HEADER IMMUNE SYSTEM 05-JUN-22 8D5K TITLE THE COMPLEX OF PRE-MRNA-PROCESSING FACTOR 19 (PRPF19) PEPTIDE TITLE 2 KYLQVASHV PRESENTED BY H2-KD COMPND MOL_ID: 1; COMPND 2 MOLECULE: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-D ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: H-2K(D); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: PRE-MRNA-PROCESSING FACTOR 19; COMPND 12 CHAIN: C; COMPND 13 FRAGMENT: UNP RESIDUES 206-214; COMPND 14 SYNONYM: NUCLEAR MATRIX PROTEIN 200,PRP19/PSO4 HOMOLOG,RING-TYPE E3 COMPND 15 UBIQUITIN TRANSFERASE PRP19,SENESCENCE EVASION FACTOR; COMPND 16 EC: 2.3.2.27; COMPND 17 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, H2-K; 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 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PGMT7; SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 20 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 21 ORGANISM_TAXID: 10090 KEYWDS COMPLEX, MHC, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.M.F.CUSTODIO,B.M.BAKER REVDAT 3 17-JAN-24 8D5K 1 JRNL REVDAT 2 18-OCT-23 8D5K 1 REMARK REVDAT 1 06-JUL-22 8D5K 0 JRNL AUTH J.M.CUSTODIO,C.M.AYRES,T.J.ROSALES,C.A.BRAMBLEY,A.G.ARBUISO, JRNL AUTH 2 L.M.LANDAU,G.L.J.KELLER,P.K.SRIVASTAVA,B.M.BAKER JRNL TITL STRUCTURAL AND PHYSICAL FEATURES THAT DISTINGUISH JRNL TITL 2 TUMOR-CONTROLLING FROM INACTIVE CANCER NEOEPITOPES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 57120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 38085776 JRNL DOI 10.1073/PNAS.2312057120 REMARK 2 REMARK 2 RESOLUTION. 2.07 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 3 NUMBER OF REFLECTIONS : 23784 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) : 0.203 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.272 REMARK 3 FREE R VALUE TEST SET COUNT : 1254 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1180 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3139 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.42600 REMARK 3 B22 (A**2) : 3.23500 REMARK 3 B33 (A**2) : -2.81200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.16300 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.253 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.191 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.146 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.527 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3236 ; 0.007 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4402 ; 1.874 ; 1.654 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 378 ; 7.677 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 28 ; 5.714 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 510 ;16.067 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.120 ; 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): 1368 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2181 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 169 ; 0.157 ; 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): 1524 ; 3.064 ; 3.668 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1898 ; 4.188 ; 5.474 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1712 ; 4.248 ; 3.999 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2504 ; 5.805 ; 5.856 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): 20.5597 25.8980 14.5167 REMARK 3 T TENSOR REMARK 3 T11: 0.1250 T22: 0.0314 REMARK 3 T33: 0.0031 T12: 0.0136 REMARK 3 T13: 0.0159 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.8750 L22: 0.4675 REMARK 3 L33: 0.8428 L12: 0.1891 REMARK 3 L13: 0.7986 L23: 0.1743 REMARK 3 S TENSOR REMARK 3 S11: -0.0045 S12: 0.1485 S13: -0.0223 REMARK 3 S21: -0.0240 S22: 0.0357 S23: -0.0217 REMARK 3 S31: -0.1251 S32: 0.1183 S33: -0.0312 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): 18.9106 28.3595 33.4409 REMARK 3 T TENSOR REMARK 3 T11: 0.0890 T22: 0.0208 REMARK 3 T33: 0.0202 T12: -0.0428 REMARK 3 T13: 0.0319 T23: -0.0145 REMARK 3 L TENSOR REMARK 3 L11: 1.2563 L22: 2.2455 REMARK 3 L33: 2.1558 L12: 0.7561 REMARK 3 L13: 0.8129 L23: 1.2803 REMARK 3 S TENSOR REMARK 3 S11: 0.1423 S12: -0.0563 S13: 0.0613 REMARK 3 S21: 0.1642 S22: -0.0643 S23: 0.0911 REMARK 3 S31: -0.0833 S32: 0.0517 S33: -0.0780 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): 5.5100 22.0031 3.2152 REMARK 3 T TENSOR REMARK 3 T11: 0.1157 T22: 0.2528 REMARK 3 T33: 0.0421 T12: 0.0594 REMARK 3 T13: -0.0306 T23: 0.0538 REMARK 3 L TENSOR REMARK 3 L11: 2.4623 L22: 1.7206 REMARK 3 L33: 1.5723 L12: 0.7712 REMARK 3 L13: 0.5637 L23: 1.6169 REMARK 3 S TENSOR REMARK 3 S11: 0.0478 S12: 0.4754 S13: 0.0995 REMARK 3 S21: -0.1291 S22: 0.0294 S23: -0.0752 REMARK 3 S31: -0.1584 S32: -0.0956 S33: -0.0772 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 8D5K 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_1000266073. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : 23784 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 41.349 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28100 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 (%): 49.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG8000, 200 MM MAGNESIUM REMARK 280 ACETATE, VAPOR DIFFUSION, HANGING DROP, 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 57.68500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.68500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.10000 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: 4580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 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 THR A 225 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 LEU A 17 CG CD1 CD2 REMARK 470 LYS A 89 CG CD CE NZ REMARK 470 VAL A 197 CG1 CG2 REMARK 470 LYS A 264 CG CD CE NZ 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: 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 ND2 ASN A 220 ND2 ASN A 220 2656 0.82 REMARK 500 CG ASN A 220 ND2 ASN A 220 2656 1.67 REMARK 500 CG ASN A 220 CG ASN A 220 2656 1.91 REMARK 500 OD1 ASN A 220 ND2 ASN A 220 2656 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 LYS A 186 CB - CA - C ANGL. DEV. = -13.0 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 -127.59 48.37 REMARK 500 TRP B 61 -11.44 87.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 105 ASP A 106 -149.17 REMARK 500 ASP A 223 LEU A 224 -148.93 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 169 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8D5K A 1 274 UNP P01902 HA1D_MOUSE 22 295 DBREF 8D5K B 2 100 UNP P01887 B2MG_MOUSE 21 119 DBREF 8D5K C 1 9 UNP Q99KP6 PRP19_MOUSE 206 214 SEQADV 8D5K GLU A 275 UNP P01902 EXPRESSION TAG SEQADV 8D5K MET B 1 UNP P01887 INITIATING METHIONINE SEQADV 8D5K ASP B 86 UNP P01887 ALA 105 CONFLICT SEQRES 1 A 275 GLY PRO HIS SER LEU ARG TYR PHE VAL THR ALA VAL SER SEQRES 2 A 275 ARG PRO GLY LEU GLY GLU PRO ARG PHE ILE ALA VAL GLY SEQRES 3 A 275 TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER ASP SEQRES 4 A 275 ALA ASP ASN PRO ARG PHE GLU PRO ARG ALA PRO TRP MET SEQRES 5 A 275 GLU GLN GLU GLY PRO GLU TYR TRP GLU GLU GLN THR GLN SEQRES 6 A 275 ARG ALA LYS SER ASP GLU GLN TRP PHE ARG VAL SER LEU SEQRES 7 A 275 ARG THR ALA GLN ARG TYR TYR ASN GLN SER LYS GLY GLY SEQRES 8 A 275 SER HIS THR PHE GLN ARG MET PHE GLY CYS ASP VAL GLY SEQRES 9 A 275 SER ASP TRP ARG LEU LEU ARG GLY TYR GLN GLN PHE ALA SEQRES 10 A 275 TYR ASP GLY ARG ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 A 275 LYS THR TRP THR ALA ALA ASP THR ALA ALA LEU ILE THR SEQRES 12 A 275 ARG ARG LYS TRP GLU GLN ALA GLY ASP ALA GLU TYR TYR SEQRES 13 A 275 ARG ALA TYR LEU GLU GLY GLU CYS VAL GLU TRP LEU ARG SEQRES 14 A 275 ARG TYR LEU GLU LEU GLY ASN GLU THR LEU LEU ARG THR SEQRES 15 A 275 ASP SER PRO LYS ALA HIS VAL THR TYR HIS PRO ARG SER SEQRES 16 A 275 GLN VAL ASP VAL THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 A 275 TYR PRO ALA ASP ILE THR LEU THR TRP GLN LEU ASN GLY SEQRES 18 A 275 GLU ASP LEU THR GLN ASP MET GLU LEU VAL GLU THR ARG SEQRES 19 A 275 PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA VAL SEQRES 20 A 275 VAL VAL PRO LEU GLY LYS GLU GLN ASN TYR THR CYS HIS SEQRES 21 A 275 VAL HIS HIS LYS GLY LEU PRO GLU PRO LEU THR LEU ARG SEQRES 22 A 275 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 ARG GLN VAL ALA SER HIS VAL FORMUL 4 HOH *55(H2 O) HELIX 1 AA1 ALA A 49 GLU A 53 5 5 HELIX 2 AA2 GLY A 56 ASN A 86 1 31 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 GLY A 175 LEU A 180 1 6 HELIX 7 AA7 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 GLY A 26 O PHE A 33 SHEET 4 AA1 8 HIS A 3 VAL A 12 -1 N PHE A 8 O VAL A 25 SHEET 5 AA1 8 THR A 94 VAL A 103 -1 O PHE A 99 N TYR A 7 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 TYR A 123 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 ALA A 245 N CYS A 203 SHEET 4 AA2 4 MET A 228 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 ALA A 245 N CYS A 203 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 260 N THR A 216 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 VAL B 94 N CYS B 81 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.08 SSBOND 2 CYS A 203 CYS A 259 1555 1555 1.98 SSBOND 3 CYS B 26 CYS B 81 1555 1555 2.06 CISPEP 1 TYR A 209 PRO A 210 0 6.11 CISPEP 2 HIS B 32 PRO B 33 0 3.62 CRYST1 115.370 66.200 56.790 90.00 92.42 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 0.008668 0.000000 0.000366 0.00000 SCALE2 0.000000 0.015106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017624 0.00000