HEADER IMMUNE SYSTEM 05-OCT-18 6MP0 TITLE CRYSTAL STRUCTURES OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY TITLE 2 COMPLEX H-2DB IN COMPLEX WITH THE TRP1-M9 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRP1-M9 PEPTIDE, BETA-2-MICROGLOBULIN,H-2 CLASS I COMPND 3 HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN, CHIMERIC CONSTRUCT; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: DHICA OXIDASE,BROWN LOCUS PROTEIN,CATALASE B,TYROSINASE- COMPND 6 RELATED PROTEIN 1,TRP1,H-2D(B); COMPND 7 EC: 1.14.18.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TYRP1, TYRP-1, B2M, H2-D1; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS MHC, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR E.CLANCY-THOMPSON,C.A.DEVLIN,M.E.BIRNBAUM,S.K.DOUGAN REVDAT 6 11-OCT-23 6MP0 1 HETSYN REVDAT 5 29-JUL-20 6MP0 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 04-DEC-19 6MP0 1 REMARK REVDAT 3 12-DEC-18 6MP0 1 JRNL REVDAT 2 28-NOV-18 6MP0 1 JRNL REVDAT 1 07-NOV-18 6MP0 0 JRNL AUTH E.CLANCY-THOMPSON,C.A.DEVLIN,P.M.TYLER,M.M.SERVOS,L.R.ALI, JRNL AUTH 2 K.S.VENTRE,M.A.BHUIYAN,P.T.BRUCK,M.E.BIRNBAUM,S.K.DOUGAN JRNL TITL ALTERED BINDING OF TUMOR ANTIGENIC PEPTIDES TO MHC CLASS I JRNL TITL 2 AFFECTS CD8+T CELL-EFFECTOR RESPONSES. JRNL REF CANCER IMMUNOL RES V. 6 1524 2018 JRNL REFN ISSN 2326-6074 JRNL PMID 30352798 JRNL DOI 10.1158/2326-6066.CIR-18-0348 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 40439 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.6860 - 4.8147 0.99 2979 170 0.1890 0.2281 REMARK 3 2 4.8147 - 3.8237 1.00 2867 142 0.1558 0.1623 REMARK 3 3 3.8237 - 3.3409 1.00 2826 166 0.1700 0.2010 REMARK 3 4 3.3409 - 3.0357 1.00 2844 158 0.1864 0.2227 REMARK 3 5 3.0357 - 2.8183 1.00 2785 155 0.2011 0.2405 REMARK 3 6 2.8183 - 2.6522 1.00 2798 134 0.2106 0.2514 REMARK 3 7 2.6522 - 2.5195 1.00 2828 134 0.2118 0.3013 REMARK 3 8 2.5195 - 2.4098 1.00 2812 131 0.2165 0.2685 REMARK 3 9 2.4098 - 2.3171 1.00 2795 139 0.2246 0.2352 REMARK 3 10 2.3171 - 2.2372 1.00 2776 151 0.2245 0.2716 REMARK 3 11 2.2372 - 2.1672 1.00 2779 133 0.2202 0.2729 REMARK 3 12 2.1672 - 2.1053 0.99 2738 158 0.2441 0.2985 REMARK 3 13 2.1053 - 2.0499 0.92 2573 110 0.2743 0.2706 REMARK 3 14 2.0499 - 1.9999 0.74 2050 108 0.3384 0.3827 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.620 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.016 3300 REMARK 3 ANGLE : 1.394 4489 REMARK 3 CHIRALITY : 0.080 457 REMARK 3 PLANARITY : 0.009 586 REMARK 3 DIHEDRAL : 16.853 1956 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 2012 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.4753 -11.4466 32.3543 REMARK 3 T TENSOR REMARK 3 T11: 0.2238 T22: 0.2228 REMARK 3 T33: 0.1910 T12: 0.0119 REMARK 3 T13: -0.0158 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 1.2570 L22: 3.2481 REMARK 3 L33: 0.4572 L12: 0.9846 REMARK 3 L13: 0.3740 L23: 0.9862 REMARK 3 S TENSOR REMARK 3 S11: 0.0044 S12: 0.1312 S13: -0.1293 REMARK 3 S21: -0.1866 S22: -0.0616 S23: -0.0404 REMARK 3 S31: -0.0280 S32: -0.0367 S33: 0.0705 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2013 THROUGH 2162 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6285 9.4687 38.7313 REMARK 3 T TENSOR REMARK 3 T11: 0.1578 T22: 0.1207 REMARK 3 T33: 0.1842 T12: -0.0274 REMARK 3 T13: -0.0115 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 3.1112 L22: 2.7261 REMARK 3 L33: 2.7666 L12: -0.0913 REMARK 3 L13: -0.3748 L23: 0.1443 REMARK 3 S TENSOR REMARK 3 S11: -0.0230 S12: 0.0909 S13: -0.0189 REMARK 3 S21: -0.0913 S22: -0.0354 S23: -0.1665 REMARK 3 S31: -0.0043 S32: 0.1330 S33: 0.0626 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2163 THROUGH 2277 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.8135 -17.2583 52.0432 REMARK 3 T TENSOR REMARK 3 T11: 0.3748 T22: 0.3699 REMARK 3 T33: 0.2103 T12: -0.0006 REMARK 3 T13: 0.0185 T23: -0.0354 REMARK 3 L TENSOR REMARK 3 L11: 1.4997 L22: 4.3684 REMARK 3 L33: 2.6037 L12: 0.5438 REMARK 3 L13: -0.0979 L23: -0.3070 REMARK 3 S TENSOR REMARK 3 S11: 0.1085 S12: -0.1610 S13: -0.3543 REMARK 3 S21: 0.4906 S22: -0.2219 S23: 0.1479 REMARK 3 S31: 0.7482 S32: 0.0719 S33: 0.0794 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6MP0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237048. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20170601 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20170601 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40488 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 31.682 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.14120 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.7 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 : 1.580 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: 4HUU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG-6000, 200 MM LICL, AND 100 MM REMARK 280 TRIS-HCL (PH 8.0), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.21800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.88600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.21800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.88600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 989 REMARK 465 SER A 990 REMARK 465 GLY A 991 REMARK 465 GLY A 992 REMARK 465 GLY A 993 REMARK 465 GLY A 994 REMARK 465 SER A 995 REMARK 465 GLY A 996 REMARK 465 GLY A 997 REMARK 465 GLY A 998 REMARK 465 GLY A 999 REMARK 465 SER A 1000 REMARK 465 GLY A 1981 REMARK 465 GLY A 1982 REMARK 465 GLY A 1983 REMARK 465 GLY A 1984 REMARK 465 SER A 1985 REMARK 465 GLY A 1986 REMARK 465 GLY A 1987 REMARK 465 GLY A 1988 REMARK 465 GLY A 1989 REMARK 465 SER A 1990 REMARK 465 GLY A 1991 REMARK 465 GLY A 1992 REMARK 465 GLY A 1993 REMARK 465 GLY A 1994 REMARK 465 SER A 1995 REMARK 465 GLY A 1996 REMARK 465 GLY A 1997 REMARK 465 GLY A 1998 REMARK 465 GLY A 1999 REMARK 465 SER A 2000 REMARK 465 ALA A 2278 REMARK 465 ALA A 2279 REMARK 465 GLY A 2280 REMARK 465 GLY A 2281 REMARK 465 GLY A 2282 REMARK 465 LEU A 2283 REMARK 465 ASN A 2284 REMARK 465 ASP A 2285 REMARK 465 ILE A 2286 REMARK 465 PHE A 2287 REMARK 465 GLU A 2288 REMARK 465 ALA A 2289 REMARK 465 GLN A 2290 REMARK 465 LYS A 2291 REMARK 465 ILE A 2292 REMARK 465 GLU A 2293 REMARK 465 TRP A 2294 REMARK 465 HIS A 2295 REMARK 465 GLU A 2296 REMARK 465 HIS A 2297 REMARK 465 HIS A 2298 REMARK 465 HIS A 2299 REMARK 465 HIS A 2300 REMARK 465 HIS A 2301 REMARK 465 HIS A 2302 REMARK 465 HIS A 2303 REMARK 465 HIS A 2304 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 O HOH A 3098 O HOH A 3284 1.87 REMARK 500 O HOH A 3286 O HOH A 3354 1.89 REMARK 500 O HOH A 3246 O HOH A 3359 1.92 REMARK 500 O HOH A 3115 O HOH A 3157 1.95 REMARK 500 O HOH A 3209 O HOH A 3279 1.96 REMARK 500 O HOH A 3035 O HOH A 3190 1.97 REMARK 500 O HOH A 3307 O HOH A 3315 2.03 REMARK 500 O HOH A 3177 O HOH A 3207 2.05 REMARK 500 O HOH A 3165 O HOH A 3192 2.08 REMARK 500 O6 NAG A 2901 O HOH A 3001 2.11 REMARK 500 O HOH A 3017 O HOH A 3103 2.13 REMARK 500 O HOH A 3301 O HOH A 3326 2.13 REMARK 500 O HOH A 3128 O HOH A 3367 2.13 REMARK 500 OE1 GLN A 2054 O HOH A 3002 2.15 REMARK 500 O GLY A 12 O HOH A 3003 2.16 REMARK 500 O HOH A 3174 O HOH A 3230 2.16 REMARK 500 OE2 GLU A 2264 O HOH A 3004 2.16 REMARK 500 O HOH A 3099 O HOH A 3285 2.17 REMARK 500 OD1 ASP A 1098 O HOH A 3005 2.18 REMARK 500 O HOH A 3231 O HOH A 3259 2.19 REMARK 500 O HOH A 3144 O HOH A 3240 2.19 REMARK 500 OH TYR A 1078 O HOH A 3006 2.19 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 3211 O HOH A 3325 3555 1.89 REMARK 500 NH2 ARG A 2079 O HOH A 3005 3555 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 A2062 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 LEU A2114 CB - CG - CD2 ANGL. DEV. = -15.2 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 LEU A 6 -101.93 -112.52 REMARK 500 TRP A1060 -11.38 82.24 REMARK 500 ASP A1098 24.70 -79.82 REMARK 500 ARG A2111 140.98 -170.59 REMARK 500 LYS A2196 -142.01 63.93 REMARK 500 PRO A2210 -178.94 -67.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A3378 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A3379 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A3380 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A3381 DISTANCE = 6.71 ANGSTROMS DBREF 6MP0 A 1 9 UNP P07147 TYRP1_MOUSE 455 463 DBREF 6MP0 A 1001 1099 UNP P01887 B2MG_MOUSE 21 119 DBREF 6MP0 A 2001 2276 UNP P01899 HA11_MOUSE 25 300 SEQADV 6MP0 MET A 9 UNP P07147 ALA 463 ENGINEERED MUTATION SEQADV 6MP0 GLY A 10 UNP P07147 LINKER SEQADV 6MP0 GLY A 11 UNP P07147 LINKER SEQADV 6MP0 GLY A 12 UNP P07147 LINKER SEQADV 6MP0 GLY A 989 UNP P07147 LINKER SEQADV 6MP0 SER A 990 UNP P07147 LINKER SEQADV 6MP0 GLY A 991 UNP P07147 LINKER SEQADV 6MP0 GLY A 992 UNP P07147 LINKER SEQADV 6MP0 GLY A 993 UNP P07147 LINKER SEQADV 6MP0 GLY A 994 UNP P07147 LINKER SEQADV 6MP0 SER A 995 UNP P07147 LINKER SEQADV 6MP0 GLY A 996 UNP P07147 LINKER SEQADV 6MP0 GLY A 997 UNP P07147 LINKER SEQADV 6MP0 GLY A 998 UNP P07147 LINKER SEQADV 6MP0 GLY A 999 UNP P07147 LINKER SEQADV 6MP0 SER A 1000 UNP P07147 LINKER SEQADV 6MP0 GLY A 1981 UNP P01887 LINKER SEQADV 6MP0 GLY A 1982 UNP P01887 LINKER SEQADV 6MP0 GLY A 1983 UNP P01887 LINKER SEQADV 6MP0 GLY A 1984 UNP P01887 LINKER SEQADV 6MP0 SER A 1985 UNP P01887 LINKER SEQADV 6MP0 GLY A 1986 UNP P01887 LINKER SEQADV 6MP0 GLY A 1987 UNP P01887 LINKER SEQADV 6MP0 GLY A 1988 UNP P01887 LINKER SEQADV 6MP0 GLY A 1989 UNP P01887 LINKER SEQADV 6MP0 SER A 1990 UNP P01887 LINKER SEQADV 6MP0 GLY A 1991 UNP P01887 LINKER SEQADV 6MP0 GLY A 1992 UNP P01887 LINKER SEQADV 6MP0 GLY A 1993 UNP P01887 LINKER SEQADV 6MP0 GLY A 1994 UNP P01887 LINKER SEQADV 6MP0 SER A 1995 UNP P01887 LINKER SEQADV 6MP0 GLY A 1996 UNP P01887 LINKER SEQADV 6MP0 GLY A 1997 UNP P01887 LINKER SEQADV 6MP0 GLY A 1998 UNP P01887 LINKER SEQADV 6MP0 GLY A 1999 UNP P01887 LINKER SEQADV 6MP0 SER A 2000 UNP P01887 LINKER SEQADV 6MP0 ALA A 2084 UNP P01899 TYR 108 ENGINEERED MUTATION SEQADV 6MP0 ALA A 2277 UNP P01899 EXPRESSION TAG SEQADV 6MP0 ALA A 2278 UNP P01899 EXPRESSION TAG SEQADV 6MP0 ALA A 2279 UNP P01899 EXPRESSION TAG SEQADV 6MP0 GLY A 2280 UNP P01899 EXPRESSION TAG SEQADV 6MP0 GLY A 2281 UNP P01899 EXPRESSION TAG SEQADV 6MP0 GLY A 2282 UNP P01899 EXPRESSION TAG SEQADV 6MP0 LEU A 2283 UNP P01899 EXPRESSION TAG SEQADV 6MP0 ASN A 2284 UNP P01899 EXPRESSION TAG SEQADV 6MP0 ASP A 2285 UNP P01899 EXPRESSION TAG SEQADV 6MP0 ILE A 2286 UNP P01899 EXPRESSION TAG SEQADV 6MP0 PHE A 2287 UNP P01899 EXPRESSION TAG SEQADV 6MP0 GLU A 2288 UNP P01899 EXPRESSION TAG SEQADV 6MP0 ALA A 2289 UNP P01899 EXPRESSION TAG SEQADV 6MP0 GLN A 2290 UNP P01899 EXPRESSION TAG SEQADV 6MP0 LYS A 2291 UNP P01899 EXPRESSION TAG SEQADV 6MP0 ILE A 2292 UNP P01899 EXPRESSION TAG SEQADV 6MP0 GLU A 2293 UNP P01899 EXPRESSION TAG SEQADV 6MP0 TRP A 2294 UNP P01899 EXPRESSION TAG SEQADV 6MP0 HIS A 2295 UNP P01899 EXPRESSION TAG SEQADV 6MP0 GLU A 2296 UNP P01899 EXPRESSION TAG SEQADV 6MP0 HIS A 2297 UNP P01899 EXPRESSION TAG SEQADV 6MP0 HIS A 2298 UNP P01899 EXPRESSION TAG SEQADV 6MP0 HIS A 2299 UNP P01899 EXPRESSION TAG SEQADV 6MP0 HIS A 2300 UNP P01899 EXPRESSION TAG SEQADV 6MP0 HIS A 2301 UNP P01899 EXPRESSION TAG SEQADV 6MP0 HIS A 2302 UNP P01899 EXPRESSION TAG SEQADV 6MP0 HIS A 2303 UNP P01899 EXPRESSION TAG SEQADV 6MP0 HIS A 2304 UNP P01899 EXPRESSION TAG SEQRES 1 A 447 THR ALA PRO ASP ASN LEU GLY TYR MET GLY GLY GLY GLY SEQRES 2 A 447 SER GLY GLY GLY GLY SER GLY GLY GLY GLY SER ILE GLN SEQRES 3 A 447 LYS THR PRO GLN ILE GLN VAL TYR SER ARG HIS PRO PRO SEQRES 4 A 447 GLU ASN GLY LYS PRO ASN ILE LEU ASN CYS TYR VAL THR SEQRES 5 A 447 GLN PHE HIS PRO PRO HIS ILE GLU ILE GLN MET LEU LYS SEQRES 6 A 447 ASN GLY LYS LYS ILE PRO LYS VAL GLU MET SER ASP MET SEQRES 7 A 447 SER PHE SER LYS ASP TRP SER PHE TYR ILE LEU ALA HIS SEQRES 8 A 447 THR GLU PHE THR PRO THR GLU THR ASP THR TYR ALA CYS SEQRES 9 A 447 ARG VAL LYS HIS ALA SER MET ALA GLU PRO LYS THR VAL SEQRES 10 A 447 TYR TRP ASP ARG ASP MET GLY GLY GLY GLY SER GLY GLY SEQRES 11 A 447 GLY GLY SER GLY GLY GLY GLY SER GLY GLY GLY GLY SER SEQRES 12 A 447 GLY PRO HIS SER MET ARG TYR PHE GLU THR ALA VAL SER SEQRES 13 A 447 ARG PRO GLY LEU GLU GLU PRO ARG TYR ILE SER VAL GLY SEQRES 14 A 447 TYR VAL ASP ASN LYS GLU PHE VAL ARG PHE ASP SER ASP SEQRES 15 A 447 ALA GLU ASN PRO ARG TYR GLU PRO ARG ALA PRO TRP MET SEQRES 16 A 447 GLU GLN GLU GLY PRO GLU TYR TRP GLU ARG GLU THR GLN SEQRES 17 A 447 LYS ALA LYS GLY GLN GLU GLN TRP PHE ARG VAL SER LEU SEQRES 18 A 447 ARG ASN LEU LEU GLY ALA TYR ASN GLN SER ALA GLY GLY SEQRES 19 A 447 SER HIS THR LEU GLN GLN MET SER GLY CYS ASP LEU GLY SEQRES 20 A 447 SER ASP TRP ARG LEU LEU ARG GLY TYR LEU GLN PHE ALA SEQRES 21 A 447 TYR GLU GLY ARG ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 22 A 447 LYS THR TRP THR ALA ALA ASP MET ALA ALA GLN ILE THR SEQRES 23 A 447 ARG ARG LYS TRP GLU GLN SER GLY ALA ALA GLU HIS TYR SEQRES 24 A 447 LYS ALA TYR LEU GLU GLY GLU CYS VAL GLU TRP LEU HIS SEQRES 25 A 447 ARG TYR LEU LYS ASN GLY ASN ALA THR LEU LEU ARG THR SEQRES 26 A 447 ASP SER PRO LYS ALA HIS VAL THR HIS HIS PRO ARG SER SEQRES 27 A 447 LYS GLY GLU VAL THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 28 A 447 TYR PRO ALA ASP ILE THR LEU THR TRP GLN LEU ASN GLY SEQRES 29 A 447 GLU GLU LEU THR GLN ASP MET GLU LEU VAL GLU THR ARG SEQRES 30 A 447 PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA SER VAL SEQRES 31 A 447 VAL VAL PRO LEU GLY LYS GLU GLN ASN TYR THR CYS ARG SEQRES 32 A 447 VAL TYR HIS GLU GLY LEU PRO GLU PRO LEU THR LEU ARG SEQRES 33 A 447 TRP GLU PRO ALA ALA ALA GLY GLY GLY LEU ASN ASP ILE SEQRES 34 A 447 PHE GLU ALA GLN LYS ILE GLU TRP HIS GLU HIS HIS HIS SEQRES 35 A 447 HIS HIS HIS HIS HIS HET NAG A2901 14 HET NAG A2902 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 4 HOH *381(H2 O) HELIX 1 AA1 ALA A 2049 GLU A 2055 5 7 HELIX 2 AA2 GLY A 2056 TYR A 2085 1 30 HELIX 3 AA3 ASP A 2137 SER A 2150 1 14 HELIX 4 AA4 GLY A 2151 GLY A 2162 1 12 HELIX 5 AA5 GLY A 2162 GLY A 2175 1 14 HELIX 6 AA6 GLY A 2175 LEU A 2180 1 6 HELIX 7 AA7 LYS A 2253 GLN A 2255 5 3 SHEET 1 AA1 4 GLN A1006 SER A1011 0 SHEET 2 AA1 4 ASN A1021 PHE A1030 -1 O ASN A1024 N TYR A1010 SHEET 3 AA1 4 PHE A1062 PHE A1070 -1 O ILE A1064 N VAL A1027 SHEET 4 AA1 4 GLU A1050 MET A1051 -1 N GLU A1050 O HIS A1067 SHEET 1 AA2 4 GLN A1006 SER A1011 0 SHEET 2 AA2 4 ASN A1021 PHE A1030 -1 O ASN A1024 N TYR A1010 SHEET 3 AA2 4 PHE A1062 PHE A1070 -1 O ILE A1064 N VAL A1027 SHEET 4 AA2 4 SER A1055 PHE A1056 -1 N SER A1055 O TYR A1063 SHEET 1 AA3 4 LYS A1044 LYS A1045 0 SHEET 2 AA3 4 GLU A1036 LYS A1041 -1 N LYS A1041 O LYS A1044 SHEET 3 AA3 4 TYR A1078 LYS A1083 -1 O LYS A1083 N GLU A1036 SHEET 4 AA3 4 LYS A1091 TYR A1094 -1 O VAL A1093 N CYS A1080 SHEET 1 AA4 8 GLU A2046 PRO A2047 0 SHEET 2 AA4 8 LYS A2031 ASP A2037 -1 N ARG A2035 O GLU A2046 SHEET 3 AA4 8 LEU A2017 VAL A2028 -1 N GLY A2026 O PHE A2033 SHEET 4 AA4 8 HIS A2003 ARG A2014 -1 N ARG A2006 O TYR A2027 SHEET 5 AA4 8 THR A2094 LEU A2103 -1 O LEU A2103 N HIS A2003 SHEET 6 AA4 8 LEU A2109 TYR A2118 -1 O LEU A2110 N ASP A2102 SHEET 7 AA4 8 ARG A2121 LEU A2126 -1 O LEU A2126 N LEU A2114 SHEET 8 AA4 8 TRP A2133 ALA A2135 -1 O THR A2134 N ALA A2125 SHEET 1 AA5 4 LYS A2186 PRO A2193 0 SHEET 2 AA5 4 GLU A2198 PHE A2208 -1 O TRP A2204 N HIS A2188 SHEET 3 AA5 4 PHE A2241 PRO A2250 -1 O ALA A2245 N CYS A2203 SHEET 4 AA5 4 GLU A2229 LEU A2230 -1 N GLU A2229 O SER A2246 SHEET 1 AA6 4 LYS A2186 PRO A2193 0 SHEET 2 AA6 4 GLU A2198 PHE A2208 -1 O TRP A2204 N HIS A2188 SHEET 3 AA6 4 PHE A2241 PRO A2250 -1 O ALA A2245 N CYS A2203 SHEET 4 AA6 4 ARG A2234 PRO A2235 -1 N ARG A2234 O GLN A2242 SHEET 1 AA7 4 GLU A2222 GLU A2223 0 SHEET 2 AA7 4 THR A2214 LEU A2219 -1 N LEU A2219 O GLU A2222 SHEET 3 AA7 4 TYR A2257 TYR A2262 -1 O ARG A2260 N THR A2216 SHEET 4 AA7 4 LEU A2270 LEU A2272 -1 O LEU A2272 N CYS A2259 SSBOND 1 CYS A 1025 CYS A 1080 1555 1555 2.07 SSBOND 2 CYS A 2101 CYS A 2164 1555 1555 2.12 SSBOND 3 CYS A 2203 CYS A 2259 1555 1555 2.02 LINK ND2 ASN A2176 C1 NAG A2901 1555 1555 1.45 LINK ND2 ASN A2256 C1 NAG A2902 1555 1555 1.45 CISPEP 1 HIS A 1031 PRO A 1032 0 5.90 CISPEP 2 TYR A 2209 PRO A 2210 0 -1.15 CRYST1 50.061 98.436 121.772 90.00 90.00 90.00 P 2 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 0.019976 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010159 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008212 0.00000