PDB Short entry for 3AVR HEADER OXIDOREDUCTASE/STRUCTURAL PROTEIN 07-MAR-11 3AVR TITLE CATALYTIC FRAGMENT OF UTX/KDM6A BOUND WITH HISTONE H3K27ME3 PEPTIDE, TITLE 2 N-OXYALYLGLYCINE, AND NI(II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 6A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 880-1401; COMPND 5 SYNONYM: HISTONE DEMETHYLASE UTX, UBIQUITOUSLY-TRANSCRIBED TPR COMPND 6 PROTEIN ON THE X CHROMOSOME, UBIQUITOUSLY-TRANSCRIBED X CHROMOSOME COMPND 7 TETRATRICOPEPTIDE REPEAT PROTEIN; COMPND 8 EC: 1.14.11.-; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: HISTONE H3; COMPND 12 CHAIN: B; COMPND 13 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: KDM6A, UTX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET47; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS CUPIN SUPERFAMILY, TRI/DIMETHYLLYSINE DEMETHYLASE, OXIDOREDUCTASE- KEYWDS 2 STRUCTURAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.SENGOKU,S.YOKOYAMA REVDAT 3 01-NOV-23 3AVR 1 REMARK SEQADV LINK REVDAT 2 14-DEC-11 3AVR 1 JRNL REVDAT 1 19-OCT-11 3AVR 0 JRNL AUTH T.SENGOKU,S.YOKOYAMA JRNL TITL STRUCTURAL BASIS FOR HISTONE H3 LYS 27 DEMETHYLATION BY JRNL TITL 2 UTX/KDM6A JRNL REF GENES DEV. V. 25 2266 2011 JRNL REFN ISSN 0890-9369 JRNL PMID 22002947 JRNL DOI 10.1101/GAD.172296.111 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 58029 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 2979 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 30.3610 - 3.8822 1.00 5814 300 0.1581 0.1648 REMARK 3 2 3.8822 - 3.0823 1.00 5561 312 0.1734 0.2010 REMARK 3 3 3.0823 - 2.6930 1.00 5548 297 0.1682 0.2085 REMARK 3 4 2.6930 - 2.4469 1.00 5522 305 0.1592 0.1982 REMARK 3 5 2.4469 - 2.2716 1.00 5516 286 0.1520 0.1799 REMARK 3 6 2.2716 - 2.1377 1.00 5448 297 0.1551 0.1826 REMARK 3 7 2.1377 - 2.0306 1.00 5471 288 0.1685 0.2326 REMARK 3 8 2.0306 - 1.9423 1.00 5431 306 0.1881 0.2353 REMARK 3 9 1.9423 - 1.8675 1.00 5458 311 0.2204 0.2443 REMARK 3 10 1.8675 - 1.8031 0.97 5281 277 0.2771 0.3444 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.89 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 41.99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.960 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) : 9.29480 REMARK 3 B22 (A**2) : 0.12400 REMARK 3 B33 (A**2) : -4.67610 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 : 0.007 4129 REMARK 3 ANGLE : 1.101 5610 REMARK 3 CHIRALITY : 0.073 607 REMARK 3 PLANARITY : 0.005 724 REMARK 3 DIHEDRAL : 13.777 1540 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 886:918) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9530 29.2656 -12.3760 REMARK 3 T TENSOR REMARK 3 T11: 0.3111 T22: 0.2528 REMARK 3 T33: 0.1882 T12: -0.0764 REMARK 3 T13: -0.0092 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.6993 L22: 0.2821 REMARK 3 L33: 0.3753 L12: -0.3698 REMARK 3 L13: -0.4521 L23: 0.1533 REMARK 3 S TENSOR REMARK 3 S11: 0.2274 S12: -0.0087 S13: 0.1142 REMARK 3 S21: -0.0893 S22: -0.2281 S23: -0.1003 REMARK 3 S31: -0.0493 S32: -0.0215 S33: 0.0144 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 919:1046) REMARK 3 ORIGIN FOR THE GROUP (A): -16.1254 -9.3398 -15.0450 REMARK 3 T TENSOR REMARK 3 T11: 0.1409 T22: 0.1559 REMARK 3 T33: 0.1367 T12: -0.0113 REMARK 3 T13: 0.0191 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.5066 L22: 1.0908 REMARK 3 L33: 1.1371 L12: 0.2577 REMARK 3 L13: -0.0045 L23: 0.2811 REMARK 3 S TENSOR REMARK 3 S11: -0.0160 S12: -0.0146 S13: -0.0136 REMARK 3 S21: 0.0091 S22: -0.0277 S23: 0.0457 REMARK 3 S31: 0.0756 S32: -0.1278 S33: 0.0310 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1047:1132) REMARK 3 ORIGIN FOR THE GROUP (A): -7.1946 -8.4648 -4.4716 REMARK 3 T TENSOR REMARK 3 T11: 0.2113 T22: 0.1934 REMARK 3 T33: 0.1464 T12: -0.0151 REMARK 3 T13: -0.0278 T23: 0.0255 REMARK 3 L TENSOR REMARK 3 L11: 0.2477 L22: 0.6474 REMARK 3 L33: 0.2611 L12: 0.1557 REMARK 3 L13: -0.2145 L23: -0.0060 REMARK 3 S TENSOR REMARK 3 S11: 0.0400 S12: -0.1031 S13: 0.0118 REMARK 3 S21: 0.2216 S22: -0.0103 S23: -0.1080 REMARK 3 S31: 0.1012 S32: -0.0050 S33: -0.0187 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1133:1285) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1125 0.4818 -15.8782 REMARK 3 T TENSOR REMARK 3 T11: 0.1259 T22: 0.1326 REMARK 3 T33: 0.1382 T12: -0.0013 REMARK 3 T13: 0.0117 T23: -0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.3192 L22: 0.6274 REMARK 3 L33: 0.5134 L12: 0.3782 REMARK 3 L13: -0.0026 L23: 0.0947 REMARK 3 S TENSOR REMARK 3 S11: 0.0085 S12: -0.0137 S13: 0.0110 REMARK 3 S21: -0.0126 S22: -0.0313 S23: 0.0230 REMARK 3 S31: -0.0219 S32: -0.0521 S33: 0.0204 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1286:1312) REMARK 3 ORIGIN FOR THE GROUP (A): 3.8780 22.5580 -8.4686 REMARK 3 T TENSOR REMARK 3 T11: 0.2470 T22: 0.1549 REMARK 3 T33: 0.1864 T12: -0.0779 REMARK 3 T13: 0.0375 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.2706 L22: 0.6443 REMARK 3 L33: 0.4462 L12: -0.2418 REMARK 3 L13: -0.0433 L23: 0.4417 REMARK 3 S TENSOR REMARK 3 S11: 0.1095 S12: -0.0313 S13: 0.0862 REMARK 3 S21: 0.0517 S22: -0.1448 S23: 0.0081 REMARK 3 S31: -0.2062 S32: 0.0906 S33: 0.0179 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1313:1395) REMARK 3 ORIGIN FOR THE GROUP (A): -2.1746 19.5760 4.5763 REMARK 3 T TENSOR REMARK 3 T11: 0.3036 T22: 0.2517 REMARK 3 T33: 0.1341 T12: -0.1148 REMARK 3 T13: 0.0526 T23: -0.0362 REMARK 3 L TENSOR REMARK 3 L11: 0.2703 L22: 0.6125 REMARK 3 L33: 0.2049 L12: 0.1939 REMARK 3 L13: 0.1574 L23: -0.1288 REMARK 3 S TENSOR REMARK 3 S11: 0.1983 S12: -0.2022 S13: -0.0279 REMARK 3 S21: 0.3667 S22: -0.1676 S23: -0.0258 REMARK 3 S31: -0.1555 S32: 0.1597 S33: -0.0072 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 17:21) REMARK 3 ORIGIN FOR THE GROUP (A): -4.2280 14.0179 14.2082 REMARK 3 T TENSOR REMARK 3 T11: 0.6635 T22: 0.5669 REMARK 3 T33: 0.2979 T12: -0.0659 REMARK 3 T13: 0.0939 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.0626 L22: 0.0165 REMARK 3 L33: 0.0099 L12: -0.0046 REMARK 3 L13: -0.0065 L23: -0.0117 REMARK 3 S TENSOR REMARK 3 S11: -0.0871 S12: -0.0149 S13: -0.0291 REMARK 3 S21: 0.0708 S22: -0.0800 S23: 0.0251 REMARK 3 S31: 0.0001 S32: -0.0114 S33: 0.1428 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 22:33) REMARK 3 ORIGIN FOR THE GROUP (A): -16.9734 2.2120 -1.9338 REMARK 3 T TENSOR REMARK 3 T11: 0.2650 T22: 0.2791 REMARK 3 T33: 0.2002 T12: -0.0425 REMARK 3 T13: 0.0724 T23: -0.0531 REMARK 3 L TENSOR REMARK 3 L11: 0.2897 L22: 0.0532 REMARK 3 L33: 0.6025 L12: -0.0366 REMARK 3 L13: 0.4120 L23: -0.0278 REMARK 3 S TENSOR REMARK 3 S11: 0.3498 S12: -0.2087 S13: 0.0916 REMARK 3 S21: 0.1286 S22: -0.0393 S23: -0.0573 REMARK 3 S31: -0.1024 S32: 0.0693 S33: -0.2241 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 3AVR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000029755. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE SI(111) CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 3AVS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL (PH 8.5), 0.2M LI2SO4, REMARK 280 18-20% PEG 3,350, VAPOR DIFFUSION, HANGING 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 39.45250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.52850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.54050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.52850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.45250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.54050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 871 REMARK 465 PRO A 872 REMARK 465 GLY A 873 REMARK 465 TYR A 874 REMARK 465 GLN A 875 REMARK 465 ASP A 876 REMARK 465 PRO A 877 REMARK 465 ASN A 878 REMARK 465 SER A 879 REMARK 465 GLN A 880 REMARK 465 ILE A 881 REMARK 465 ILE A 882 REMARK 465 PRO A 883 REMARK 465 SER A 884 REMARK 465 MET A 885 REMARK 465 LEU A 903 REMARK 465 GLY A 904 REMARK 465 LYS A 905 REMARK 465 ASN A 906 REMARK 465 GLY A 907 REMARK 465 LEU A 908 REMARK 465 SER A 909 REMARK 465 ARG A 1048 REMARK 465 GLU A 1049 REMARK 465 GLU A 1050 REMARK 465 ASN A 1051 REMARK 465 GLU A 1052 REMARK 465 LYS A 1053 REMARK 465 ARG A 1054 REMARK 465 SER A 1055 REMARK 465 HIS A 1056 REMARK 465 HIS A 1057 REMARK 465 LYS A 1058 REMARK 465 ASP A 1059 REMARK 465 HIS A 1060 REMARK 465 SER A 1061 REMARK 465 ASP A 1062 REMARK 465 SER A 1063 REMARK 465 GLU A 1064 REMARK 465 SER A 1065 REMARK 465 THR A 1066 REMARK 465 SER A 1067 REMARK 465 SER A 1068 REMARK 465 ASP A 1069 REMARK 465 ASN A 1070 REMARK 465 SER A 1071 REMARK 465 GLY A 1072 REMARK 465 ARG A 1073 REMARK 465 ARG A 1074 REMARK 465 ARG A 1075 REMARK 465 LYS A 1076 REMARK 465 GLY A 1077 REMARK 465 LEU A 1396 REMARK 465 PRO A 1397 REMARK 465 SER A 1398 REMARK 465 ALA A 1399 REMARK 465 SER A 1400 REMARK 465 SER A 1401 REMARK 465 GLY B 34 REMARK 465 VAL B 35 REMARK 465 LYS B 36 REMARK 465 LYS B 37 REMARK 465 PRO B 38 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 277 O HOH A 354 1.84 REMARK 500 O HOH A 336 O HOH A 360 2.03 REMARK 500 O HOH A 383 O HOH A 388 2.05 REMARK 500 O HOH A 226 O HOH A 287 2.06 REMARK 500 O HOH A 308 O HOH A 367 2.07 REMARK 500 O HOH A 337 O HOH A 340 2.11 REMARK 500 O HOH A 363 O HOH A 377 2.12 REMARK 500 O HOH A 276 O HOH A 354 2.13 REMARK 500 OD2 ASP A 934 O HOH A 196 2.19 REMARK 500 OE2 GLU A 1325 O HOH A 352 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 280 O HOH A 300 3544 2.17 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 916 -25.56 84.33 REMARK 500 ALA A1008 -125.27 45.90 REMARK 500 SER A1025 89.55 -154.55 REMARK 500 SER A1025 89.55 -162.50 REMARK 500 LEU A1090 44.47 -96.78 REMARK 500 MET A1129 -60.66 -102.04 REMARK 500 ILE A1333 -62.13 -95.03 REMARK 500 ASP A1340 -65.08 76.90 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 NI A1503 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 265 O REMARK 620 2 HIS A1146 NE2 90.8 REMARK 620 3 GLU A1148 OE2 80.6 101.0 REMARK 620 4 HIS A1226 NE2 167.6 83.8 89.4 REMARK 620 5 OGA A1501 O2 92.7 166.3 92.6 95.1 REMARK 620 6 OGA A1501 O2' 89.9 88.7 166.4 101.2 78.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1331 SG REMARK 620 2 CYS A1334 SG 108.5 REMARK 620 3 CYS A1358 SG 114.1 111.8 REMARK 620 4 CYS A1361 SG 105.0 114.5 102.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AVS RELATED DB: PDB REMARK 900 H3-FREE UTX/KDM6A DBREF 3AVR A 880 1401 UNP O15550 KDM6A_HUMAN 880 1401 DBREF 3AVR B 17 38 PDB 3AVR 3AVR 17 38 SEQADV 3AVR GLY A 871 UNP O15550 EXPRESSION TAG SEQADV 3AVR PRO A 872 UNP O15550 EXPRESSION TAG SEQADV 3AVR GLY A 873 UNP O15550 EXPRESSION TAG SEQADV 3AVR TYR A 874 UNP O15550 EXPRESSION TAG SEQADV 3AVR GLN A 875 UNP O15550 EXPRESSION TAG SEQADV 3AVR ASP A 876 UNP O15550 EXPRESSION TAG SEQADV 3AVR PRO A 877 UNP O15550 EXPRESSION TAG SEQADV 3AVR ASN A 878 UNP O15550 EXPRESSION TAG SEQADV 3AVR SER A 879 UNP O15550 EXPRESSION TAG SEQRES 1 A 531 GLY PRO GLY TYR GLN ASP PRO ASN SER GLN ILE ILE PRO SEQRES 2 A 531 SER MET SER VAL SER ILE TYR PRO SER SER ALA GLU VAL SEQRES 3 A 531 LEU LYS ALA CYS ARG ASN LEU GLY LYS ASN GLY LEU SER SEQRES 4 A 531 ASN SER SER ILE LEU LEU ASP LYS CYS PRO PRO PRO ARG SEQRES 5 A 531 PRO PRO SER SER PRO TYR PRO PRO LEU PRO LYS ASP LYS SEQRES 6 A 531 LEU ASN PRO PRO THR PRO SER ILE TYR LEU GLU ASN LYS SEQRES 7 A 531 ARG ASP ALA PHE PHE PRO PRO LEU HIS GLN PHE CYS THR SEQRES 8 A 531 ASN PRO ASN ASN PRO VAL THR VAL ILE ARG GLY LEU ALA SEQRES 9 A 531 GLY ALA LEU LYS LEU ASP LEU GLY LEU PHE SER THR LYS SEQRES 10 A 531 THR LEU VAL GLU ALA ASN ASN GLU HIS MET VAL GLU VAL SEQRES 11 A 531 ARG THR GLN LEU LEU GLN PRO ALA ASP GLU ASN TRP ASP SEQRES 12 A 531 PRO THR GLY THR LYS LYS ILE TRP HIS CYS GLU SER ASN SEQRES 13 A 531 ARG SER HIS THR THR ILE ALA LYS TYR ALA GLN TYR GLN SEQRES 14 A 531 ALA SER SER PHE GLN GLU SER LEU ARG GLU GLU ASN GLU SEQRES 15 A 531 LYS ARG SER HIS HIS LYS ASP HIS SER ASP SER GLU SER SEQRES 16 A 531 THR SER SER ASP ASN SER GLY ARG ARG ARG LYS GLY PRO SEQRES 17 A 531 PHE LYS THR ILE LYS PHE GLY THR ASN ILE ASP LEU SER SEQRES 18 A 531 ASP ASP LYS LYS TRP LYS LEU GLN LEU HIS GLU LEU THR SEQRES 19 A 531 LYS LEU PRO ALA PHE VAL ARG VAL VAL SER ALA GLY ASN SEQRES 20 A 531 LEU LEU SER HIS VAL GLY HIS THR ILE LEU GLY MET ASN SEQRES 21 A 531 THR VAL GLN LEU TYR MET LYS VAL PRO GLY SER ARG THR SEQRES 22 A 531 PRO GLY HIS GLN GLU ASN ASN ASN PHE CYS SER VAL ASN SEQRES 23 A 531 ILE ASN ILE GLY PRO GLY ASP CYS GLU TRP PHE VAL VAL SEQRES 24 A 531 PRO GLU GLY TYR TRP GLY VAL LEU ASN ASP PHE CYS GLU SEQRES 25 A 531 LYS ASN ASN LEU ASN PHE LEU MET GLY SER TRP TRP PRO SEQRES 26 A 531 ASN LEU GLU ASP LEU TYR GLU ALA ASN VAL PRO VAL TYR SEQRES 27 A 531 ARG PHE ILE GLN ARG PRO GLY ASP LEU VAL TRP ILE ASN SEQRES 28 A 531 ALA GLY THR VAL HIS TRP VAL GLN ALA ILE GLY TRP CYS SEQRES 29 A 531 ASN ASN ILE ALA TRP ASN VAL GLY PRO LEU THR ALA CYS SEQRES 30 A 531 GLN TYR LYS LEU ALA VAL GLU ARG TYR GLU TRP ASN LYS SEQRES 31 A 531 LEU GLN SER VAL LYS SER ILE VAL PRO MET VAL HIS LEU SEQRES 32 A 531 SER TRP ASN MET ALA ARG ASN ILE LYS VAL SER ASP PRO SEQRES 33 A 531 LYS LEU PHE GLU MET ILE LYS TYR CYS LEU LEU ARG THR SEQRES 34 A 531 LEU LYS GLN CYS GLN THR LEU ARG GLU ALA LEU ILE ALA SEQRES 35 A 531 ALA GLY LYS GLU ILE ILE TRP HIS GLY ARG THR LYS GLU SEQRES 36 A 531 GLU PRO ALA HIS TYR CYS SER ILE CYS GLU VAL GLU VAL SEQRES 37 A 531 PHE ASP LEU LEU PHE VAL THR ASN GLU SER ASN SER ARG SEQRES 38 A 531 LYS THR TYR ILE VAL HIS CYS GLN ASP CYS ALA ARG LYS SEQRES 39 A 531 THR SER GLY ASN LEU GLU ASN PHE VAL VAL LEU GLU GLN SEQRES 40 A 531 TYR LYS MET GLU ASP LEU MET GLN VAL TYR ASP GLN PHE SEQRES 41 A 531 THR LEU ALA PRO PRO LEU PRO SER ALA SER SER SEQRES 1 B 22 ARG LYS GLN LEU ALA THR LYS ALA ALA ARG M3L SER ALA SEQRES 2 B 22 PRO ALA THR GLY GLY VAL LYS LYS PRO MODRES 3AVR M3L B 27 LYS N-TRIMETHYLLYSINE HET M3L B 27 31 HET OGA A1501 13 HET ZN A1502 1 HET NI A1503 1 HET EDO A 1 10 HET EDO A 2 10 HET EDO A 3 10 HET EDO A 4 10 HET EDO A 5 10 HET EDO A 6 10 HET EDO A 7 10 HET EDO A 8 10 HET EDO A 9 10 HET CL A1402 1 HET CL A1403 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM OGA N-OXALYLGLYCINE HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 OGA C4 H5 N O5 FORMUL 4 ZN ZN 2+ FORMUL 5 NI NI 2+ FORMUL 6 EDO 9(C2 H6 O2) FORMUL 15 CL 2(CL 1-) FORMUL 17 HOH *388(H2 O) HELIX 1 1 SER A 892 ARG A 901 1 10 HELIX 2 2 PRO A 932 LEU A 936 5 5 HELIX 3 3 ASN A 947 PHE A 952 1 6 HELIX 4 4 PHE A 953 ASN A 962 1 10 HELIX 5 5 GLY A 972 LYS A 978 1 7 HELIX 6 6 ASP A 980 PHE A 984 5 5 HELIX 7 7 SER A 985 ASN A 993 1 9 HELIX 8 8 ILE A 1032 SER A 1046 1 15 HELIX 9 9 TRP A 1096 LEU A 1103 1 8 HELIX 10 10 THR A 1104 LEU A 1106 5 3 HELIX 11 11 PRO A 1107 ARG A 1111 5 5 HELIX 12 12 ASN A 1117 VAL A 1122 5 6 HELIX 13 13 GLU A 1148 PHE A 1152 5 5 HELIX 14 14 PRO A 1170 GLY A 1172 5 3 HELIX 15 15 TYR A 1173 ASN A 1184 1 12 HELIX 16 16 ASN A 1196 ALA A 1203 1 8 HELIX 17 17 THR A 1245 SER A 1263 1 19 HELIX 18 18 PRO A 1269 ILE A 1281 1 13 HELIX 19 19 ASP A 1285 ALA A 1313 1 29 HELIX 20 20 CYS A 1358 SER A 1366 1 9 HELIX 21 21 LYS A 1379 GLN A 1389 1 11 SHEET 1 A 9 SER A 942 TYR A 944 0 SHEET 2 A 9 VAL A 967 ARG A 971 1 O ARG A 971 N ILE A 943 SHEET 3 A 9 LEU A1217 ILE A1220 -1 O LEU A1217 N ILE A 970 SHEET 4 A 9 CYS A1153 PRO A1161 -1 N ASN A1156 O VAL A1218 SHEET 5 A 9 CYS A1234 VAL A1241 -1 O ILE A1237 N ILE A1157 SHEET 6 A 9 GLN A1133 LYS A1137 -1 N LYS A1137 O CYS A1234 SHEET 7 A 9 THR A1081 ASP A1089 -1 N ILE A1088 O LEU A1134 SHEET 8 A 9 MET A 997 LEU A1004 -1 N GLU A 999 O THR A1086 SHEET 9 A 9 SER A1025 THR A1031 -1 O SER A1028 N VAL A1000 SHEET 1 B 4 ARG A1142 HIS A1146 0 SHEET 2 B 4 VAL A1225 ALA A1230 -1 O VAL A1228 N THR A1143 SHEET 3 B 4 CYS A1164 VAL A1169 -1 N GLU A1165 O GLN A1229 SHEET 4 B 4 TYR A1208 GLN A1212 -1 O GLN A1212 N CYS A1164 SHEET 1 C 5 ILE A1317 TRP A1319 0 SHEET 2 C 5 VAL A1373 GLU A1376 1 O VAL A1374 N ILE A1318 SHEET 3 C 5 LEU A1341 ASN A1346 -1 N LEU A1342 O LEU A1375 SHEET 4 C 5 THR A1353 HIS A1357 -1 O ILE A1355 N THR A1345 SHEET 5 C 5 GLN B 19 LEU B 20 1 O GLN B 19 N TYR A1354 SHEET 1 D 2 HIS A1329 TYR A1330 0 SHEET 2 D 2 GLU A1337 VAL A1338 -1 O VAL A1338 N HIS A1329 LINK C ARG B 26 N M3L B 27 1555 1555 1.32 LINK C M3L B 27 N SER B 28 1555 1555 1.33 LINK O HOH A 265 NI NI A1503 1555 1555 2.36 LINK NE2 HIS A1146 NI NI A1503 1555 1555 2.19 LINK OE2 GLU A1148 NI NI A1503 1555 1555 2.13 LINK NE2 HIS A1226 NI NI A1503 1555 1555 2.18 LINK SG CYS A1331 ZN ZN A1502 1555 1555 2.27 LINK SG CYS A1334 ZN ZN A1502 1555 1555 2.35 LINK SG CYS A1358 ZN ZN A1502 1555 1555 2.34 LINK SG CYS A1361 ZN ZN A1502 1555 1555 2.44 LINK O2 OGA A1501 NI NI A1503 1555 1555 2.20 LINK O2' OGA A1501 NI NI A1503 1555 1555 2.21 CISPEP 1 TYR A 928 PRO A 929 0 0.38 CISPEP 2 GLY A 1160 PRO A 1161 0 5.68 SITE 1 AC1 12 HOH A 63 LYS A1137 THR A1143 HIS A1146 SITE 2 AC1 12 GLU A1148 SER A1154 ASN A1156 TRP A1166 SITE 3 AC1 12 HIS A1226 ALA A1238 NI A1503 M3L B 27 SITE 1 AC2 4 CYS A1331 CYS A1334 CYS A1358 CYS A1361 SITE 1 AC3 5 HOH A 265 HIS A1146 GLU A1148 HIS A1226 SITE 2 AC3 5 OGA A1501 SITE 1 AC4 2 HOH A 295 SER A1120 SITE 1 AC5 4 HOH A 115 HOH A 198 GLU A 946 MET A1291 SITE 1 AC6 4 HOH A 343 PRO A 932 LYS A 933 ASN A1204 SITE 1 AC7 7 HOH A 60 HOH A 99 HOH A 104 ILE A 889 SITE 2 AC7 7 TYR A 890 PRO A 891 THR A 940 SITE 1 AC8 5 HOH A 55 HOH A 210 GLN A1039 ALA A1040 SITE 2 AC8 5 TRP A1233 SITE 1 AC9 6 HOH A 275 HOH A 296 THR A1030 LYS A1034 SITE 2 AC9 6 TYR A1035 LYS A1083 SITE 1 BC1 2 ALA A1108 ARG A1111 SITE 1 BC2 6 HOH A 329 THR A 961 ASN A1221 ALA A1222 SITE 2 BC2 6 THR A1245 CYS A1247 SITE 1 BC3 5 HOH A 56 HOH A 368 LEU A 981 GLY A 982 SITE 2 BC3 5 ILE A1159 SITE 1 BC4 1 ARG A1322 SITE 1 BC5 2 SER A1114 ALA A1115 CRYST1 78.905 83.081 95.057 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 0.012673 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012036 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010520 0.00000