PDB Short entry for 2XDP HEADER OXIDOREDUCTASE 06-MAY-10 2XDP TITLE CRYSTAL STRUCTURE OF THE TUDOR DOMAIN OF HUMAN JMJD2C COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TUDOR DOMAIN, RESIDUES 875-995; COMPND 5 SYNONYM: JMJD2C, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN COMPND 6 3C, JUMONJI DOMAIN-CONTAINING PROTEIN 2C, GENE AMPLIFIED IN SQUAMOUS COMPND 7 CELL CARCINOMA 1 PROTEIN, GASC-1 PROTEIN; COMPND 8 EC: 1.14.11.-; COMPND 9 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: R3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PNIC28-BSA4 KEYWDS OXIDOREDUCTASE, HISTONE MODIFICATION EXPDTA X-RAY DIFFRACTION AUTHOR W.W.YUE,C.GILEADI,T.KROJER,H.WEISBACH,E.UGOCHUKWU,M.DANIEL, AUTHOR 2 C.PHILLIPS,A.CHAIKUAD,F.VON DELFT,C.ALLERSTON,C.ARROWSMITH, AUTHOR 3 J.WEIGELT,A.EDWARDS,C.BOUNTRA,U.OPPERMANN REVDAT 4 20-DEC-23 2XDP 1 REMARK REVDAT 3 24-JAN-18 2XDP 1 JRNL REVDAT 2 05-DEC-12 2XDP 1 SOURCE AUTHOR JRNL REMARK REVDAT 2 2 1 VERSN MASTER REVDAT 1 09-JUN-10 2XDP 0 JRNL AUTH W.W.YUE,C.GILEADI,T.KROJER,H.WEISBACH,E.UGOCHUKWU,M.DANIEL, JRNL AUTH 2 C.PHILLIPS,A.CHAIKUAD,F.VON DELFT,C.ALLERSTON,C.ARROWSMITH, JRNL AUTH 3 J.WEIGELT,A.EDWARDS,C.BOUNTRA,U.OPPERMANN JRNL TITL CRYSTAL STRUCTURE OF THE TUDOR DOMAIN OF HUMAN JMJD2C JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 46098 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2355 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 18.5128 - 3.9987 0.98 2595 137 0.1672 0.1790 REMARK 3 2 3.9987 - 3.1791 0.99 2597 153 0.1668 0.1733 REMARK 3 3 3.1791 - 2.7788 0.99 2578 180 0.1755 0.1977 REMARK 3 4 2.7788 - 2.5254 1.00 2643 113 0.1754 0.1829 REMARK 3 5 2.5254 - 2.3448 0.99 2655 147 0.1771 0.2036 REMARK 3 6 2.3448 - 2.2068 0.99 2624 137 0.1729 0.2120 REMARK 3 7 2.2068 - 2.0964 0.99 2592 136 0.1709 0.2009 REMARK 3 8 2.0964 - 2.0053 1.00 2670 155 0.1782 0.2070 REMARK 3 9 2.0053 - 1.9282 1.00 2650 133 0.1718 0.1946 REMARK 3 10 1.9282 - 1.8617 1.00 2602 142 0.1791 0.2125 REMARK 3 11 1.8617 - 1.8035 1.00 2624 139 0.1968 0.2310 REMARK 3 12 1.8035 - 1.7520 0.99 2638 138 0.1985 0.2176 REMARK 3 13 1.7520 - 1.7059 1.00 2602 148 0.2219 0.2210 REMARK 3 14 1.7059 - 1.6643 1.00 2692 136 0.2354 0.3225 REMARK 3 15 1.6643 - 1.6265 0.99 2585 136 0.2672 0.2371 REMARK 3 16 1.6265 - 1.5919 0.87 2331 120 0.3064 0.3632 REMARK 3 17 1.5919 - 1.5601 0.78 2065 105 0.3564 0.3197 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 : 0.37 REMARK 3 B_SOL : 50.38 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.30420 REMARK 3 B22 (A**2) : 10.27400 REMARK 3 B33 (A**2) : -0.96980 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.009 993 REMARK 3 ANGLE : 1.240 1346 REMARK 3 CHIRALITY : 0.100 145 REMARK 3 PLANARITY : 0.006 172 REMARK 3 DIHEDRAL : 12.253 375 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 877:889) REMARK 3 ORIGIN FOR THE GROUP (A): 44.8309 22.2944 -1.9359 REMARK 3 T TENSOR REMARK 3 T11: 0.1403 T22: 0.2846 REMARK 3 T33: 0.1663 T12: 0.0378 REMARK 3 T13: 0.0038 T23: 0.0092 REMARK 3 L TENSOR REMARK 3 L11: 0.2473 L22: 1.9509 REMARK 3 L33: 2.0424 L12: -0.0286 REMARK 3 L13: -0.3788 L23: 0.6423 REMARK 3 S TENSOR REMARK 3 S11: 0.0341 S12: -0.6502 S13: 0.3044 REMARK 3 S21: -0.0465 S22: 0.0467 S23: 0.2943 REMARK 3 S31: -0.1443 S32: -0.2442 S33: -0.0168 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 890:903) REMARK 3 ORIGIN FOR THE GROUP (A): 12.9735 17.0104 2.0051 REMARK 3 T TENSOR REMARK 3 T11: 0.0992 T22: 0.3574 REMARK 3 T33: 0.1467 T12: -0.0061 REMARK 3 T13: -0.0050 T23: -0.0652 REMARK 3 L TENSOR REMARK 3 L11: 1.8892 L22: 1.0117 REMARK 3 L33: 1.0442 L12: -0.3297 REMARK 3 L13: 0.6558 L23: -0.4348 REMARK 3 S TENSOR REMARK 3 S11: 0.0196 S12: 0.7649 S13: -0.1019 REMARK 3 S21: -0.0084 S22: -0.0527 S23: -0.2312 REMARK 3 S31: 0.0211 S32: 0.3811 S33: 0.0163 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 904:939) REMARK 3 ORIGIN FOR THE GROUP (A): 23.2499 28.8135 19.6942 REMARK 3 T TENSOR REMARK 3 T11: 0.2281 T22: 0.1425 REMARK 3 T33: 0.2217 T12: -0.0361 REMARK 3 T13: 0.0030 T23: 0.0389 REMARK 3 L TENSOR REMARK 3 L11: 1.5986 L22: 0.5575 REMARK 3 L33: 0.8229 L12: -0.4835 REMARK 3 L13: -0.1330 L23: 0.6265 REMARK 3 S TENSOR REMARK 3 S11: -0.0561 S12: 0.1217 S13: 0.3571 REMARK 3 S21: -0.2205 S22: 0.0653 S23: -0.0299 REMARK 3 S31: -0.0837 S32: 0.0208 S33: -0.0080 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 940:962) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5273 27.9296 17.6071 REMARK 3 T TENSOR REMARK 3 T11: 0.2505 T22: 0.2038 REMARK 3 T33: 0.2718 T12: -0.0402 REMARK 3 T13: 0.0083 T23: 0.0352 REMARK 3 L TENSOR REMARK 3 L11: 2.1667 L22: 0.1100 REMARK 3 L33: 0.7112 L12: -0.1648 REMARK 3 L13: -0.1069 L23: 0.3418 REMARK 3 S TENSOR REMARK 3 S11: -0.0113 S12: 0.5141 S13: 0.3886 REMARK 3 S21: -0.1873 S22: -0.0289 S23: -0.1233 REMARK 3 S31: -0.0937 S32: 0.1395 S33: 0.0899 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 963:982) REMARK 3 ORIGIN FOR THE GROUP (A): 10.6582 17.9853 7.5417 REMARK 3 T TENSOR REMARK 3 T11: 0.1697 T22: 0.2543 REMARK 3 T33: 0.2203 T12: -0.0215 REMARK 3 T13: -0.0028 T23: -0.0468 REMARK 3 L TENSOR REMARK 3 L11: 0.8425 L22: 1.9723 REMARK 3 L33: 1.2458 L12: 0.2430 REMARK 3 L13: 0.3347 L23: 0.0840 REMARK 3 S TENSOR REMARK 3 S11: -0.0782 S12: 0.0982 S13: -0.2064 REMARK 3 S21: 0.0728 S22: 0.1139 S23: -0.3975 REMARK 3 S31: 0.0103 S32: 0.4297 S33: -0.1037 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 983:993) REMARK 3 ORIGIN FOR THE GROUP (A): 14.6656 25.3287 -4.9500 REMARK 3 T TENSOR REMARK 3 T11: 0.1748 T22: 0.4111 REMARK 3 T33: 0.2065 T12: -0.0173 REMARK 3 T13: 0.0436 T23: -0.0334 REMARK 3 L TENSOR REMARK 3 L11: 0.4968 L22: 0.7917 REMARK 3 L33: 2.4717 L12: 0.4560 REMARK 3 L13: -0.8896 L23: -0.1531 REMARK 3 S TENSOR REMARK 3 S11: 0.2650 S12: -0.3865 S13: 0.1637 REMARK 3 S21: -0.0546 S22: -0.1282 S23: -0.1283 REMARK 3 S31: -0.0201 S32: 0.7786 S33: -0.0639 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 2XDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1290043857. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-10 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 : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24650 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 18.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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 2GFA REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M (NH4)2SO4; 0.1M TRIS PH 8.5; 25% REMARK 280 PEG 3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 26.40750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.82300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.80700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.40750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.82300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.80700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.40750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.82300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.80700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.40750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.82300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 40.80700 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.6 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 52.81500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A2053 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2064 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2124 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 SER A 873 REMARK 465 MET A 874 REMARK 465 CYS A 875 REMARK 465 LYS A 995 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 876 CG CD OE1 OE2 REMARK 470 GLN A 944 CD OE1 NE2 REMARK 470 GLU A 981 CD OE1 OE2 REMARK 470 ARG A 993 NE CZ NH1 NH2 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 2006 O HOH A 2081 1.95 REMARK 500 O HOH A 2028 O HOH A 2158 1.98 REMARK 500 O HOH A 2135 O HOH A 2136 2.01 REMARK 500 O HOH A 2023 O HOH A 2136 2.02 REMARK 500 O HOH A 2017 O HOH A 2114 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 2140 O HOH A 2180 3655 2.15 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 ASN A 891 55.32 -146.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2038 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A2040 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A2041 DISTANCE = 6.66 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1995 DBREF 2XDP A 875 995 UNP Q9H3R0 KDM4C_HUMAN 875 995 SEQADV 2XDP SER A 873 UNP Q9H3R0 EXPRESSION TAG SEQADV 2XDP MET A 874 UNP Q9H3R0 EXPRESSION TAG SEQRES 1 A 123 SER MET CYS GLU LYS VAL ILE SER VAL GLY GLN THR VAL SEQRES 2 A 123 ILE THR LYS HIS ARG ASN THR ARG TYR TYR SER CYS ARG SEQRES 3 A 123 VAL MET ALA VAL THR SER GLN THR PHE TYR GLU VAL MET SEQRES 4 A 123 PHE ASP ASP GLY SER PHE SER ARG ASP THR PHE PRO GLU SEQRES 5 A 123 ASP ILE VAL SER ARG ASP CYS LEU LYS LEU GLY PRO PRO SEQRES 6 A 123 ALA GLU GLY GLU VAL VAL GLN VAL LYS TRP PRO ASP GLY SEQRES 7 A 123 LYS LEU TYR GLY ALA LYS TYR PHE GLY SER ASN ILE ALA SEQRES 8 A 123 HIS MET TYR GLN VAL GLU PHE GLU ASP GLY SER GLN ILE SEQRES 9 A 123 ALA MET LYS ARG GLU ASP ILE TYR THR LEU ASP GLU GLU SEQRES 10 A 123 LEU PRO LYS ARG VAL LYS HET SO4 A1995 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *186(H2 O) HELIX 1 1 PHE A 922 ASP A 925 5 4 HELIX 2 2 ASP A 930 GLY A 935 1 6 HELIX 3 3 GLU A 981 ILE A 983 5 3 SHEET 1 AA 4 PHE A 917 THR A 921 0 SHEET 2 AA 4 ARG A 898 PHE A 912 -1 O TYR A 908 N THR A 921 SHEET 3 AA 4 LEU A 952 GLU A 969 -1 O LYS A 956 N MET A 911 SHEET 4 AA 4 GLN A 975 LYS A 979 -1 O ILE A 976 N VAL A 968 SHEET 1 AB 4 PHE A 917 THR A 921 0 SHEET 2 AB 4 ARG A 898 PHE A 912 -1 O TYR A 908 N THR A 921 SHEET 3 AB 4 LEU A 952 GLU A 969 -1 O LYS A 956 N MET A 911 SHEET 4 AB 4 VAL A 942 LYS A 946 -1 O VAL A 943 N ALA A 955 SHEET 1 AC 2 GLN A 975 LYS A 979 0 SHEET 2 AC 2 LEU A 952 GLU A 969 -1 O TYR A 966 N MET A 978 SITE 1 AC1 6 HIS A 964 TYR A 966 ARG A 980 HOH A2153 SITE 2 AC1 6 HOH A2185 HOH A2186 CRYST1 52.815 79.646 81.614 90.00 90.00 90.00 I 2 2 2 8 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 0.018934 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012253 0.00000