HEADER OXIDOREDUCTASE 23-JAN-21 7DYU TITLE HUMAN JMJD5 IN COMPLEX WITH MN AND 5-((4-PHENYLBUTYL)AMINO)PYRIDINE-2, TITLE 2 4-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 7DYU 1 JRNL REVDAT 3 29-NOV-23 7DYU 1 REMARK REVDAT 2 16-AUG-23 7DYU 1 JRNL REVDAT 1 02-FEB-22 7DYU 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. 1.72 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.3 REMARK 3 NUMBER OF REFLECTIONS : 38768 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1849 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 49.8600 - 4.0400 1.00 3770 175 0.1590 0.1775 REMARK 3 2 4.0400 - 3.2100 1.00 3755 211 0.1225 0.1528 REMARK 3 3 3.2100 - 2.8000 1.00 3774 185 0.1310 0.1740 REMARK 3 4 2.8000 - 2.5500 1.00 3798 182 0.1397 0.1802 REMARK 3 5 2.5500 - 2.3700 1.00 3727 215 0.1551 0.2148 REMARK 3 6 2.3700 - 2.2300 1.00 3784 179 0.1686 0.2125 REMARK 3 7 2.2300 - 2.1100 0.98 3704 166 0.1954 0.2468 REMARK 3 8 2.1100 - 2.0200 0.86 3222 168 0.2066 0.2366 REMARK 3 9 2.0200 - 1.9400 0.74 2803 124 0.2277 0.2371 REMARK 3 10 1.9400 - 1.8800 0.58 2227 99 0.2648 0.3819 REMARK 3 11 1.8800 - 1.8200 0.37 1333 94 0.2867 0.2977 REMARK 3 12 1.8200 - 1.7700 0.21 802 39 0.3274 0.3733 REMARK 3 13 1.7700 - 1.7200 0.06 220 12 0.3717 0.4085 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) : 0.126 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.67 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 : 0.017 2072 REMARK 3 ANGLE : 1.271 2844 REMARK 3 CHIRALITY : 0.087 291 REMARK 3 PLANARITY : 0.010 374 REMARK 3 DIHEDRAL : 18.296 765 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): -25.6429 22.4474 -21.2721 REMARK 3 T TENSOR REMARK 3 T11: 0.1369 T22: 0.2138 REMARK 3 T33: 0.2145 T12: 0.0877 REMARK 3 T13: 0.0286 T23: 0.0583 REMARK 3 L TENSOR REMARK 3 L11: 3.0319 L22: 1.6227 REMARK 3 L33: 2.7218 L12: -0.0073 REMARK 3 L13: -0.1801 L23: 0.9984 REMARK 3 S TENSOR REMARK 3 S11: -0.0839 S12: 0.0656 S13: 0.2820 REMARK 3 S21: 0.1661 S22: 0.2669 S23: 0.3599 REMARK 3 S31: -0.2522 S32: -0.5155 S33: -0.0579 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 206 THROUGH 230 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.3725 13.8386 -5.9073 REMARK 3 T TENSOR REMARK 3 T11: 0.3163 T22: 0.2420 REMARK 3 T33: 0.1627 T12: 0.0705 REMARK 3 T13: 0.0403 T23: -0.0168 REMARK 3 L TENSOR REMARK 3 L11: 1.7458 L22: 1.4552 REMARK 3 L33: 2.0187 L12: -1.3600 REMARK 3 L13: 0.5804 L23: -0.5214 REMARK 3 S TENSOR REMARK 3 S11: -0.3962 S12: -0.4531 S13: -0.0129 REMARK 3 S21: 0.6914 S22: 0.4189 S23: 0.0978 REMARK 3 S31: -0.3116 S32: -0.1568 S33: -0.0108 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 231 THROUGH 262 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9361 2.9285 -15.0395 REMARK 3 T TENSOR REMARK 3 T11: 0.1092 T22: 0.1557 REMARK 3 T33: 0.1729 T12: 0.0555 REMARK 3 T13: 0.0319 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 6.3747 L22: 7.8006 REMARK 3 L33: 6.8928 L12: 1.9789 REMARK 3 L13: -2.2696 L23: -0.7815 REMARK 3 S TENSOR REMARK 3 S11: -0.0529 S12: 0.4957 S13: -0.3225 REMARK 3 S21: -0.2246 S22: -0.0792 S23: -0.3220 REMARK 3 S31: 0.2248 S32: 0.1699 S33: 0.0890 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 263 THROUGH 297 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6405 7.2407 -13.0082 REMARK 3 T TENSOR REMARK 3 T11: 0.1792 T22: 0.1327 REMARK 3 T33: 0.1746 T12: -0.0083 REMARK 3 T13: 0.0445 T23: 0.0264 REMARK 3 L TENSOR REMARK 3 L11: 2.8217 L22: 1.8994 REMARK 3 L33: 1.4422 L12: -0.7163 REMARK 3 L13: 1.0831 L23: -0.3251 REMARK 3 S TENSOR REMARK 3 S11: -0.0697 S12: -0.1442 S13: -0.3478 REMARK 3 S21: 0.1681 S22: 0.0771 S23: 0.0503 REMARK 3 S31: 0.1107 S32: -0.0680 S33: -0.0295 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 298 THROUGH 312 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.3974 4.7774 -18.4273 REMARK 3 T TENSOR REMARK 3 T11: 0.1643 T22: 0.1074 REMARK 3 T33: 0.2467 T12: -0.0565 REMARK 3 T13: 0.0523 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 2.5578 L22: 3.0780 REMARK 3 L33: 2.8213 L12: 0.2996 REMARK 3 L13: 0.0390 L23: 0.2253 REMARK 3 S TENSOR REMARK 3 S11: -0.0900 S12: -0.0471 S13: -0.4013 REMARK 3 S21: 0.0976 S22: 0.1296 S23: 0.6103 REMARK 3 S31: 0.5572 S32: -0.7074 S33: -0.0175 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 313 THROUGH 416 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.8737 17.3506 -28.1510 REMARK 3 T TENSOR REMARK 3 T11: 0.0738 T22: 0.0609 REMARK 3 T33: 0.0826 T12: 0.0196 REMARK 3 T13: -0.0010 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 2.0034 L22: 1.7951 REMARK 3 L33: 2.1554 L12: 0.2336 REMARK 3 L13: -0.8990 L23: -0.8013 REMARK 3 S TENSOR REMARK 3 S11: 0.0297 S12: 0.2132 S13: -0.0407 REMARK 3 S21: -0.0574 S22: 0.0346 S23: -0.0364 REMARK 3 S31: -0.0266 S32: -0.0483 S33: -0.0855 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 7DYU 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_1300020474. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-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 : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96862 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38768 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 49.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.15500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 1.80500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 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 (%): 47.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 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 24.68600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.24300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.28200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.24300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.68600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.28200 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: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11170 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 465 GLU A 247 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 GLN A 193 OE1 NE2 REMARK 470 ARG A 196 CZ NH1 NH2 REMARK 470 GLN A 219 CD OE1 NE2 REMARK 470 GLU A 284 CD OE1 OE2 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 872 O HOH A 943 1.87 REMARK 500 O HOH A 917 O HOH A 943 1.88 REMARK 500 O HOH A 824 O HOH A 899 1.89 REMARK 500 O HOH A 872 O HOH A 917 1.91 REMARK 500 O HOH A 958 O HOH A 973 1.91 REMARK 500 O HOH A 948 O HOH A 968 1.96 REMARK 500 O HOH A 886 O HOH A 950 1.96 REMARK 500 O HOH A 876 O HOH A 895 1.96 REMARK 500 O HOH A 918 O HOH A 956 1.97 REMARK 500 O HOH A 842 O HOH A 967 2.00 REMARK 500 O HOH A 828 O HOH A 908 2.01 REMARK 500 O HOH A 925 O HOH A 934 2.01 REMARK 500 O HOH A 870 O HOH A 946 2.02 REMARK 500 O HOH A 951 O HOH A 952 2.03 REMARK 500 O HOH A 808 O HOH A 915 2.06 REMARK 500 O HOH A 894 O HOH A 972 2.07 REMARK 500 O HOH A 960 O HOH A 962 2.08 REMARK 500 O HOH A 932 O HOH A 949 2.11 REMARK 500 O HOH A 956 O HOH A 978 2.11 REMARK 500 O HOH A 892 O HOH A 929 2.12 REMARK 500 O HOH A 889 O HOH A 949 2.13 REMARK 500 O HOH A 891 O HOH A 908 2.15 REMARK 500 O HOH A 914 O HOH A 942 2.15 REMARK 500 O HOH A 911 O HOH A 937 2.18 REMARK 500 O HOH A 860 O HOH A 951 2.19 REMARK 500 O HOH A 847 O HOH A 902 2.19 REMARK 500 O HOH A 926 O HOH A 981 2.19 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 ARG A 189 61.47 33.37 REMARK 500 PHE A 199 -50.57 -131.99 REMARK 500 GLU A 266 98.98 -54.12 REMARK 500 ASN A 367 68.46 -150.59 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 702 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 321 NE2 REMARK 620 2 ASP A 323 OD2 107.2 REMARK 620 3 HIS A 400 NE2 82.9 85.3 REMARK 620 4 HR9 A 704 O2 165.8 86.7 95.9 REMARK 620 5 HR9 A 704 N1 92.4 160.3 98.2 73.7 REMARK 620 6 HOH A 846 O 83.1 87.7 161.8 100.4 94.0 REMARK 620 N 1 2 3 4 5 DBREF 7DYU A 183 416 UNP Q8N371 KDM8_HUMAN 183 416 SEQADV 7DYU 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 TRS A 701 20 HET MN A 702 1 HET TRS A 703 20 HET HR9 A 704 39 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM MN MANGANESE (II) ION HETNAM HR9 5-(4-PHENYLBUTYLAMINO)PYRIDINE-2,4-DICARBOXYLIC ACID HETSYN TRS TRIS BUFFER FORMUL 2 TRS 2(C4 H12 N O3 1+) FORMUL 3 MN MN 2+ FORMUL 5 HR9 C17 H18 N2 O4 FORMUL 6 HOH *182(H2 O) HELIX 1 AA1 SER A 191 PHE A 199 1 9 HELIX 2 AA2 PRO A 216 TRP A 221 1 6 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 PRO A 283 ILE A 289 5 7 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 THR A 354 HIS A 358 5 5 HELIX 11 AB2 PHE A 373 ALA A 379 5 7 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 ILE A 391 N LEU A 208 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 GLY A 271 HIS A 276 -1 N HIS A 276 O ALA A 309 SHEET 8 AA1 9 THR A 234 VAL A 239 -1 N GLU A 238 O TYR A 272 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 702 1555 1555 2.18 LINK OD2 ASP A 323 MN MN A 702 1555 1555 2.21 LINK NE2 HIS A 400 MN MN A 702 1555 1555 2.41 LINK MN MN A 702 O2 HR9 A 704 1555 1555 2.18 LINK MN MN A 702 N1 HR9 A 704 1555 1555 2.34 LINK MN MN A 702 O HOH A 846 1555 1555 2.16 CRYST1 49.372 64.564 78.486 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 0.020254 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015489 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012741 0.00000