PDB Short entry for 4GAF HEADER SIGNALING PROTEIN 25-JUL-12 4GAF TITLE CRYSTAL STRUCTURE OF EBI-005, A CHIMERA OF HUMAN IL-1BETA AND IL-1RA, TITLE 2 BOUND TO HUMAN INTERLEUKIN-1 RECEPTOR TYPE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EBI-005; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: INTERLEUKIN-1 RECEPTOR TYPE 1; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: UNP RESIDUES 18-336; COMPND 9 SYNONYM: IL-1R-1, IL-1RT-1, IL-1RT1, CD121 ANTIGEN-LIKE FAMILY MEMBER COMPND 10 A, INTERLEUKIN-1 RECEPTOR ALPHA, IL-1R-ALPHA, INTERLEUKIN-1 RECEPTOR COMPND 11 TYPE I, P80, INTERLEUKIN-1 RECEPTOR TYPE 1, MEMBRANE FORM, MIL-1R1, COMPND 12 MIL-1RI, INTERLEUKIN-1 RECEPTOR TYPE 1, SOLUBLE FORM, SIL-1R1, SIL- COMPND 13 1RI; COMPND 14 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; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: IL1R1, IL1R, IL1RA, IL1RT1; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IL-1BETA, IL-1RA, IL-1R1, IL-1 SIGNALING, BETA-TREFOIL, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.HOU,S.A.TOWNSON,J.T.KOVALCHIN,A.MASCI,O.KINER,Y.SHU,B.KING, AUTHOR 2 C.THOMAS,K.C.GARCIA,E.S.FURFINE,T.M.BARNES REVDAT 4 29-JUL-20 4GAF 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 15-NOV-17 4GAF 1 REMARK REVDAT 2 27-MAR-13 4GAF 1 JRNL REVDAT 1 20-FEB-13 4GAF 0 JRNL AUTH J.HOU,S.A.TOWNSON,J.T.KOVALCHIN,A.MASCI,O.KINER,Y.SHU, JRNL AUTH 2 B.M.KING,E.SCHIRMER,K.GOLDEN,C.THOMAS,K.C.GARCIA, JRNL AUTH 3 G.ZARBIS-PAPASTOITSIS,E.S.FURFINE,T.M.BARNES JRNL TITL DESIGN OF A SUPERIOR CYTOKINE ANTAGONIST FOR TOPICAL JRNL TITL 2 OPHTHALMIC USE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 3913 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23431173 JRNL DOI 10.1073/PNAS.1217996110 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31383 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1585 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2148 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3716 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 209 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : -0.59000 REMARK 3 B33 (A**2) : 0.41000 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): 0.255 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.218 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.350 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3904 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5304 ; 1.983 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 465 ; 7.479 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 186 ;37.358 ;25.161 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 688 ;18.993 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;22.557 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 583 ; 0.145 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2960 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2314 ; 1.232 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3779 ; 2.209 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1590 ; 3.324 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1521 ; 5.356 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 21 REMARK 3 RESIDUE RANGE : A 22 A 53 REMARK 3 RESIDUE RANGE : A 54 A 116 REMARK 3 RESIDUE RANGE : A 117 A 152 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5020 -33.2310 11.5070 REMARK 3 T TENSOR REMARK 3 T11: 0.1166 T22: 0.1142 REMARK 3 T33: 0.0474 T12: -0.1007 REMARK 3 T13: 0.0193 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 2.5823 L22: 4.1355 REMARK 3 L33: 3.4976 L12: 1.2555 REMARK 3 L13: -0.4896 L23: -1.0404 REMARK 3 S TENSOR REMARK 3 S11: 0.2051 S12: -0.1420 S13: 0.1352 REMARK 3 S21: 0.1936 S22: -0.1081 S23: -0.0933 REMARK 3 S31: -0.1646 S32: 0.1422 S33: -0.0971 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 69 REMARK 3 RESIDUE RANGE : B 70 B 166 REMARK 3 RESIDUE RANGE : B 167 B 204 REMARK 3 RESIDUE RANGE : B 205 B 313 REMARK 3 ORIGIN FOR THE GROUP (A): -5.8510 -39.8700 16.7530 REMARK 3 T TENSOR REMARK 3 T11: 0.1543 T22: 0.2238 REMARK 3 T33: 0.0691 T12: -0.0812 REMARK 3 T13: -0.0034 T23: 0.0380 REMARK 3 L TENSOR REMARK 3 L11: 0.3040 L22: 3.6745 REMARK 3 L33: 0.0348 L12: 0.9541 REMARK 3 L13: 0.0355 L23: 0.0008 REMARK 3 S TENSOR REMARK 3 S11: -0.0685 S12: 0.0839 S13: 0.0208 REMARK 3 S21: -0.2749 S22: 0.0696 S23: -0.0530 REMARK 3 S31: 0.0046 S32: 0.0567 S33: -0.0011 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 4GAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073940. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9755 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31476 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 100 MM TRIS, 200 MM REMARK 280 LITHIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, REMARK 280 PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.08500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.08500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.17500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 74.63500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.17500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 74.63500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.08500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.17500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 74.63500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.08500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.17500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 74.63500 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER A 153 REMARK 465 LEU B 1 REMARK 465 GLU B 2 REMARK 465 ALA B 3 REMARK 465 ARG B 82 REMARK 465 ASN B 83 REMARK 465 SER B 84 REMARK 465 SER B 85 REMARK 465 VAL B 314 REMARK 465 THR B 315 REMARK 465 ASN B 316 REMARK 465 PHE B 317 REMARK 465 GLN B 318 REMARK 465 LYS B 319 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 NH2 ARG A 21 OE2 GLU B 11 2.15 REMARK 500 O SER B 93 O HOH B 741 2.18 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 VAL B 24 CB - CA - C ANGL. DEV. = -14.6 DEGREES REMARK 500 PRO B 206 C - N - CA ANGL. DEV. = 9.8 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 ASN A 22 -121.83 45.45 REMARK 500 ASN A 118 -2.74 78.98 REMARK 500 LYS B 5 119.85 84.11 REMARK 500 ASN B 32 -40.52 128.98 REMARK 500 LYS B 35 71.13 120.31 REMARK 500 ASP B 43 -129.16 62.64 REMARK 500 ASN B 102 18.63 58.15 REMARK 500 ALA B 118 -0.85 78.79 REMARK 500 LYS B 161 -112.83 53.68 REMARK 500 VAL B 169 127.08 -37.81 REMARK 500 GLU B 202 150.06 -48.70 REMARK 500 ASN B 204 92.11 -65.06 REMARK 500 PRO B 206 92.48 -58.31 REMARK 500 PRO B 214 -178.53 -69.12 REMARK 500 ALA B 215 47.13 -140.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 505 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 18 OG REMARK 620 2 GLU B 21 OE1 84.0 REMARK 620 3 THR B 193 O 171.1 90.0 REMARK 620 4 THR B 193 OG1 93.1 78.7 79.3 REMARK 620 5 HOH B 627 O 84.3 167.5 101.2 97.7 REMARK 620 6 HOH B 642 O 92.8 85.3 93.2 162.2 99.6 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GAI RELATED DB: PDB DBREF 4GAF B 1 319 UNP P14778 IL1R1_HUMAN 18 336 DBREF 4GAF A 1 153 PDB 4GAF 4GAF 1 153 SEQRES 1 A 153 ALA PRO VAL ARG SER LEU ASN CYS ARG ILE TRP ASP VAL SEQRES 2 A 153 ASN GLN LYS THR PHE TYR LEU ARG ASN ASN GLN LEU VAL SEQRES 3 A 153 ALA GLY TYR LEU GLN GLY PRO ASN VAL ASN LEU GLU GLU SEQRES 4 A 153 LYS PHE SER MET SER PHE VAL GLN GLY GLU GLU SER ASN SEQRES 5 A 153 ASP LYS ILE PRO VAL ALA LEU GLY LEU LYS GLU LYS ASN SEQRES 6 A 153 LEU TYR LEU SER CYS VAL LEU LYS ASP ASP LYS PRO THR SEQRES 7 A 153 LEU GLN LEU GLU SER VAL ASP PRO LYS ASN TYR PRO LYS SEQRES 8 A 153 LYS LYS MET GLU LYS ARG PHE VAL PHE ASN LYS ILE GLU SEQRES 9 A 153 ILE ASN ASN LYS LEU GLU PHE GLU SER ALA GLN PHE PRO SEQRES 10 A 153 ASN TRP PHE LEU CYS THR ALA MET GLU ALA ASP GLN PRO SEQRES 11 A 153 VAL SER LEU THR ASN MET PRO ASP GLU GLY VAL MET VAL SEQRES 12 A 153 THR LYS PHE TYR MET GLN PHE VAL SER SER SEQRES 1 B 319 LEU GLU ALA ASP LYS CYS LYS GLU ARG GLU GLU LYS ILE SEQRES 2 B 319 ILE LEU VAL SER SER ALA ASN GLU ILE ASP VAL ARG PRO SEQRES 3 B 319 CYS PRO LEU ASN PRO ASN GLU HIS LYS GLY THR ILE THR SEQRES 4 B 319 TRP TYR LYS ASP ASP SER LYS THR PRO VAL SER THR GLU SEQRES 5 B 319 GLN ALA SER ARG ILE HIS GLN HIS LYS GLU LYS LEU TRP SEQRES 6 B 319 PHE VAL PRO ALA LYS VAL GLU ASP SER GLY HIS TYR TYR SEQRES 7 B 319 CYS VAL VAL ARG ASN SER SER TYR CYS LEU ARG ILE LYS SEQRES 8 B 319 ILE SER ALA LYS PHE VAL GLU ASN GLU PRO ASN LEU CYS SEQRES 9 B 319 TYR ASN ALA GLN ALA ILE PHE LYS GLN LYS LEU PRO VAL SEQRES 10 B 319 ALA GLY ASP GLY GLY LEU VAL CYS PRO TYR MET GLU PHE SEQRES 11 B 319 PHE LYS ASN GLU ASN ASN GLU LEU PRO LYS LEU GLN TRP SEQRES 12 B 319 TYR LYS ASP CYS LYS PRO LEU LEU LEU ASP ASN ILE HIS SEQRES 13 B 319 PHE SER GLY VAL LYS ASP ARG LEU ILE VAL MET ASN VAL SEQRES 14 B 319 ALA GLU LYS HIS ARG GLY ASN TYR THR CYS HIS ALA SER SEQRES 15 B 319 TYR THR TYR LEU GLY LYS GLN TYR PRO ILE THR ARG VAL SEQRES 16 B 319 ILE GLU PHE ILE THR LEU GLU GLU ASN LYS PRO THR ARG SEQRES 17 B 319 PRO VAL ILE VAL SER PRO ALA ASN GLU THR MET GLU VAL SEQRES 18 B 319 ASP LEU GLY SER GLN ILE GLN LEU ILE CYS ASN VAL THR SEQRES 19 B 319 GLY GLN LEU SER ASP ILE ALA TYR TRP LYS TRP ASN GLY SEQRES 20 B 319 SER VAL ILE ASP GLU ASP ASP PRO VAL LEU GLY GLU ASP SEQRES 21 B 319 TYR TYR SER VAL GLU ASN PRO ALA ASN LYS ARG ARG SER SEQRES 22 B 319 THR LEU ILE THR VAL LEU ASN ILE SER GLU ILE GLU SER SEQRES 23 B 319 ARG PHE TYR LYS HIS PRO PHE THR CYS PHE ALA LYS ASN SEQRES 24 B 319 THR HIS GLY ILE ASP ALA ALA TYR ILE GLN LEU ILE TYR SEQRES 25 B 319 PRO VAL THR ASN PHE GLN LYS MODRES 4GAF ASN B 216 ASN GLYCOSYLATION SITE MODRES 4GAF ASN B 232 ASN GLYCOSYLATION SITE MODRES 4GAF ASN B 246 ASN GLYCOSYLATION SITE MODRES 4GAF ASN B 176 ASN GLYCOSYLATION SITE HET NAG B 501 14 HET NAG B 502 14 HET NAG B 503 14 HET NAG B 504 14 HET NA B 505 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 7 NA NA 1+ FORMUL 8 HOH *209(H2 O) HELIX 1 1 GLN A 31 GLU A 38 5 8 HELIX 2 2 GLU A 95 PHE A 98 5 4 HELIX 3 3 LYS B 70 SER B 74 5 5 HELIX 4 4 ASN B 106 GLN B 108 5 3 HELIX 5 5 MET B 128 LYS B 132 5 5 HELIX 6 6 ALA B 170 ARG B 174 5 5 HELIX 7 7 ASN B 269 ARG B 272 5 4 HELIX 8 8 GLU B 285 LYS B 290 5 6 SHEET 1 A 7 SER A 5 ASP A 12 0 SHEET 2 A 7 PHE A 41 SER A 44 -1 O MET A 43 N LEU A 6 SHEET 3 A 7 LYS A 54 LEU A 61 -1 O GLY A 60 N SER A 42 SHEET 4 A 7 PHE A 100 ILE A 105 -1 O PHE A 100 N VAL A 57 SHEET 5 A 7 LYS A 108 SER A 113 -1 O GLU A 112 N ASN A 101 SHEET 6 A 7 PHE A 146 PHE A 150 -1 O PHE A 146 N LEU A 109 SHEET 7 A 7 SER A 5 ASP A 12 -1 N TRP A 11 O TYR A 147 SHEET 1 B 3 THR A 17 ARG A 21 0 SHEET 2 B 3 GLN A 24 GLY A 28 -1 O VAL A 26 N TYR A 19 SHEET 3 B 3 GLN A 129 PRO A 130 -1 O GLN A 129 N ALA A 27 SHEET 1 C 2 LEU A 66 LYS A 73 0 SHEET 2 C 2 LYS A 76 SER A 83 -1 O THR A 78 N VAL A 71 SHEET 1 D 2 PHE A 120 CYS A 122 0 SHEET 2 D 2 SER A 132 THR A 134 -1 O SER A 132 N CYS A 122 SHEET 1 E 3 LYS B 7 GLU B 10 0 SHEET 2 E 3 LEU B 88 VAL B 97 1 O LYS B 91 N ARG B 9 SHEET 3 E 3 LEU B 15 SER B 18 1 N SER B 17 O LYS B 95 SHEET 1 F 4 LYS B 7 GLU B 10 0 SHEET 2 F 4 LEU B 88 VAL B 97 1 O LYS B 91 N ARG B 9 SHEET 3 F 4 GLY B 75 VAL B 80 -1 N TYR B 77 O ILE B 92 SHEET 4 F 4 THR B 39 LYS B 42 -1 N TYR B 41 O TYR B 78 SHEET 1 G 3 ASP B 23 PRO B 26 0 SHEET 2 G 3 LYS B 63 PHE B 66 -1 O PHE B 66 N ASP B 23 SHEET 3 G 3 ILE B 57 HIS B 60 -1 N HIS B 58 O TRP B 65 SHEET 1 H 5 ILE B 110 PRO B 116 0 SHEET 2 H 5 LYS B 188 LEU B 201 1 O GLU B 197 N GLN B 113 SHEET 3 H 5 GLY B 175 TYR B 185 -1 N TYR B 183 O TYR B 190 SHEET 4 H 5 GLN B 142 LYS B 145 -1 N GLN B 142 O HIS B 180 SHEET 5 H 5 LYS B 148 PRO B 149 -1 O LYS B 148 N LYS B 145 SHEET 1 I 3 GLY B 121 VAL B 124 0 SHEET 2 I 3 ARG B 163 VAL B 166 -1 O VAL B 166 N GLY B 121 SHEET 3 I 3 PHE B 157 VAL B 160 -1 N SER B 158 O ILE B 165 SHEET 1 J 4 VAL B 210 SER B 213 0 SHEET 2 J 4 ILE B 227 GLY B 235 -1 O ASN B 232 N VAL B 212 SHEET 3 J 4 SER B 273 ILE B 281 -1 O LEU B 275 N VAL B 233 SHEET 4 J 4 LEU B 257 VAL B 264 -1 N GLY B 258 O ASN B 280 SHEET 1 K 5 GLU B 217 GLU B 220 0 SHEET 2 K 5 GLY B 302 ILE B 311 1 O GLN B 309 N GLU B 217 SHEET 3 K 5 PHE B 293 ASN B 299 -1 N PHE B 293 O ILE B 308 SHEET 4 K 5 ILE B 240 TRP B 245 -1 N TYR B 242 O PHE B 296 SHEET 5 K 5 SER B 248 VAL B 249 -1 O SER B 248 N TRP B 245 SSBOND 1 CYS B 6 CYS B 87 1555 1555 2.04 SSBOND 2 CYS B 27 CYS B 79 1555 1555 2.05 SSBOND 3 CYS B 104 CYS B 147 1555 1555 2.14 SSBOND 4 CYS B 125 CYS B 179 1555 1555 2.09 SSBOND 5 CYS B 231 CYS B 295 1555 1555 1.94 LINK ND2 ASN B 176 C1 NAG B 503 1555 1555 1.45 LINK ND2 ASN B 216 C1 NAG B 502 1555 1555 1.43 LINK ND2 ASN B 232 C1 NAG B 501 1555 1555 1.44 LINK ND2 ASN B 246 C1 NAG B 504 1555 1555 1.44 LINK OG SER B 18 NA NA B 505 1555 1555 2.55 LINK OE1 GLU B 21 NA NA B 505 1555 1555 2.58 LINK O THR B 193 NA NA B 505 1555 1555 2.32 LINK OG1 THR B 193 NA NA B 505 1555 1555 2.56 LINK NA NA B 505 O HOH B 627 1555 1555 2.34 LINK NA NA B 505 O HOH B 642 1555 1555 2.33 CISPEP 1 TYR A 89 PRO A 90 0 -0.10 CISPEP 2 VAL B 67 PRO B 68 0 -7.76 CISPEP 3 GLU B 134 ASN B 135 0 15.92 CISPEP 4 SER B 213 PRO B 214 0 -0.51 CRYST1 60.350 149.270 126.170 90.00 90.00 90.00 C 2 2 21 8 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 0.016570 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007926 0.00000