HEADER OXIDOREDUCTASE 05-DEC-11 4AAP TITLE CRYSTAL STRUCTURE OF JMJD5 DOMAIN OF HUMAN LYSINE-SPECIFIC DEMETHYLASE TITLE 2 8 (KDM8) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 8; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: JMJD5 DOMAIN, RESIDUES 218-454; COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING PROTEIN 5, JUMONJI DOMAIN-CONTAINING COMPND 6 PROTEIN 5; COMPND 7 EC: 1.14.11.27; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.VOLLMAR,C.JOHANSSON,T.KROJER,P.CANNING,C.ALLERSTON,A.GADHAVE,F.VON AUTHOR 2 DELFT,C.BOUNTRA,C.H.ARROWSMITH,J.WEIGELT,A.EDWARDS,U.OPPERMANN REVDAT 2 24-JAN-18 4AAP 1 JRNL REVDAT 1 29-FEB-12 4AAP 0 JRNL AUTH M.VOLLMAR,C.JOHANSSON,T.KROJER,P.CANNING,C.ALLERSTON, JRNL AUTH 2 A.GADHAVE,F.VON DELFT,C.BOUNTRA,C.H.ARROWSMITH,J.WEIGELT, JRNL AUTH 3 A.EDWARDS,U.OPPERMANN JRNL TITL CRYSTAL STRUCTURE OF JMJD5 DOMAIN OF HUMAN LYSINE- SPECIFIC JRNL TITL 2 DEMETHYLASE 8 (KDM8) IN COMPLEX WITH N- OXALYLGLYCINE (NOG) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 89.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 22281 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1210 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1448 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.4770 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.5990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3672 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 88.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25000 REMARK 3 B22 (A**2) : 0.25000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.13000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.391 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.274 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.213 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.432 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3808 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2513 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5205 ; 1.295 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6107 ; 0.975 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 462 ; 6.780 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;34.763 ;23.533 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 547 ;13.992 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;23.232 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 560 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4253 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 814 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 282 REMARK 3 ORIGIN FOR THE GROUP (A): 24.6652 -12.0809 -1.9943 REMARK 3 T TENSOR REMARK 3 T11: 0.4192 T22: 0.0631 REMARK 3 T33: 0.2853 T12: -0.0753 REMARK 3 T13: -0.0888 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 4.8088 L22: 2.0349 REMARK 3 L33: 5.2214 L12: 1.9192 REMARK 3 L13: -2.8134 L23: -1.5470 REMARK 3 S TENSOR REMARK 3 S11: 0.1240 S12: -0.1738 S13: -0.0407 REMARK 3 S21: 0.0578 S22: -0.0546 S23: -0.0382 REMARK 3 S31: 0.1487 S32: -0.3229 S33: -0.0693 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 283 A 379 REMARK 3 ORIGIN FOR THE GROUP (A): 33.1157 -7.6050 -3.3437 REMARK 3 T TENSOR REMARK 3 T11: 0.4114 T22: 0.0405 REMARK 3 T33: 0.2454 T12: -0.0938 REMARK 3 T13: -0.0476 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 3.8459 L22: 2.8458 REMARK 3 L33: 3.8113 L12: 2.0047 REMARK 3 L13: -0.5720 L23: -1.1430 REMARK 3 S TENSOR REMARK 3 S11: 0.2002 S12: -0.2452 S13: -0.0413 REMARK 3 S21: 0.0255 S22: -0.2125 S23: -0.2259 REMARK 3 S31: -0.1039 S32: 0.1092 S33: 0.0124 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 380 A 410 REMARK 3 ORIGIN FOR THE GROUP (A): 38.4239 -10.5823 17.0958 REMARK 3 T TENSOR REMARK 3 T11: 0.6386 T22: 0.6932 REMARK 3 T33: 0.3986 T12: -0.3294 REMARK 3 T13: -0.1949 T23: -0.0189 REMARK 3 L TENSOR REMARK 3 L11: 14.3354 L22: 7.7460 REMARK 3 L33: 3.0030 L12: -5.7384 REMARK 3 L13: 0.0724 L23: -0.3397 REMARK 3 S TENSOR REMARK 3 S11: 0.2227 S12: -0.6083 S13: 0.2145 REMARK 3 S21: 0.8438 S22: -0.2116 S23: -0.9340 REMARK 3 S31: -0.3142 S32: 0.2660 S33: -0.0111 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 411 A 454 REMARK 3 ORIGIN FOR THE GROUP (A): 30.2036 -13.6034 6.4862 REMARK 3 T TENSOR REMARK 3 T11: 0.4623 T22: 0.4304 REMARK 3 T33: 0.1978 T12: -0.1852 REMARK 3 T13: -0.0682 T23: 0.0387 REMARK 3 L TENSOR REMARK 3 L11: 2.5268 L22: 2.8148 REMARK 3 L33: 5.4384 L12: 0.1474 REMARK 3 L13: 1.5225 L23: -2.1471 REMARK 3 S TENSOR REMARK 3 S11: 0.2164 S12: -0.7272 S13: -0.2095 REMARK 3 S21: 0.5007 S22: -0.2057 S23: -0.2881 REMARK 3 S31: -0.2922 S32: 0.4145 S33: -0.0107 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 0 B 284 REMARK 3 ORIGIN FOR THE GROUP (A): 25.7995 -31.4620 43.4268 REMARK 3 T TENSOR REMARK 3 T11: 0.0756 T22: 0.2858 REMARK 3 T33: 0.2985 T12: -0.0920 REMARK 3 T13: 0.0323 T23: -0.0259 REMARK 3 L TENSOR REMARK 3 L11: 4.0304 L22: 2.1713 REMARK 3 L33: 4.9644 L12: -1.8230 REMARK 3 L13: 2.3864 L23: -0.9413 REMARK 3 S TENSOR REMARK 3 S11: -0.1688 S12: -0.1033 S13: 0.1082 REMARK 3 S21: 0.0571 S22: 0.1658 S23: 0.0254 REMARK 3 S31: 0.1209 S32: 0.2397 S33: 0.0030 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 285 B 379 REMARK 3 ORIGIN FOR THE GROUP (A): 18.2031 -26.9873 41.1524 REMARK 3 T TENSOR REMARK 3 T11: 0.0399 T22: 0.3080 REMARK 3 T33: 0.2137 T12: -0.0619 REMARK 3 T13: 0.0256 T23: -0.0279 REMARK 3 L TENSOR REMARK 3 L11: 4.0641 L22: 1.9456 REMARK 3 L33: 4.4913 L12: -0.9102 REMARK 3 L13: 1.3661 L23: -0.5851 REMARK 3 S TENSOR REMARK 3 S11: -0.2481 S12: -0.1854 S13: 0.1640 REMARK 3 S21: 0.0600 S22: 0.1552 S23: 0.0337 REMARK 3 S31: 0.0360 S32: -0.1675 S33: 0.0929 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 380 B 410 REMARK 3 ORIGIN FOR THE GROUP (A): 18.4830 -20.1395 62.2273 REMARK 3 T TENSOR REMARK 3 T11: 0.4496 T22: 0.6943 REMARK 3 T33: 0.3425 T12: 0.1554 REMARK 3 T13: 0.0780 T23: -0.1491 REMARK 3 L TENSOR REMARK 3 L11: 5.2946 L22: 18.6089 REMARK 3 L33: 4.6127 L12: 0.9943 REMARK 3 L13: 0.9535 L23: -1.8944 REMARK 3 S TENSOR REMARK 3 S11: -0.0042 S12: -0.9170 S13: 0.5560 REMARK 3 S21: -0.1074 S22: -0.2687 S23: 0.6147 REMARK 3 S31: -0.1307 S32: -0.0675 S33: 0.2729 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 411 B 454 REMARK 3 ORIGIN FOR THE GROUP (A): 24.9320 -26.3808 50.9644 REMARK 3 T TENSOR REMARK 3 T11: 0.1471 T22: 0.3930 REMARK 3 T33: 0.2136 T12: 0.0332 REMARK 3 T13: -0.0146 T23: -0.0350 REMARK 3 L TENSOR REMARK 3 L11: 3.9750 L22: 2.2712 REMARK 3 L33: 4.2718 L12: -0.2984 REMARK 3 L13: 0.9046 L23: 0.3754 REMARK 3 S TENSOR REMARK 3 S11: -0.2406 S12: -0.6336 S13: 0.3233 REMARK 3 S21: 0.4995 S22: 0.2824 S23: -0.0120 REMARK 3 S31: -0.2296 S32: -0.0875 S33: -0.0417 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES WITH TLS ADDED. REMARK 4 REMARK 4 4AAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1290050598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-11 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 : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23473 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.77000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG_3350, 0.007M NICL, 0M CDCL, REMARK 280 0.007M MGCL, 0.1M HEPES PH 7.3 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 179.33533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.66767 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 89.66767 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 179.33533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 -1 REMARK 465 GLU A 304 REMARK 465 PRO A 305 REMARK 465 LEU A 395 REMARK 465 SER B -1 REMARK 465 GLU B 304 REMARK 465 PRO B 305 REMARK 465 LEU B 394 REMARK 465 LEU B 395 REMARK 465 HIS B 396 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 MET A 0 CG SD CE REMARK 470 LEU A 218 CG CD1 CD2 REMARK 470 LYS A 220 CD CE NZ REMARK 470 GLN A 257 CG CD OE1 NE2 REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 LYS A 299 CG CD CE NZ REMARK 470 VAL A 302 CG1 CG2 REMARK 470 ASN A 303 CG OD1 ND2 REMARK 470 ARG A 306 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 322 CG CD OE1 OE2 REMARK 470 LYS A 324 CD CE NZ REMARK 470 GLU A 339 CG CD OE1 OE2 REMARK 470 GLU A 341 CG CD OE1 OE2 REMARK 470 GLU A 342 CG CD OE1 OE2 REMARK 470 ASP A 391 CG OD1 OD2 REMARK 470 LEU A 394 CG CD1 CD2 REMARK 470 HIS A 396 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 397 CG OD1 ND2 REMARK 470 THR A 398 OG1 CG2 REMARK 470 VAL A 401 CG1 CG2 REMARK 470 ASN A 405 CG OD1 ND2 REMARK 470 ASP A 407 CG OD1 OD2 REMARK 470 LEU A 408 CG CD1 CD2 REMARK 470 GLU A 409 CG CD OE1 OE2 REMARK 470 LYS A 410 CG CD CE NZ REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 MET B 0 CG SD CE REMARK 470 GLN B 236 CG CD OE1 NE2 REMARK 470 GLN B 257 CG CD OE1 NE2 REMARK 470 GLU B 262 CG CD OE1 OE2 REMARK 470 SER B 279 OG REMARK 470 ARG B 280 NE CZ NH1 NH2 REMARK 470 GLU B 285 CG CD OE1 OE2 REMARK 470 ASN B 303 CG OD1 ND2 REMARK 470 ARG B 306 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 307 CG OD1 OD2 REMARK 470 GLU B 339 CG CD OE1 OE2 REMARK 470 GLU B 341 CG CD OE1 OE2 REMARK 470 GLN B 382 CD OE1 NE2 REMARK 470 ASP B 391 CG OD1 OD2 REMARK 470 THR B 392 OG1 CG2 REMARK 470 ASN B 397 CG OD1 ND2 REMARK 470 THR B 398 OG1 CG2 REMARK 470 ASN B 405 CG OD1 ND2 REMARK 470 ASP B 407 CG OD1 OD2 REMARK 470 LEU B 408 CG CD1 CD2 REMARK 470 GLU B 409 CG CD OE1 OE2 REMARK 470 LYS B 410 CG CD CE NZ REMARK 470 LYS B 413 CG CD CE NZ REMARK 470 LYS B 416 CG CD CE NZ REMARK 470 LYS B 435 CE NZ 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 237 -47.26 -135.31 REMARK 500 ARG A 280 34.57 -82.86 REMARK 500 ASN A 405 57.93 -164.90 REMARK 500 LYS A 416 33.98 -99.03 REMARK 500 PHE B 237 -47.43 -135.08 REMARK 500 ARG B 280 35.60 -81.68 REMARK 500 ASN B 405 58.08 -165.03 REMARK 500 LYS B 416 33.61 -98.85 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 ZN A 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 361 OD2 REMARK 620 2 OGA A 501 O1 71.1 REMARK 620 3 OGA A 501 O2' 150.8 84.3 REMARK 620 4 HIS A 359 NE2 121.7 153.3 75.4 REMARK 620 5 HIS A 438 NE2 71.8 80.7 89.2 81.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 252 NE2 REMARK 620 2 ASP A 283 OD2 84.7 REMARK 620 3 HIS A 393 NE2 83.3 167.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 438 NE2 REMARK 620 2 OGA B 501 O2' 97.4 REMARK 620 3 ASP B 361 OD2 73.1 156.4 REMARK 620 4 HIS B 359 NE2 85.4 74.8 124.5 REMARK 620 5 OGA B 501 O1 90.3 84.9 73.7 158.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 502 DBREF 4AAP A 218 454 UNP Q8N371 KDM8_HUMAN 218 454 DBREF 4AAP B 218 454 UNP Q8N371 KDM8_HUMAN 218 454 SEQADV 4AAP SER A -1 UNP Q8N371 EXPRESSION TAG SEQADV 4AAP MET A 0 UNP Q8N371 EXPRESSION TAG SEQADV 4AAP SER B -1 UNP Q8N371 EXPRESSION TAG SEQADV 4AAP MET B 0 UNP Q8N371 EXPRESSION TAG SEQRES 1 A 239 SER MET LEU GLU LYS THR VAL PRO ARG LEU HIS ARG PRO SEQRES 2 A 239 SER LEU GLN HIS PHE ARG GLU GLN PHE LEU VAL PRO GLY SEQRES 3 A 239 ARG PRO VAL ILE LEU LYS GLY VAL ALA ASP HIS TRP PRO SEQRES 4 A 239 CYS MET GLN LYS TRP SER LEU GLU TYR ILE GLN GLU ILE SEQRES 5 A 239 ALA GLY CYS ARG THR VAL PRO VAL GLU VAL GLY SER ARG SEQRES 6 A 239 TYR THR ASP GLU GLU TRP SER GLN THR LEU MET THR VAL SEQRES 7 A 239 ASN GLU PHE ILE SER LYS TYR ILE VAL ASN GLU PRO ARG SEQRES 8 A 239 ASP VAL GLY TYR LEU ALA GLN HIS GLN LEU PHE ASP GLN SEQRES 9 A 239 ILE PRO GLU LEU LYS GLN ASP ILE SER ILE PRO ASP TYR SEQRES 10 A 239 CYS SER LEU GLY ASP GLY GLU GLU GLU GLU ILE THR ILE SEQRES 11 A 239 ASN ALA TRP PHE GLY PRO GLN GLY THR ILE SER PRO LEU SEQRES 12 A 239 HIS GLN ASP PRO GLN GLN ASN PHE LEU VAL GLN VAL MET SEQRES 13 A 239 GLY ARG LYS TYR ILE ARG LEU TYR SER PRO GLN GLU SER SEQRES 14 A 239 GLY ALA LEU TYR PRO HIS ASP THR HIS LEU LEU HIS ASN SEQRES 15 A 239 THR SER GLN VAL ASP VAL GLU ASN PRO ASP LEU GLU LYS SEQRES 16 A 239 PHE PRO LYS PHE ALA LYS ALA PRO PHE LEU SER CYS ILE SEQRES 17 A 239 LEU SER PRO GLY GLU ILE LEU PHE ILE PRO VAL LYS TYR SEQRES 18 A 239 TRP HIS TYR VAL ARG ALA LEU ASP LEU SER PHE SER VAL SEQRES 19 A 239 SER PHE TRP TRP SER SEQRES 1 B 239 SER MET LEU GLU LYS THR VAL PRO ARG LEU HIS ARG PRO SEQRES 2 B 239 SER LEU GLN HIS PHE ARG GLU GLN PHE LEU VAL PRO GLY SEQRES 3 B 239 ARG PRO VAL ILE LEU LYS GLY VAL ALA ASP HIS TRP PRO SEQRES 4 B 239 CYS MET GLN LYS TRP SER LEU GLU TYR ILE GLN GLU ILE SEQRES 5 B 239 ALA GLY CYS ARG THR VAL PRO VAL GLU VAL GLY SER ARG SEQRES 6 B 239 TYR THR ASP GLU GLU TRP SER GLN THR LEU MET THR VAL SEQRES 7 B 239 ASN GLU PHE ILE SER LYS TYR ILE VAL ASN GLU PRO ARG SEQRES 8 B 239 ASP VAL GLY TYR LEU ALA GLN HIS GLN LEU PHE ASP GLN SEQRES 9 B 239 ILE PRO GLU LEU LYS GLN ASP ILE SER ILE PRO ASP TYR SEQRES 10 B 239 CYS SER LEU GLY ASP GLY GLU GLU GLU GLU ILE THR ILE SEQRES 11 B 239 ASN ALA TRP PHE GLY PRO GLN GLY THR ILE SER PRO LEU SEQRES 12 B 239 HIS GLN ASP PRO GLN GLN ASN PHE LEU VAL GLN VAL MET SEQRES 13 B 239 GLY ARG LYS TYR ILE ARG LEU TYR SER PRO GLN GLU SER SEQRES 14 B 239 GLY ALA LEU TYR PRO HIS ASP THR HIS LEU LEU HIS ASN SEQRES 15 B 239 THR SER GLN VAL ASP VAL GLU ASN PRO ASP LEU GLU LYS SEQRES 16 B 239 PHE PRO LYS PHE ALA LYS ALA PRO PHE LEU SER CYS ILE SEQRES 17 B 239 LEU SER PRO GLY GLU ILE LEU PHE ILE PRO VAL LYS TYR SEQRES 18 B 239 TRP HIS TYR VAL ARG ALA LEU ASP LEU SER PHE SER VAL SEQRES 19 B 239 SER PHE TRP TRP SER HET ZN A 500 1 HET OGA A 501 10 HET ZN A 502 1 HET ZN B 500 1 HET OGA B 501 10 HET ZN B 502 1 HETNAM ZN ZINC ION HETNAM OGA N-OXALYLGLYCINE FORMUL 3 ZN 4(ZN 2+) FORMUL 4 OGA 2(C4 H5 N O5) FORMUL 9 HOH *29(H2 O) HELIX 1 1 SER A 229 PHE A 237 1 9 HELIX 2 2 TRP A 253 TRP A 259 1 7 HELIX 3 3 SER A 260 GLY A 269 1 10 HELIX 4 4 VAL A 293 ILE A 301 1 9 HELIX 5 5 GLN A 315 ILE A 320 1 6 HELIX 6 6 PRO A 321 ILE A 327 5 7 HELIX 7 7 PRO A 330 GLY A 336 5 7 HELIX 8 8 GLU A 339 ILE A 343 5 5 HELIX 9 9 SER A 380 TYR A 388 5 9 HELIX 10 10 SER B 229 PHE B 237 1 9 HELIX 11 11 TRP B 253 TRP B 259 1 7 HELIX 12 12 SER B 260 GLY B 269 1 10 HELIX 13 13 VAL B 293 ILE B 301 1 9 HELIX 14 14 GLN B 315 ILE B 320 1 6 HELIX 15 15 ILE B 320 GLN B 325 1 6 HELIX 16 16 PRO B 330 GLY B 336 5 7 HELIX 17 17 GLU B 339 ILE B 343 5 5 HELIX 18 18 SER B 380 TYR B 388 5 9 SHEET 1 AA 5 GLU A 219 THR A 221 0 SHEET 2 AA 5 PHE A 419 LEU A 424 1 O PHE A 419 N LYS A 220 SHEET 3 AA 5 LYS A 374 TYR A 379 -1 O LYS A 374 N LEU A 424 SHEET 4 AA 5 TRP A 437 ALA A 442 -1 O TRP A 437 N TYR A 379 SHEET 5 AA 5 ILE A 355 HIS A 359 -1 O SER A 356 N VAL A 440 SHEET 1 AB 7 ARG A 224 HIS A 226 0 SHEET 2 AB 7 VAL A 244 LYS A 247 1 O ILE A 245 N LEU A 225 SHEET 3 AB 7 ILE A 429 ILE A 432 -1 O ILE A 429 N LEU A 246 SHEET 4 AB 7 GLN A 364 MET A 371 -1 O ASN A 365 N ILE A 432 SHEET 5 AB 7 SER A 446 TRP A 453 -1 O PHE A 447 N VAL A 370 SHEET 6 AB 7 THR A 344 GLY A 350 -1 O THR A 344 N TRP A 452 SHEET 7 AB 7 LEU A 311 HIS A 314 -1 O LEU A 311 N PHE A 349 SHEET 1 AC 2 THR A 272 GLY A 278 0 SHEET 2 AC 2 TRP A 286 THR A 292 -1 O SER A 287 N VAL A 277 SHEET 1 BA 5 GLU B 219 THR B 221 0 SHEET 2 BA 5 PHE B 419 LEU B 424 1 O PHE B 419 N LYS B 220 SHEET 3 BA 5 LYS B 374 TYR B 379 -1 O LYS B 374 N LEU B 424 SHEET 4 BA 5 TRP B 437 ALA B 442 -1 O TRP B 437 N TYR B 379 SHEET 5 BA 5 ILE B 355 HIS B 359 -1 O SER B 356 N VAL B 440 SHEET 1 BB 7 ARG B 224 HIS B 226 0 SHEET 2 BB 7 VAL B 244 LYS B 247 1 O ILE B 245 N LEU B 225 SHEET 3 BB 7 ILE B 429 ILE B 432 -1 O ILE B 429 N LEU B 246 SHEET 4 BB 7 GLN B 364 MET B 371 -1 O ASN B 365 N ILE B 432 SHEET 5 BB 7 SER B 446 TRP B 453 -1 O PHE B 447 N VAL B 370 SHEET 6 BB 7 THR B 344 GLY B 350 -1 O THR B 344 N TRP B 452 SHEET 7 BB 7 LEU B 311 HIS B 314 -1 O LEU B 311 N PHE B 349 SHEET 1 BC 2 THR B 272 GLY B 278 0 SHEET 2 BC 2 TRP B 286 THR B 292 -1 O SER B 287 N VAL B 277 LINK ZN ZN A 500 OD2 ASP A 361 1555 1555 2.12 LINK ZN ZN A 500 O1 OGA A 501 1555 1555 2.13 LINK ZN ZN A 500 O2' OGA A 501 1555 1555 1.94 LINK ZN ZN A 500 NE2 HIS A 359 1555 1555 2.08 LINK ZN ZN A 500 NE2 HIS A 438 1555 1555 2.33 LINK ZN ZN A 502 NE2 HIS A 252 1555 4655 2.56 LINK ZN ZN A 502 OD2 ASP A 283 1555 1555 2.50 LINK ZN ZN A 502 NE2 HIS A 393 1555 1555 2.01 LINK ZN ZN B 500 NE2 HIS B 438 1555 1555 2.22 LINK ZN ZN B 500 O2' OGA B 501 1555 1555 1.94 LINK ZN ZN B 500 OD2 ASP B 361 1555 1555 2.14 LINK ZN ZN B 500 NE2 HIS B 359 1555 1555 2.02 LINK ZN ZN B 500 O1 OGA B 501 1555 1555 2.14 LINK ZN ZN B 502 NE2 HIS B 252 1555 5445 2.36 SITE 1 AC1 4 HIS A 359 ASP A 361 HIS A 438 OGA A 501 SITE 1 AC2 10 TYR A 310 TRP A 348 SER A 356 HIS A 359 SITE 2 AC2 10 ASP A 361 ASN A 365 LYS A 374 HIS A 438 SITE 3 AC2 10 VAL A 440 ZN A 500 SITE 1 AC3 3 HIS A 252 ASP A 283 HIS A 393 SITE 1 AC4 4 HIS B 359 ASP B 361 HIS B 438 OGA B 501 SITE 1 AC5 11 TYR B 310 TRP B 348 SER B 356 HIS B 359 SITE 2 AC5 11 ASP B 361 ASN B 365 LYS B 374 HIS B 438 SITE 3 AC5 11 VAL B 440 TRP B 452 ZN B 500 SITE 1 AC6 3 HIS B 252 ASP B 283 HIS B 393 CRYST1 68.575 68.575 269.003 90.00 90.00 120.00 P 32 2 1 12 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 0.014583 0.008419 0.000000 0.00000 SCALE2 0.000000 0.016839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003717 0.00000