HEADER CYTOKINE 29-JAN-91 8I1B TITLE A COMPARISON OF THE HIGH RESOLUTION STRUCTURES OF HUMAN AND MURINE TITLE 2 INTERLEUKIN-1B 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: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090 KEYWDS CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR D.H.OHLENDORF,P.C.WEBER,F.R.SALEMME REVDAT 5 14-FEB-24 8I1B 1 REMARK REVDAT 4 29-NOV-17 8I1B 1 HELIX REVDAT 3 24-FEB-09 8I1B 1 VERSN REVDAT 2 15-OCT-94 8I1B 1 AUTHOR REVDAT 1 15-JUL-92 8I1B 0 JRNL AUTH D.H.OHLENDORF,A.C.TREHARNE,P.C.WEBER,J.J.WENDOLOSKI, JRNL AUTH 2 F.R.SALEMME JRNL TITL A COMPARISON OF THE HIGH RESOLUTION STRUCTURES OF HUMAN AND JRNL TITL 2 MURINE INTERLEUKIN-1B JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6771 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) : 0.159 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 : 1179 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 86 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) : 0.021 ; 0.030 REMARK 3 ANGLE DISTANCE (A) : 0.038 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.038 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.015 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.260 ; 0.300 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.217 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.253 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.220 ; 0.500 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) : 1.047 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.917 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.521 ; 1.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.551 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8I1B 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_1000179978. 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 (%): 65.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 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 39.50000 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 59.25000 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 19.75000 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 400 REMARK 400 COMPOUND REMARK 400 THE MOLECULE CAN BE DIVIDED INTO THREE SIMILAR MOTIFS, REMARK 400 (RESIDUES 1 - 55, RESIDUES 56 - 107, AND RESIDUES 108 - REMARK 400 153). THESE MOTIFS ARE RELATED BY A LOCAL THREE-FOLD AXIS. REMARK 400 THE TRANSFORMATION PRESENTED IN MTRIX 1 PRODUCES MOTIFS BCA REMARK 400 FROM MOTIFS ABC. THE TRANSFORMATION PRESENTED IN MTRIX 2 REMARK 400 PRODUCES MOTIFS CAB FROM MOTIFS ABC. 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 VAL A 1 REMARK 465 PRO A 2 REMARK 465 ILE A 3 REMARK 465 ARG A 4 REMARK 465 SER A 152 REMARK 465 SER A 153 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 OE2 GLU A 111 OD1 ASP A 145 2.19 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 9 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 9 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 11 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 LYS A 27 N - CA - CB ANGL. DEV. = 12.0 DEGREES REMARK 500 ILE A 36 CB - CA - C ANGL. DEV. = 13.2 DEGREES REMARK 500 SER A 43 N - CA - CB ANGL. DEV. = 10.9 DEGREES REMARK 500 PRO A 51 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 ASP A 54 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 SER A 70 N - CA - CB ANGL. DEV. = -11.7 DEGREES REMARK 500 LYS A 92 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 MET A 95 CA - CB - CG ANGL. DEV. = 13.4 DEGREES REMARK 500 GLU A 128 OE1 - CD - OE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 THR A 147 CA - CB - CG2 ANGL. DEV. = 11.6 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 ASP A 22 -63.29 -4.02 REMARK 500 PRO A 23 37.89 -70.25 REMARK 500 ASN A 35 43.94 -93.35 REMARK 500 PRO A 51 136.79 -16.18 REMARK 500 SER A 52 -168.36 -54.18 REMARK 500 ASN A 53 22.66 138.79 REMARK 500 ASP A 54 37.31 76.15 REMARK 500 ASN A 66 48.73 -92.56 REMARK 500 SER A 108 -14.94 79.58 REMARK 500 GLN A 141 -36.28 78.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 SOLVENT MOLECULES 201, 202 AND 204 COORDINATE THE REMARK 600 INTERSECTIONS OF THREE BETA STRANDS. REMARK 700 REMARK 700 SHEET REMARK 700 THE ARRANGEMENT OF THE STRANDS IN IL-1 MAKES A SHEET REMARK 700 DESIGNATION MEANINGLESS. THE 12 STRANDS HAVE BEEN REMARK 700 PRESENTED AS 12 SHEETS OF ONE STRAND EACH ON THE SHEET REMARK 700 RECORDS BELOW. THE FIRST GROUP OF FOUR STRANDS ARE PART OF REMARK 700 MOTIF A. THE SECOND GROUP OF FOUR STRANDS ARE PART OF REMARK 700 MOTIF B. THE THIRD GROUP OF FOUR STRANDS ARE PART OF MOTIF REMARK 700 C. REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES HAVE BEEN NUMBERED TO AGREE WITH HUMAN IL-1BETA. REMARK 999 THIS MEANS THERE IS NO RESIDUE 140. DBREF 8I1B A 1 153 UNP P10749 IL1B_MOUSE 118 269 SEQRES 1 A 152 VAL PRO ILE ARG GLN LEU HIS TYR ARG LEU ARG ASP GLU SEQRES 2 A 152 GLN GLN LYS SER LEU VAL LEU SER ASP PRO TYR GLU LEU SEQRES 3 A 152 LYS ALA LEU HIS LEU ASN GLY GLN ASN ILE ASN GLN GLN SEQRES 4 A 152 VAL ILE PHE SER MET SER PHE VAL GLN GLY GLU PRO SER SEQRES 5 A 152 ASN ASP LYS ILE PRO VAL ALA LEU GLY LEU LYS GLY LYS SEQRES 6 A 152 ASN LEU TYR LEU SER CYS VAL MET LYS ASP GLY THR PRO SEQRES 7 A 152 THR LEU GLN LEU GLU SER VAL ASP PRO LYS GLN TYR PRO SEQRES 8 A 152 LYS LYS LYS MET GLU LYS ARG PHE VAL PHE ASN LYS ILE SEQRES 9 A 152 GLU VAL LYS SER LYS VAL GLU PHE GLU SER ALA GLU PHE SEQRES 10 A 152 PRO ASN TRP TYR ILE SER THR SER GLN ALA GLU HIS LYS SEQRES 11 A 152 PRO VAL PHE LEU GLY ASN ASN SER GLY GLN ASP ILE ILE SEQRES 12 A 152 ASP PHE THR MET GLU SER VAL SER SER FORMUL 2 HOH *86(H2 O) HELIX 1 HA GLY A 33 GLN A 38 5MOTIF A LOOP 3 (KINKED) 6 SHEET 1 SA1 1 LEU A 6 ASP A 12 0 SHEET 1 SA2 1 SER A 17 SER A 21 0 SHEET 1 SA3 1 GLU A 25 LEU A 29 0 SHEET 1 SA4 1 PHE A 42 PHE A 46 0 SHEET 1 SB1 1 LYS A 55 LEU A 62 0 SHEET 1 SB2 1 LEU A 67 LYS A 74 0 SHEET 1 SB3 1 THR A 77 SER A 84 0 SHEET 1 SB4 1 VAL A 100 VAL A 106 0 SHEET 1 SC1 1 LYS A 109 SER A 114 0 SHEET 1 SC2 1 TYR A 121 SER A 123 0 SHEET 1 SC3 1 LYS A 130 GLY A 135 0 SHEET 1 SC4 1 PHE A 146 SER A 150 0 CISPEP 1 TYR A 90 PRO A 91 0 0.29 CRYST1 55.710 55.710 79.000 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 0.017950 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017950 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012658 0.00000 MTRIX1 1 -0.454410 -0.688380 0.565370 29.25200 1 MTRIX2 1 0.227770 0.523790 0.820830 7.63800 1 MTRIX3 1 -0.861180 0.501770 -0.081230 -1.70600 1 MTRIX1 2 -0.454410 0.227770 -0.861180 10.08300 1 MTRIX2 2 -0.688380 0.523790 0.501770 16.99200 1 MTRIX3 2 0.565370 0.820830 -0.082130 -22.94600 1