PDB Short entry for 4I1B HEADER CYTOKINE 27-MAR-90 4I1B TITLE FUNCTIONAL IMPLICATIONS OF INTERLEUKIN-1BETA BASED ON THE THREE- TITLE 2 DIMENSIONAL STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 BETA; COMPND 3 CHAIN: A; 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 CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR B.VEERAPANDIAN,T.L.POULOS,G.L.GILLILAND,R.RAAG,L.A.SVENSSON,Y.MASUI, AUTHOR 2 Y.HIRAI REVDAT 5 28-FEB-24 4I1B 1 REMARK REVDAT 4 24-FEB-09 4I1B 1 VERSN REVDAT 3 15-JAN-93 4I1B 1 SOURCE JRNL REMARK REVDAT 2 15-JUL-92 4I1B 1 AUTHOR REVDAT 1 15-APR-90 4I1B 0 JRNL AUTH B.VEERAPANDIAN,G.L.GILLILAND,R.RAAG,A.L.SVENSSON,Y.MASUI, JRNL AUTH 2 Y.HIRAI,T.L.POULOS JRNL TITL FUNCTIONAL IMPLICATIONS OF INTERLEUKIN-1 BETA BASED ON THE JRNL TITL 2 THREE-DIMENSIONAL STRUCTURE. JRNL REF PROTEINS V. 12 10 1992 JRNL REFN ISSN 0887-3585 JRNL PMID 1553379 JRNL DOI 10.1002/PROT.340120103 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.L.GILLILAND,E.L.WINBORNE,Y.MASUI,Y.HIRAI REMARK 1 TITL A PRELIMINARY CRYSTALLOGRAPHIC STUDY OF RECOMBINANT HUMAN REMARK 1 TITL 2 INTERLEUKIN 1BETA REMARK 1 REF J.BIOL.CHEM. V. 262 12323 1987 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : RESTRAIN REMARK 3 AUTHORS : MOSS,DRIESSEN,HANEEF,HOWLIN,HARRIS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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 + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1207 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 91 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.020 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.039 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4I1B 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_1000179346. 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 38.33000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.49500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.16500 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 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 ALA A 1 REMARK 465 PRO A 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 20 CG - SD - CE ANGL. DEV. = 11.4 DEGREES REMARK 500 MET A 44 CG - SD - CE ANGL. DEV. = 11.0 DEGREES REMARK 500 ASP A 54 CB - CG - OD1 ANGL. DEV. = 8.2 DEGREES REMARK 500 LEU A 60 CB - CG - CD1 ANGL. DEV. = 11.4 DEGREES REMARK 500 VAL A 85 CA - CB - CG2 ANGL. DEV. = 12.6 DEGREES REMARK 500 MET A 95 CG - SD - CE ANGL. DEV. = 13.9 DEGREES REMARK 500 VAL A 100 CA - CB - CG2 ANGL. DEV. = 9.4 DEGREES REMARK 500 GLN A 141 N - CA - CB ANGL. DEV. = 12.2 DEGREES REMARK 500 MET A 148 CG - SD - CE ANGL. DEV. = 10.2 DEGREES REMARK 500 SER A 153 C - N - CA ANGL. DEV. = 21.5 DEGREES 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 CYS A 8 146.01 -175.35 REMARK 500 SER A 21 -78.57 -80.31 REMARK 500 TYR A 24 10.64 -147.38 REMARK 500 GLN A 38 5.02 -65.61 REMARK 500 ASP A 75 41.66 90.29 REMARK 500 ASN A 107 67.44 78.45 REMARK 500 GLN A 141 -76.66 -150.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 4I1B A 1 153 UNP P01584 IL1B_HUMAN 117 269 SEQRES 1 A 153 ALA PRO VAL ARG SER LEU ASN CYS THR LEU ARG ASP SER SEQRES 2 A 153 GLN GLN LYS SER LEU VAL MET SER GLY PRO TYR GLU LEU SEQRES 3 A 153 LYS ALA LEU HIS LEU GLN GLY GLN ASP MET GLU GLN GLN SEQRES 4 A 153 VAL VAL PHE SER MET SER PHE VAL GLN GLY GLU GLU SER SEQRES 5 A 153 ASN ASP LYS ILE PRO VAL ALA LEU GLY LEU LYS GLU LYS SEQRES 6 A 153 ASN LEU TYR LEU SER CYS VAL LEU LYS ASP ASP LYS PRO SEQRES 7 A 153 THR LEU GLN LEU GLU SER VAL ASP PRO LYS ASN TYR PRO SEQRES 8 A 153 LYS LYS LYS MET GLU LYS ARG PHE VAL PHE ASN LYS ILE SEQRES 9 A 153 GLU ILE ASN ASN LYS LEU GLU PHE GLU SER ALA GLN PHE SEQRES 10 A 153 PRO ASN TRP TYR ILE SER THR SER GLN ALA GLU ASN MET SEQRES 11 A 153 PRO VAL PHE LEU GLY GLY THR LYS GLY GLY GLN ASP ILE SEQRES 12 A 153 THR ASP PHE THR MET GLN PHE VAL SER SER FORMUL 2 HOH *91(H2 O) HELIX 1 1 GLN A 32 GLN A 39 5 8 HELIX 2 2 GLU A 96 PHE A 99 5 4 SHEET 1 BAR 7 ARG A 4 ASP A 12 0 SHEET 2 BAR 7 VAL A 40 GLN A 48 -1 O MET A 44 N LEU A 6 SHEET 3 BAR 7 LYS A 55 LEU A 62 -1 O ALA A 59 N SER A 45 SHEET 4 BAR 7 VAL A 100 ILE A 106 -1 O LYS A 103 N ILE A 56 SHEET 5 BAR 7 LYS A 109 ALA A 115 -1 O LYS A 109 N ILE A 106 SHEET 6 BAR 7 ILE A 143 VAL A 151 -1 O PHE A 146 N LEU A 110 SHEET 7 BAR 7 ARG A 4 ASP A 12 -1 N THR A 9 O GLN A 149 SHEET 1 S2 2 SER A 17 SER A 21 0 SHEET 2 S2 2 GLU A 25 LEU A 29 -1 O LEU A 29 N SER A 17 SHEET 1 S3 2 ASN A 66 LYS A 74 0 SHEET 2 S3 2 LYS A 77 VAL A 85 -1 O LYS A 77 N LYS A 74 SHEET 1 S4 2 TRP A 120 SER A 125 0 SHEET 2 S4 2 MET A 130 GLY A 135 -1 O GLY A 135 N TYR A 121 CISPEP 1 TYR A 90 PRO A 91 0 8.37 CRYST1 55.140 55.140 76.660 90.00 90.00 90.00 P 43 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 0.018136 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018136 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013045 0.00000