 465 SER 1 7 REMARK 465 ARG 2 1 REMARK 465 PRO 2 2 REMARK 465 SER 2 3 REMARK 465 GLY 2 4 REMARK 465 ARG 2 5 REMARK 465 LYS 2 6 REMARK 465 SER 2 7 REMARK 465 SER 2 8 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP 1 74 CG OD1 OD2 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 SER 1 132 -158.49 -143.91 REMARK 500 GLU 1 139 31.06 -86.57 REMARK 500 PRO 2 53 -81.19 -69.00 REMARK 500 SER 2 72 78.45 -158.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 1ILR 1 1 152 UNP P18510 IL1RA_HUMAN 26 177 DBREF 1ILR 2 1 152 UNP P18510 IL1RA_HUMAN 26 177 SEQRES 1 1 152 ARG PRO SER GLY ARG LYS SER SER LYS MET GLN ALA PHE SEQRES 2 1 152 ARG ILE TRP ASP VAL ASN GLN LYS THR PHE TYR LEU ARG SEQRES 3 1 152 ASN ASN GLN LEU VAL ALA GLY TYR LEU GLN GLY PRO ASN SEQRES 4 1 152 VAL ASN LEU GLU GLU LYS ILE ASP VAL VAL PRO ILE GLU SEQRES 5 1 152 PRO HIS ALA LEU PHE LEU GLY ILE HIS GLY GLY LYS MET SEQRES 6 1 152 CYS LEU SER CYS VAL LYS SER GLY ASP GLU THR ARG LEU SEQRES 7 1 152 GLN LEU GLU ALA VAL ASN ILE THR ASP LEU SER GLU ASN SEQRES 8 1 152 ARG LYS GLN ASP LYS ARG PHE ALA PHE ILE ARG SER ASP SEQRES 9 1 152 SER GLY PRO THR THR SER PHE GLU SER ALA ALA CYS PRO SEQRES 10 1 152 GLY TRP PHE LEU CYS THR ALA MET GLU ALA ASP GLN PRO SEQRES 11 1 152 VAL SER LEU THR ASN MET PRO ASP GLU GLY VAL MET VAL SEQRES 12 1 152 THR LYS PHE TYR PHE GLN GLU ASP GLU SEQRES 1 2 152 ARG PRO SER GLY ARG LYS SER SER LYS MET GLN ALA PHE SEQRES 2 2 152 ARG ILE TRP ASP VAL ASN GLN LYS THR PHE TYR LEU ARG SEQRES 3 2 152 ASN ASN GLN LEU VAL ALA GLY TYR LEU GLN GLY PRO ASN SEQRES 4 2 152 VAL ASN LEU GLU GLU LYS ILE ASP VAL VAL PRO ILE GLU SEQRES 5 2 152 PRO HIS ALA LEU PHE LEU GLY ILE HIS GLY GLY LYS MET SEQRES 6 2 152 CYS LEU SER CYS VAL LYS SER GLY ASP GLU THR ARG LEU SEQRES 7 2 152 GLN LEU GLU ALA VAL ASN ILE THR ASP LEU SER GLU ASN SEQRES 8 2 152 ARG LYS GLN ASP LYS ARG PHE ALA PHE ILE ARG SER ASP SEQRES 9 2 152 SER GLY PRO THR THR SER PHE GLU SER ALA ALA CYS PRO SEQRES 10 2 152 GLY TRP PHE LEU CYS THR ALA MET GLU ALA ASP GLN PRO SEQRES 11 2 152 VAL SER LEU THR ASN MET PRO ASP GLU GLY VAL MET VAL SEQRES 12 2 152 THR LYS PHE TYR PHE GLN GLU ASP GLU FORMUL 3 HOH *139(H2 O) HELIX 1 H1 GLY 1 37 LEU 1 42 5 6 HELIX 2 H2A ILE 1 85 ASP 1 87 5ONLY IN MOLECULE 1 3 HELIX 3 H2 LYS 1 93 PHE 1 98 5 6 HELIX 4 BH1 GLY 2 37 LEU 2 42 5 6 HELIX 5 BH2 LYS 2 93 PHE 2 98 5 6 SHEET 1 B1 7 GLN 1 11 ASP 1 17 0 SHEET 2 B1 7 ILE 1 46 ILE 1 51 -1 SHEET 3 B1 7 ALA 1 55 ILE 1 60 -1 SHEET 4 B1 7 ALA 1 99 SER 1 105 -1 SHEET 5 B1 7 THR 1 108 SER 1 113 -1 SHEET 6 B1 7 PHE 1 146 GLU 1 150 -1 SHEET 7 B1 7 GLN 1 11 ASP 1 17 -1 SHEET 1 B2 7 GLN 2 11 ASP 2 17 0 SHEET 2 B2 7 ILE 2 46 ILE 2 51 -1 SHEET 3 B2 7 ALA 2 55 ILE 2 60 -1 SHEET 4 B2 7 ALA 2 99 SER 2 105 -1 SHEET 5 B2 7 THR 2 108 SER 2 113 -1 SHEET 6 B2 7 PHE 2 146 GLU 2 150 -1 SHEET 7 B2 7 GLN 2 11 ASP 2 17 -1 SSBOND 1 CYS 1 69 CYS 1 116 1555 1555 2.03 SSBOND 2 CYS 2 69 CYS 2 116 1555 1555 2.03 CISPEP 1 GLU 1 52 PRO 1 53 0 -0.32 CISPEP 2 GLU 2 52 PRO 2 53 0 1.86 CRYST1 71.300 71.300 117.300 90.00 90.00 90.00 P 43 21 2 16 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 0.014025 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008525 0.00000 MTRIX1 1 0.342973 0.714236 -0.610110 13.45390 1 MTRIX2 1 -0.829805 0.534758 0.159550 50.85968 1 MTRIX3 1 0.440219 0.451551 0.776085 -7.88375 1