HEADER IMMUNE SYSTEM 04-JUN-22 8D5J TITLE THE COMPLEX OF PRE-MRNA-PROCESSING FACTOR 19 (PRPF19) NEOANTIGEN TITLE 2 KYLQVASHV PRESENTED BY H2-KD COMPND MOL_ID: 1; COMPND 2 MOLECULE: MHC CLASS I HEAVY CHAIN MATURATION PEPTIDE H-2K(D); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PRE-MRNA-PROCESSING FACTOR 19; COMPND 11 CHAIN: C; COMPND 12 FRAGMENT: UNP RESIDUES 206-214; COMPND 13 SYNONYM: NUCLEAR MATRIX PROTEIN 200,PRP19/PSO4 HOMOLOG,RING-TYPE E3 COMPND 14 UBIQUITIN TRANSFERASE PRP19,SENESCENCE EVASION FACTOR; COMPND 15 EC: 2.3.2.27; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: H2-K1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 GENE: B2M; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 18 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 19 ORGANISM_TAXID: 10090 KEYWDS COMPLEX, MHC, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.M.F.CUSTODIO,B.M.BAKER REVDAT 2 18-OCT-23 8D5J 1 REMARK REVDAT 1 06-JUL-22 8D5J 0 JRNL AUTH J.M.F.CUSTODIO,B.M.BAKER JRNL TITL THE COMPLEX OF PRE-MRNA-PROCESSING FACTOR 19 (PRPF19) JRNL TITL 2 NEOANTIGEN KYLQVASHV PRESENTED BY H2-KD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0350 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 30593 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.102 REMARK 3 FREE R VALUE TEST SET COUNT : 1561 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2118 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3151 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.59600 REMARK 3 B22 (A**2) : 0.59500 REMARK 3 B33 (A**2) : -0.00300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.06200 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.169 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.752 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3249 ; 0.008 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4421 ; 1.701 ; 1.654 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 381 ; 6.622 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 27 ;12.567 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 516 ;15.184 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 451 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2537 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1196 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2193 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 163 ; 0.131 ; 0.200 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): 1533 ; 2.666 ; 2.856 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1911 ; 3.907 ; 4.264 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1716 ; 4.027 ; 3.222 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2510 ; 6.137 ; 4.652 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 180 REMARK 3 RESIDUE RANGE : A 181 A 274 REMARK 3 ORIGIN FOR THE GROUP (A): 20.6360 25.6559 14.6311 REMARK 3 T TENSOR REMARK 3 T11: 0.1217 T22: 0.0995 REMARK 3 T33: 0.0031 T12: -0.0041 REMARK 3 T13: 0.0026 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.4368 L22: 0.2672 REMARK 3 L33: 0.3853 L12: 0.1341 REMARK 3 L13: 0.3961 L23: 0.1423 REMARK 3 S TENSOR REMARK 3 S11: 0.0040 S12: 0.0853 S13: -0.0336 REMARK 3 S21: -0.0027 S22: 0.0253 S23: -0.0093 REMARK 3 S31: -0.0519 S32: 0.0671 S33: -0.0294 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): 19.1847 28.1511 33.6841 REMARK 3 T TENSOR REMARK 3 T11: 0.1116 T22: 0.1102 REMARK 3 T33: 0.0249 T12: -0.0409 REMARK 3 T13: 0.0023 T23: -0.0300 REMARK 3 L TENSOR REMARK 3 L11: 0.5382 L22: 0.9587 REMARK 3 L33: 1.3095 L12: 0.6292 REMARK 3 L13: 0.4385 L23: 0.7615 REMARK 3 S TENSOR REMARK 3 S11: 0.1277 S12: -0.0325 S13: 0.0167 REMARK 3 S21: 0.0803 S22: -0.1172 S23: 0.0647 REMARK 3 S31: -0.0408 S32: 0.0439 S33: -0.0105 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): 5.4901 21.4014 3.6313 REMARK 3 T TENSOR REMARK 3 T11: 0.0709 T22: 0.1310 REMARK 3 T33: 0.0360 T12: 0.0366 REMARK 3 T13: -0.0279 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.3268 L22: 5.5382 REMARK 3 L33: 0.8413 L12: 0.7559 REMARK 3 L13: -0.3500 L23: 0.4959 REMARK 3 S TENSOR REMARK 3 S11: 0.0418 S12: 0.0825 S13: 0.0266 REMARK 3 S21: -0.0370 S22: 0.0224 S23: -0.0061 REMARK 3 S31: -0.0646 S32: -0.1121 S33: -0.0642 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 NOT BEEN USED REMARK 4 REMARK 4 8D5J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1000266070. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30593 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 40.902 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 40.87 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.06800 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1VGK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG3000, 100 MM HEPES, 200 MM REMARK 280 SODIUM ACETATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 57.72000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.28500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.72000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.28500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 379 LIES ON A SPECIAL POSITION. 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 GLU A 275 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 LYS A 89 CG CD CE NZ REMARK 470 GLN A 196 CG CD OE1 NE2 REMARK 470 THR A 225 OG1 CG2 REMARK 470 ASP A 227 CG OD1 OD2 REMARK 470 GLU A 268 CG CD OE1 OE2 REMARK 470 LYS B 49 CG CD CE NZ 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 6 CG - CD - NE ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG A 111 CG - CD - NE ANGL. DEV. = -17.6 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 29 -122.63 53.44 REMARK 500 GLN A 114 87.83 -156.52 REMARK 500 TYR A 123 -60.19 -120.79 REMARK 500 LEU A 180 -26.32 85.46 REMARK 500 ARG A 194 -65.16 -124.17 REMARK 500 TRP B 61 -13.29 84.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 6 0.13 SIDE CHAIN REMARK 500 ARG A 145 0.08 SIDE CHAIN REMARK 500 ARG A 157 0.19 SIDE CHAIN REMARK 500 ARG A 273 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8D5J A 0 274 UNP Q6RJ37 Q6RJ37_MOUSE 1 275 DBREF 8D5J B 2 100 UNP P01887 B2MG_MOUSE 21 119 DBREF 8D5J C 1 9 UNP Q99KP6 PRP19_MOUSE 206 214 SEQADV 8D5J GLU A 275 UNP Q6RJ37 EXPRESSION TAG SEQADV 8D5J MET B 1 UNP P01887 INITIATING METHIONINE SEQADV 8D5J ASP B 86 UNP P01887 ALA 105 CONFLICT SEQADV 8D5J LEU C 3 UNP Q99KP6 ARG 208 CONFLICT SEQRES 1 A 276 MET GLY PRO HIS SER LEU ARG TYR PHE VAL THR ALA VAL SEQRES 2 A 276 SER ARG PRO GLY LEU GLY GLU PRO ARG PHE ILE ALA VAL SEQRES 3 A 276 GLY TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER SEQRES 4 A 276 ASP ALA ASP ASN PRO ARG PHE GLU PRO ARG ALA PRO TRP SEQRES 5 A 276 MET GLU GLN GLU GLY PRO GLU TYR TRP GLU GLU GLN THR SEQRES 6 A 276 GLN ARG ALA LYS SER ASP GLU GLN TRP PHE ARG VAL SER SEQRES 7 A 276 LEU ARG THR ALA GLN ARG TYR TYR ASN GLN SER LYS GLY SEQRES 8 A 276 GLY SER HIS THR PHE GLN ARG MET PHE GLY CYS ASP VAL SEQRES 9 A 276 GLY SER ASP TRP ARG LEU LEU ARG GLY TYR GLN GLN PHE SEQRES 10 A 276 ALA TYR ASP GLY ARG ASP TYR ILE ALA LEU ASN GLU ASP SEQRES 11 A 276 LEU LYS THR TRP THR ALA ALA ASP THR ALA ALA LEU ILE SEQRES 12 A 276 THR ARG ARG LYS TRP GLU GLN ALA GLY ASP ALA GLU TYR SEQRES 13 A 276 TYR ARG ALA TYR LEU GLU GLY GLU CYS VAL GLU TRP LEU SEQRES 14 A 276 ARG ARG TYR LEU GLU LEU GLY ASN GLU THR LEU LEU ARG SEQRES 15 A 276 THR ASP SER PRO LYS ALA HIS VAL THR TYR HIS PRO ARG SEQRES 16 A 276 SER GLN VAL ASP VAL THR LEU ARG CYS TRP ALA LEU GLY SEQRES 17 A 276 PHE TYR PRO ALA ASP ILE THR LEU THR TRP GLN LEU ASN SEQRES 18 A 276 GLY GLU ASP LEU THR GLN ASP MET GLU LEU VAL GLU THR SEQRES 19 A 276 ARG PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA SEQRES 20 A 276 VAL VAL VAL PRO LEU GLY LYS GLU GLN ASN TYR THR CYS SEQRES 21 A 276 HIS VAL HIS HIS LYS GLY LEU PRO GLU PRO LEU THR LEU SEQRES 22 A 276 ARG TRP GLU SEQRES 1 B 100 MET ILE GLN LYS THR PRO GLN ILE GLN VAL TYR SER ARG SEQRES 2 B 100 HIS PRO PRO GLU ASN GLY LYS PRO ASN ILE LEU ASN CYS SEQRES 3 B 100 TYR VAL THR GLN PHE HIS PRO PRO HIS ILE GLU ILE GLN SEQRES 4 B 100 MET LEU LYS ASN GLY LYS LYS ILE PRO LYS VAL GLU MET SEQRES 5 B 100 SER ASP MET SER PHE SER LYS ASP TRP SER PHE TYR ILE SEQRES 6 B 100 LEU ALA HIS THR GLU PHE THR PRO THR GLU THR ASP THR SEQRES 7 B 100 TYR ALA CYS ARG VAL LYS HIS ASP SER MET ALA GLU PRO SEQRES 8 B 100 LYS THR VAL TYR TRP ASP ARG ASP MET SEQRES 1 C 9 LYS TYR LEU GLN VAL ALA SER HIS VAL FORMUL 4 HOH *123(H2 O) HELIX 1 AA1 ALA A 49 GLU A 53 5 5 HELIX 2 AA2 GLY A 56 TYR A 85 1 30 HELIX 3 AA3 ASP A 137 GLY A 151 1 15 HELIX 4 AA4 GLY A 151 GLY A 162 1 12 HELIX 5 AA5 GLY A 162 GLY A 175 1 14 HELIX 6 AA6 LYS A 253 GLN A 255 5 3 SHEET 1 AA1 8 GLU A 46 PRO A 47 0 SHEET 2 AA1 8 THR A 31 ASP A 37 -1 N ARG A 35 O GLU A 46 SHEET 3 AA1 8 ARG A 21 VAL A 28 -1 N VAL A 28 O THR A 31 SHEET 4 AA1 8 HIS A 3 VAL A 12 -1 N ARG A 6 O TYR A 27 SHEET 5 AA1 8 THR A 94 VAL A 103 -1 O ARG A 97 N VAL A 9 SHEET 6 AA1 8 LEU A 109 TYR A 118 -1 O GLN A 115 N MET A 98 SHEET 7 AA1 8 ARG A 121 LEU A 126 -1 O ILE A 124 N PHE A 116 SHEET 8 AA1 8 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 AA2 4 LYS A 186 PRO A 193 0 SHEET 2 AA2 4 ASP A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 AA2 4 PHE A 241 PRO A 250 -1 O VAL A 249 N VAL A 199 SHEET 4 AA2 4 GLU A 229 LEU A 230 -1 N GLU A 229 O ALA A 246 SHEET 1 AA3 4 LYS A 186 PRO A 193 0 SHEET 2 AA3 4 ASP A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 AA3 4 PHE A 241 PRO A 250 -1 O VAL A 249 N VAL A 199 SHEET 4 AA3 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 AA4 4 GLU A 222 ASP A 223 0 SHEET 2 AA4 4 THR A 214 LEU A 219 -1 N LEU A 219 O GLU A 222 SHEET 3 AA4 4 TYR A 257 HIS A 262 -1 O HIS A 262 N THR A 214 SHEET 4 AA4 4 LEU A 270 LEU A 272 -1 O LEU A 272 N CYS A 259 SHEET 1 AA5 4 GLN B 7 SER B 12 0 SHEET 2 AA5 4 ASN B 22 PHE B 31 -1 O ASN B 25 N TYR B 11 SHEET 3 AA5 4 PHE B 63 PHE B 71 -1 O ALA B 67 N CYS B 26 SHEET 4 AA5 4 GLU B 51 MET B 52 -1 N GLU B 51 O HIS B 68 SHEET 1 AA6 4 GLN B 7 SER B 12 0 SHEET 2 AA6 4 ASN B 22 PHE B 31 -1 O ASN B 25 N TYR B 11 SHEET 3 AA6 4 PHE B 63 PHE B 71 -1 O ALA B 67 N CYS B 26 SHEET 4 AA6 4 SER B 56 PHE B 57 -1 N SER B 56 O TYR B 64 SHEET 1 AA7 4 LYS B 45 LYS B 46 0 SHEET 2 AA7 4 GLU B 37 LYS B 42 -1 N LYS B 42 O LYS B 45 SHEET 3 AA7 4 TYR B 79 LYS B 84 -1 O ARG B 82 N GLN B 39 SHEET 4 AA7 4 LYS B 92 TYR B 95 -1 O LYS B 92 N VAL B 83 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.16 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.00 SSBOND 3 CYS B 26 CYS B 81 1555 1555 2.06 CISPEP 1 TYR A 209 PRO A 210 0 2.61 CISPEP 2 HIS B 32 PRO B 33 0 1.91 CRYST1 115.440 66.570 56.960 90.00 92.01 90.00 C 1 2 1 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 0.008663 0.000000 0.000304 0.00000 SCALE2 0.000000 0.015022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017567 0.00000