HEADER OXIDOREDUCTASE 23-JAN-21 7DYV TITLE HUMAN JMJD5 IN COMPLEX WITH MN AND 5-(BENZYLAMINO)PYRIDINE-2,4- TITLE 2 DICARBOXYLIC ACID. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL PEPTIDASE AND ARGINYL-HYDROXYLASE JMJD5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING PROTEIN 5,JUMONJI C DOMAIN-CONTAINING COMPND 5 PROTEIN 5,L-ARGININE (3R)-HYDROXYLASE KDM8; COMPND 6 EC: 1.14.11.-,3.4.-.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM8, JMJD5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS JMJC DOMAIN-CONTAINING PROTEIN 5, JMJD5, DIOXYGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.NAKASHIMA,L.BREWITZ,C.J.SCHOFIELD REVDAT 4 06-DEC-23 7DYV 1 JRNL REVDAT 3 29-NOV-23 7DYV 1 REMARK REVDAT 2 16-AUG-23 7DYV 1 JRNL REVDAT 1 02-FEB-22 7DYV 0 JRNL AUTH L.BREWITZ,Y.NAKASHIMA,S.K.PIASECKA,E.SALAH,S.C.FLETCHER, JRNL AUTH 2 A.TUMBER,T.P.CORNER,T.J.KENNEDY,G.FIORINI,A.THALHAMMER, JRNL AUTH 3 K.E.CHRISTENSEN,M.L.COLEMAN,C.J.SCHOFIELD JRNL TITL 5-SUBSTITUTED PYRIDINE-2,4-DICARBOXYLATE DERIVATIVES HAVE JRNL TITL 2 POTENTIAL FOR SELECTIVE INHIBITION OF HUMAN JUMONJI-C JRNL TITL 3 DOMAIN-CONTAINING PROTEIN 5. JRNL REF J.MED.CHEM. V. 66 10849 2023 JRNL REFN ISSN 0022-2623 JRNL PMID 37527664 JRNL DOI 10.1021/ACS.JMEDCHEM.3C01114 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 37023 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3705 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 50.2500 - 5.6900 1.00 1286 145 0.2220 0.2789 REMARK 3 2 5.6800 - 4.5200 1.00 1305 141 0.1648 0.1694 REMARK 3 3 4.5100 - 3.9400 1.00 1294 141 0.1446 0.1689 REMARK 3 4 3.9400 - 3.5800 1.00 1304 144 0.1553 0.1764 REMARK 3 5 3.5800 - 3.3300 1.00 1289 147 0.1701 0.2151 REMARK 3 6 3.3300 - 3.1300 1.00 1298 145 0.1664 0.1944 REMARK 3 7 3.1300 - 2.9700 1.00 1297 148 0.1806 0.2141 REMARK 3 8 2.9700 - 2.8400 1.00 1287 133 0.2011 0.3024 REMARK 3 9 2.8400 - 2.7300 0.98 1265 137 0.2088 0.2932 REMARK 3 10 2.7300 - 2.6400 0.99 1301 142 0.2284 0.2353 REMARK 3 11 2.6400 - 2.5600 0.99 1290 149 0.2112 0.2426 REMARK 3 12 2.5600 - 2.4800 0.99 1289 145 0.2098 0.2473 REMARK 3 13 2.4800 - 2.4200 1.00 1294 140 0.2129 0.3059 REMARK 3 14 2.4200 - 2.3600 0.99 1281 144 0.2164 0.2593 REMARK 3 15 2.3600 - 2.3100 0.99 1299 145 0.2270 0.2559 REMARK 3 16 2.3100 - 2.2600 1.00 1281 143 0.2314 0.2845 REMARK 3 17 2.2600 - 2.2100 0.99 1268 143 0.2825 0.2615 REMARK 3 18 2.2100 - 2.1700 0.99 1305 145 0.2546 0.3104 REMARK 3 19 2.1700 - 2.1300 0.98 1279 143 0.2662 0.2723 REMARK 3 20 2.1300 - 2.1000 0.98 1253 140 0.2642 0.3129 REMARK 3 21 2.1000 - 2.0600 0.99 1267 135 0.2984 0.3093 REMARK 3 22 2.0600 - 2.0300 0.98 1302 146 0.3067 0.3860 REMARK 3 23 2.0300 - 2.0000 0.97 1246 141 0.2918 0.2953 REMARK 3 24 2.0000 - 1.9700 0.96 1234 139 0.3372 0.3825 REMARK 3 25 1.9700 - 1.9500 0.95 1240 144 0.3587 0.3553 REMARK 3 26 1.9500 - 1.9200 0.97 1264 140 0.3843 0.4089 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.291 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.19 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 : 0.003 2131 REMARK 3 ANGLE : 0.588 2933 REMARK 3 CHIRALITY : 0.047 301 REMARK 3 PLANARITY : 0.004 393 REMARK 3 DIHEDRAL : 13.214 798 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 182 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.1018 22.0214 -21.2270 REMARK 3 T TENSOR REMARK 3 T11: 0.2545 T22: 0.3956 REMARK 3 T33: 0.3467 T12: 0.0865 REMARK 3 T13: 0.0096 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 4.5605 L22: 3.1891 REMARK 3 L33: 4.8973 L12: -0.1859 REMARK 3 L13: 0.2274 L23: 0.4257 REMARK 3 S TENSOR REMARK 3 S11: -0.1525 S12: -0.2750 S13: 0.2815 REMARK 3 S21: 0.0769 S22: 0.1574 S23: 0.5635 REMARK 3 S31: -0.1716 S32: -0.6119 S33: -0.1012 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 206 THROUGH 230 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7606 12.7582 -5.6623 REMARK 3 T TENSOR REMARK 3 T11: 0.3244 T22: 0.3902 REMARK 3 T33: 0.2633 T12: 0.0371 REMARK 3 T13: 0.0200 T23: -0.0324 REMARK 3 L TENSOR REMARK 3 L11: 1.6235 L22: 0.7339 REMARK 3 L33: 3.4107 L12: -1.0212 REMARK 3 L13: 2.0012 L23: -1.5076 REMARK 3 S TENSOR REMARK 3 S11: -0.2847 S12: -0.4673 S13: 0.1085 REMARK 3 S21: 0.4430 S22: 0.2908 S23: -0.0756 REMARK 3 S31: -0.2502 S32: -0.2788 S33: -0.0228 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 231 THROUGH 248 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.7718 2.5352 -17.6595 REMARK 3 T TENSOR REMARK 3 T11: 0.2287 T22: 0.2171 REMARK 3 T33: 0.2810 T12: 0.0693 REMARK 3 T13: -0.0370 T23: -0.0365 REMARK 3 L TENSOR REMARK 3 L11: 7.1487 L22: 2.2823 REMARK 3 L33: 9.3454 L12: 0.3899 REMARK 3 L13: -3.4448 L23: 0.1775 REMARK 3 S TENSOR REMARK 3 S11: 0.1489 S12: 0.1533 S13: 0.1180 REMARK 3 S21: -0.0194 S22: 0.1009 S23: -0.0160 REMARK 3 S31: -0.0465 S32: -0.0844 S33: -0.2830 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 249 THROUGH 262 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8941 3.4245 -13.9367 REMARK 3 T TENSOR REMARK 3 T11: 0.2187 T22: 0.3289 REMARK 3 T33: 0.3133 T12: 0.0403 REMARK 3 T13: -0.0170 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 4.9286 L22: 7.8694 REMARK 3 L33: 6.4566 L12: -0.4090 REMARK 3 L13: -3.3568 L23: -0.5486 REMARK 3 S TENSOR REMARK 3 S11: -0.0675 S12: -0.1219 S13: -0.1364 REMARK 3 S21: 0.0838 S22: -0.3490 S23: -0.1664 REMARK 3 S31: 0.3122 S32: 0.4947 S33: 0.1527 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 263 THROUGH 333 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.4865 8.3366 -16.4989 REMARK 3 T TENSOR REMARK 3 T11: 0.2769 T22: 0.2732 REMARK 3 T33: 0.2606 T12: -0.0137 REMARK 3 T13: 0.0170 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 1.5804 L22: 1.7092 REMARK 3 L33: 2.0871 L12: -0.6436 REMARK 3 L13: 0.7012 L23: -0.9597 REMARK 3 S TENSOR REMARK 3 S11: -0.0411 S12: -0.1880 S13: -0.0638 REMARK 3 S21: 0.0552 S22: 0.0330 S23: 0.0210 REMARK 3 S31: 0.1270 S32: -0.1561 S33: -0.0559 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 334 THROUGH 416 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.7537 18.3657 -29.3485 REMARK 3 T TENSOR REMARK 3 T11: 0.2163 T22: 0.1804 REMARK 3 T33: 0.2236 T12: 0.0148 REMARK 3 T13: -0.0016 T23: -0.0155 REMARK 3 L TENSOR REMARK 3 L11: 1.9134 L22: 1.3842 REMARK 3 L33: 2.2706 L12: 0.2939 REMARK 3 L13: -0.8266 L23: -0.8828 REMARK 3 S TENSOR REMARK 3 S11: 0.0015 S12: 0.2012 S13: -0.0133 REMARK 3 S21: -0.0372 S22: 0.0692 S23: 0.0361 REMARK 3 S31: -0.0062 S32: -0.0089 S33: -0.0356 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 7DYV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020468. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-19 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97622 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37023 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 50.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.71100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 1.27700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.800 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: 6F4P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES SODIUM, 200MM MAGNESIUM REMARK 280 CHLORIDE HEXAHYDRATE, 25% W/V PEG 3350, 1MM MANGANESE CHLORIDE, REMARK 280 PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 24.66900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.30500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.66950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.30500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.66900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.66950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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 SER A 241 REMARK 465 ARG A 242 REMARK 465 TYR A 243 REMARK 465 THR A 244 REMARK 465 ASP A 245 REMARK 465 GLU A 246 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 GLU A 247 CG CD OE1 OE2 REMARK 470 ASP A 353 CG OD1 OD2 REMARK 470 LEU A 356 CG CD1 CD2 REMARK 470 LYS A 378 CE NZ 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 632 O HOH A 692 2.10 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 PHE A 199 -51.48 -142.78 REMARK 500 ILE A 263 -55.67 -123.82 REMARK 500 ILE A 263 -59.16 -121.16 REMARK 500 ASN A 265 67.86 -101.18 REMARK 500 GLU A 266 72.18 31.58 REMARK 500 ASN A 367 65.67 -155.69 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 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 321 NE2 REMARK 620 2 ASP A 323 OD2 108.8 REMARK 620 3 HIS A 400 NE2 82.9 83.6 REMARK 620 4 HRF A 502 O2 158.7 91.5 93.3 REMARK 620 5 HRF A 502 N1 89.7 158.7 109.8 71.8 REMARK 620 6 HOH A 637 O 78.3 88.9 156.3 109.4 84.6 REMARK 620 N 1 2 3 4 5 DBREF 7DYV A 183 416 UNP Q8N371 KDM8_HUMAN 183 416 SEQADV 7DYV SER A 182 UNP Q8N371 EXPRESSION TAG SEQRES 1 A 235 SER THR VAL PRO ARG LEU HIS ARG PRO SER LEU GLN HIS SEQRES 2 A 235 PHE ARG GLU GLN PHE LEU VAL PRO GLY ARG PRO VAL ILE SEQRES 3 A 235 LEU LYS GLY VAL ALA ASP HIS TRP PRO CYS MET GLN LYS SEQRES 4 A 235 TRP SER LEU GLU TYR ILE GLN GLU ILE ALA GLY CYS ARG SEQRES 5 A 235 THR VAL PRO VAL GLU VAL GLY SER ARG TYR THR ASP GLU SEQRES 6 A 235 GLU TRP SER GLN THR LEU MET THR VAL ASN GLU PHE ILE SEQRES 7 A 235 SER LYS TYR ILE VAL ASN GLU PRO ARG ASP VAL GLY TYR SEQRES 8 A 235 LEU ALA GLN HIS GLN LEU PHE ASP GLN ILE PRO GLU LEU SEQRES 9 A 235 LYS GLN ASP ILE SER ILE PRO ASP TYR CYS SER LEU GLY SEQRES 10 A 235 ASP GLY GLU GLU GLU GLU ILE THR ILE ASN ALA TRP PHE SEQRES 11 A 235 GLY PRO GLN GLY THR ILE SER PRO LEU HIS GLN ASP PRO SEQRES 12 A 235 GLN GLN ASN PHE LEU VAL GLN VAL MET GLY ARG LYS TYR SEQRES 13 A 235 ILE ARG LEU TYR SER PRO GLN GLU SER GLY ALA LEU TYR SEQRES 14 A 235 PRO HIS ASP THR HIS LEU LEU HIS ASN THR SER GLN VAL SEQRES 15 A 235 ASP VAL GLU ASN PRO ASP LEU GLU LYS PHE PRO LYS PHE SEQRES 16 A 235 ALA LYS ALA PRO PHE LEU SER CYS ILE LEU SER PRO GLY SEQRES 17 A 235 GLU ILE LEU PHE ILE PRO VAL LYS TYR TRP HIS TYR VAL SEQRES 18 A 235 ARG ALA LEU ASP LEU SER PHE SER VAL SER PHE TRP TRP SEQRES 19 A 235 SER HET MN A 501 1 HET HRF A 502 30 HETNAM MN MANGANESE (II) ION HETNAM HRF 5-(BENZYLAMINO)PYRIDINE-2,4-DICARBOXYLIC ACID FORMUL 2 MN MN 2+ FORMUL 3 HRF C14 H12 N2 O4 FORMUL 4 HOH *129(H2 O) HELIX 1 AA1 SER A 191 PHE A 199 1 9 HELIX 2 AA2 TRP A 215 TRP A 221 1 7 HELIX 3 AA3 SER A 222 GLY A 231 1 10 HELIX 4 AA4 VAL A 255 ILE A 263 1 9 HELIX 5 AA5 GLN A 277 ILE A 282 1 6 HELIX 6 AA6 ILE A 282 GLN A 287 1 6 HELIX 7 AA7 PRO A 292 GLY A 298 5 7 HELIX 8 AA8 GLU A 301 ILE A 305 5 5 HELIX 9 AA9 SER A 342 TYR A 350 5 9 HELIX 10 AB1 PHE A 373 ALA A 377 5 5 SHEET 1 AA1 9 ARG A 186 HIS A 188 0 SHEET 2 AA1 9 VAL A 206 LYS A 209 1 O LYS A 209 N LEU A 187 SHEET 3 AA1 9 ILE A 391 ILE A 394 -1 O PHE A 393 N VAL A 206 SHEET 4 AA1 9 GLN A 326 MET A 333 -1 N LEU A 329 O LEU A 392 SHEET 5 AA1 9 SER A 408 TRP A 415 -1 O VAL A 411 N VAL A 330 SHEET 6 AA1 9 THR A 306 GLY A 312 -1 N THR A 306 O TRP A 414 SHEET 7 AA1 9 VAL A 270 HIS A 276 -1 N HIS A 276 O ALA A 309 SHEET 8 AA1 9 THR A 234 GLY A 240 -1 N GLY A 240 O VAL A 270 SHEET 9 AA1 9 SER A 249 THR A 254 -1 O SER A 249 N VAL A 239 SHEET 1 AA2 3 LEU A 382 LEU A 386 0 SHEET 2 AA2 3 LYS A 336 TYR A 341 -1 N LEU A 340 O LEU A 382 SHEET 3 AA2 3 TRP A 399 ALA A 404 -1 O ARG A 403 N TYR A 337 LINK NE2 HIS A 321 MN MN A 501 1555 1555 2.35 LINK OD2 ASP A 323 MN MN A 501 1555 1555 2.19 LINK NE2 HIS A 400 MN MN A 501 1555 1555 2.36 LINK MN MN A 501 O2 HRF A 502 1555 1555 2.16 LINK MN MN A 501 N1 HRF A 502 1555 1555 2.41 LINK MN MN A 501 O HOH A 637 1555 1555 2.03 CRYST1 49.338 65.339 78.610 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020268 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012721 0.00000