HEADER IMMUNE SYSTEM 28-NOV-14 4X38 TITLE GALLUS INTERLEUKIN-1 BETA MUTANT - E118A COMPND MOL_ID: 1; COMPND 2 MOLECULE: IL-1 BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: INTERLEUKIN-1 BETA,INTERLEUKIN-1BETA; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: IL-1BETA, IL1B, IL1BETA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR H.S.YIN,W.T.CHENG REVDAT 1 09-DEC-15 4X38 0 JRNL AUTH H.S.YIN,W.T.CHENG JRNL TITL GALLUS INTERLEUKIN-1 BETA MUTANT - E118A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 6564 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 324 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.12 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 213 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 40.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 14 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1174 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : 0.22000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.354 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.239 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.425 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1199 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1149 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1624 ; 1.456 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2636 ; 0.796 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 146 ; 7.885 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 53 ;34.955 ;23.019 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 201 ;16.221 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;14.977 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 185 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1338 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 282 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 593 ; 2.082 ; 2.489 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 592 ; 2.083 ; 2.485 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 736 ; 3.684 ; 3.685 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 737 ; 3.682 ; 3.689 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 606 ; 2.337 ; 2.698 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 607 ; 2.336 ; 2.701 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 889 ; 3.903 ; 3.939 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1271 ; 6.365 ;19.009 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1269 ; 6.366 ;19.018 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4X38 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000204989. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : DENZO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7853 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.120 REMARK 200 RESOLUTION RANGE LOW (A) : 24.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2WRY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.15 M (NH4)2SO4, 0.1 M TRIS, 0.2 M REMARK 280 LISO4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.83500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.13700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.87900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.13700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.83500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.87900 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 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 ALA A 1 REMARK 465 PRO A 2 REMARK 465 GLY A 37 REMARK 465 PRO A 38 REMARK 465 SER A 39 REMARK 465 SER A 40 REMARK 465 PRO A 56 REMARK 465 ARG A 57 REMARK 465 GLY A 58 REMARK 465 SER A 59 REMARK 465 ALA A 60 REMARK 465 GLY A 61 REMARK 465 ARG A 162 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 GLN A 36 CG CD OE1 NE2 REMARK 470 GLN A 42 CG CD OE1 NE2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4X37 RELATED DB: PDB REMARK 900 RELATED ID: 4X39 RELATED DB: PDB REMARK 900 RELATED ID: 4X3A RELATED DB: PDB DBREF 4X38 A 1 162 UNP O73909 O73909_CHICK 106 267 SEQADV 4X38 HIS A -5 UNP O73909 EXPRESSION TAG SEQADV 4X38 HIS A -4 UNP O73909 EXPRESSION TAG SEQADV 4X38 HIS A -3 UNP O73909 EXPRESSION TAG SEQADV 4X38 HIS A -2 UNP O73909 EXPRESSION TAG SEQADV 4X38 HIS A -1 UNP O73909 EXPRESSION TAG SEQADV 4X38 HIS A 0 UNP O73909 EXPRESSION TAG SEQADV 4X38 ALA A 118 UNP O73909 GLU 223 ENGINEERED MUTATION SEQRES 1 A 168 HIS HIS HIS HIS HIS HIS ALA PRO ALA PHE ARG TYR THR SEQRES 2 A 168 ARG SER GLN SER PHE ASP ILE PHE ASP ILE ASN GLN LYS SEQRES 3 A 168 CYS PHE VAL LEU GLU SER PRO THR GLN LEU VAL ALA LEU SEQRES 4 A 168 HIS LEU GLN GLY PRO SER SER SER GLN LYS VAL ARG LEU SEQRES 5 A 168 ASN ILE ALA LEU TYR ARG PRO ARG GLY PRO ARG GLY SER SEQRES 6 A 168 ALA GLY THR GLY GLN MET PRO VAL ALA LEU GLY ILE LYS SEQRES 7 A 168 GLY TYR LYS LEU TYR MET SER CYS VAL MET SER GLY THR SEQRES 8 A 168 GLU PRO THR LEU GLN LEU GLU GLU ALA ASP VAL MET ARG SEQRES 9 A 168 ASP ILE ASP SER VAL GLU LEU THR ARG PHE ILE PHE TYR SEQRES 10 A 168 ARG LEU ASP SER PRO THR ALA GLY THR THR ARG PHE GLU SEQRES 11 A 168 SER ALA ALA PHE PRO GLY TRP PHE ILE CYS THR SER LEU SEQRES 12 A 168 GLN PRO ARG GLN PRO VAL GLY ILE THR ASN GLN PRO ASP SEQRES 13 A 168 GLN VAL ASN ILE ALA THR TYR LYS LEU SER GLY ARG FORMUL 2 HOH *27(H2 O) HELIX 1 AA1 VAL A 103 ARG A 107 5 5 SHEET 1 AA1 6 GLU A 86 GLU A 92 0 SHEET 2 AA1 6 LEU A 76 SER A 83 -1 N SER A 79 O GLN A 90 SHEET 3 AA1 6 MET A 65 ILE A 71 -1 N ILE A 71 O LEU A 76 SHEET 4 AA1 6 LEU A 46 ARG A 52 -1 N TYR A 51 O PRO A 66 SHEET 5 AA1 6 PHE A 4 ASP A 16 -1 N ARG A 8 O LEU A 50 SHEET 6 AA1 6 ASP A 99 ILE A 100 -1 O ILE A 100 N PHE A 4 SHEET 1 AA2 8 GLU A 86 GLU A 92 0 SHEET 2 AA2 8 LEU A 76 SER A 83 -1 N SER A 79 O GLN A 90 SHEET 3 AA2 8 MET A 65 ILE A 71 -1 N ILE A 71 O LEU A 76 SHEET 4 AA2 8 ILE A 109 ASP A 114 -1 O PHE A 110 N VAL A 67 SHEET 5 AA2 8 THR A 121 SER A 125 -1 O ARG A 122 N LEU A 113 SHEET 6 AA2 8 TYR A 157 SER A 160 -1 O TYR A 157 N THR A 121 SHEET 7 AA2 8 PHE A 4 ASP A 16 -1 N ASP A 13 O SER A 160 SHEET 8 AA2 8 ASP A 99 ILE A 100 -1 O ILE A 100 N PHE A 4 SHEET 1 AA3 3 CYS A 21 SER A 26 0 SHEET 2 AA3 3 GLN A 29 LEU A 33 -1 O GLN A 29 N GLU A 25 SHEET 3 AA3 3 GLN A 141 PRO A 142 -1 O GLN A 141 N ALA A 32 SHEET 1 AA4 2 PHE A 132 CYS A 134 0 SHEET 2 AA4 2 GLY A 144 THR A 146 -1 O GLY A 144 N CYS A 134 CRYST1 35.670 35.758 102.274 90.00 90.00 90.00 P 21 21 21 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 0.028035 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009778 0.00000 MASTER 272 0 0 1 19 0 0 6 0 0 0 13 END