HEADER CYTOKINE 02-JAN-90 2I1B TITLE CRYSTALLOGRAPHIC REFINEMENT OF INTERLEUKIN-1 BETA AT 2.0 ANGSTROMS TITLE 2 RESOLUTION 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; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR J.P.PRIESTLE,H.-P.SCHAER,M.G.GRUETTER REVDAT 7 09-SEP-20 2I1B 1 JRNL REVDAT 6 29-NOV-17 2I1B 1 HELIX REVDAT 5 24-FEB-09 2I1B 1 VERSN REVDAT 4 01-APR-03 2I1B 1 JRNL REVDAT 3 15-JUL-93 2I1B 1 REMARK REVDAT 2 15-OCT-90 2I1B 1 HEADER REVDAT 1 15-APR-90 2I1B 0 JRNL AUTH J.P.PRIESTLE,H.P.SCHAR,M.G.GRUTTER JRNL TITL CRYSTALLOGRAPHIC REFINEMENT OF INTERLEUKIN 1 BETA AT 2.0 A JRNL TITL 2 RESOLUTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 86 9667 1989 JRNL REFN ISSN 0027-8424 JRNL PMID 2602367 JRNL DOI 10.1073/PNAS.86.24.9667 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.P.PRIESTLE,H.-P.SCHAER,M.G.GRUETTER REMARK 1 TITL THE THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN-1BETA REMARK 1 REF BIOCHEM.SOC.TRANS. V. 16 949 1988 REMARK 1 REFN ISSN 0300-5127 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.P.PRIESTLE,H.-P.SCHAER,M.G.GRUETTER REMARK 1 TITL CRYSTAL STRUCTURE OF THE CYTOKINE INTERLEUKIN-1BETA REMARK 1 REF EMBO J. V. 7 339 1988 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.-P.SCHAER,J.P.PRIESTLE,M.G.GRUETTER REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION STUDIES OF REMARK 1 TITL 2 RECOMBINANT HUMAN INTERLEUKIN-1BETA REMARK 1 REF J.BIOL.CHEM. V. 262 13724 1987 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 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) : 0.172 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 : 1219 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 168 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) : 0.010 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.035 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.033 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.010 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.129 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.193 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.240 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.338 ; 0.500 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 2.000 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 17.000; 15.000 REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.995 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.781 ; 6.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.901 ; 10.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 11.476; 15.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AUTHORS DECLARE THAT THE POSITIONS OF REMARK 3 ALA 1, PRO 2, AND SER 153 ARE QUESTIONABLE. ALSO THE POSITIONS REMARK 3 OF THE SIDE CHAINS OF GLN 34, GLU 37, GLN 48, GLU 50, GLU 51, REMARK 3 ASN 53, ASP 54, GLU 64, ASP 75, LYS 77, LYS 88, LYS 93, LYS 94, REMARK 3 LYS 97, AND GLU 141 ARE QUESTIONABLE. REMARK 4 REMARK 4 2I1B 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_1000178237. 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 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 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 (%): 63.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 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 38.40000 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 57.60000 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 19.20000 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 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 OE1 GLU A 111 O HOH A 201 1.86 REMARK 500 O ASP A 76 O HOH A 290 2.10 REMARK 500 O HOH A 237 O HOH A 248 2.12 REMARK 500 N GLY A 33 O HOH A 230 2.13 REMARK 500 O HOH A 224 O HOH A 252 2.15 REMARK 500 O TYR A 24 O HOH A 189 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 192 O HOH A 215 3554 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 LEU A 6 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 ALA A 59 N - CA - CB ANGL. DEV. = 9.0 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 PRO A 2 -94.73 -29.18 REMARK 500 SER A 21 -84.11 -84.69 REMARK 500 ASP A 35 3.82 -67.66 REMARK 500 ILE A 106 -95.33 -103.83 REMARK 500 ASN A 107 -109.49 -58.44 REMARK 500 SER A 152 9.50 -68.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET PRESENTED AS * B1* ON SHEET RECORDS BELOW IS REMARK 700 ACTUALLY A SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED REMARK 700 BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST REMARK 700 STRANDS ARE IDENTICAL. DBREF 2I1B 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 *168(H2 O) HELIX 1 1 GLN A 32 GLU A 37 5 6 HELIX 2 2 GLU A 96 ARG A 98 5 3 SHEET 1 B1 7 ARG A 4 ASP A 12 0 SHEET 2 B1 7 GLN A 39 PHE A 46 -1 N MET A 44 O LEU A 6 SHEET 3 B1 7 ASP A 54 LYS A 63 -1 N ALA A 59 O SER A 45 SHEET 4 B1 7 PHE A 99 ILE A 104 -1 N PHE A 101 O VAL A 58 SHEET 5 B1 7 LYS A 109 ALA A 115 -1 N GLU A 111 O ILE A 104 SHEET 6 B1 7 ILE A 143 SER A 152 -1 N PHE A 146 O LEU A 110 SHEET 7 B1 7 ARG A 4 ASP A 12 -1 N THR A 9 O GLN A 149 SHEET 1 B2 2 LYS A 16 MET A 20 0 SHEET 2 B2 2 GLU A 25 HIS A 30 -1 N LYS A 27 O VAL A 19 SHEET 1 B3 2 ASN A 66 LEU A 73 0 SHEET 2 B3 2 LYS A 77 ASP A 86 -1 N GLN A 81 O SER A 70 SHEET 1 B4 2 TRP A 120 ALA A 127 0 SHEET 2 B4 2 PRO A 131 LYS A 138 -1 N PHE A 133 O SER A 123 CISPEP 1 TYR A 90 PRO A 91 0 -0.51 CRYST1 54.900 54.900 76.800 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 0.018215 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018215 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013021 0.00000 MASTER 298 0 0 2 13 0 0 6 0 0 0 12 END