HEADER HYDROLASE 21-SEP-15 5DV4 TITLE CRYSTAL STRUCTURE OF HUMAN CNOT6L IN COMPLEX WITH NEOMYCIN CAVEAT 5DV4 NMY A 601 HAS WRONG CHIRALITY AT ATOM C1 NMY A 601 HAS WRONG CAVEAT 2 5DV4 CHIRALITY AT ATOM C10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 6-LIKE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARBON CATABOLITE REPRESSOR PROTEIN 4 HOMOLOG B; COMPND 5 EC: 3.1.13.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CNOT6L, CCR4B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEASE DOMAIN, DEADENYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.ZHANG,M.BARTLAM REVDAT 2 19-FEB-20 5DV4 1 JRNL REMARK REVDAT 1 26-OCT-16 5DV4 0 JRNL AUTH Q.ZHANG,D.YAN,E.GUO,B.DING,W.YANG,R.LIU,T.YAMAMOTO,M.BARTLAM JRNL TITL STRUCTURAL BASIS FOR INHIBITION OF THE DEADENYLASE ACTIVITY JRNL TITL 2 OF HUMAN CNOT6L JRNL REF FEBS LETT. V. 590 1270 2016 JRNL REFN ISSN 0014-5793 JRNL PMID 27013054 JRNL DOI 10.1002/1873-3468.12160 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 35.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 54475 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2013 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 35.4722 - 4.3361 0.99 3956 152 0.1910 0.1918 REMARK 3 2 4.3361 - 3.4426 1.00 3835 149 0.1578 0.1773 REMARK 3 3 3.4426 - 3.0077 1.00 3785 142 0.1808 0.2057 REMARK 3 4 3.0077 - 2.7328 1.00 3773 146 0.1958 0.2439 REMARK 3 5 2.7328 - 2.5370 1.00 3763 144 0.1900 0.2353 REMARK 3 6 2.5370 - 2.3874 1.00 3747 141 0.1939 0.2198 REMARK 3 7 2.3874 - 2.2679 1.00 3707 144 0.1894 0.2369 REMARK 3 8 2.2679 - 2.1692 1.00 3704 144 0.2095 0.2625 REMARK 3 9 2.1692 - 2.0857 1.00 3705 142 0.1961 0.2417 REMARK 3 10 2.0857 - 2.0137 1.00 3735 144 0.1967 0.2375 REMARK 3 11 2.0137 - 1.9508 1.00 3684 142 0.1987 0.2200 REMARK 3 12 1.9508 - 1.8950 1.00 3689 140 0.2603 0.3519 REMARK 3 13 1.8950 - 1.8451 1.00 3694 142 0.2613 0.3000 REMARK 3 14 1.8451 - 1.8001 1.00 3685 141 0.2990 0.3366 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.280 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) : 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 : 0.015 2913 REMARK 3 ANGLE : 1.813 3948 REMARK 3 CHIRALITY : 0.085 440 REMARK 3 PLANARITY : 0.009 497 REMARK 3 DIHEDRAL : 14.624 1715 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 169 THROUGH 231 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.0054 0.8798 8.3374 REMARK 3 T TENSOR REMARK 3 T11: 0.3194 T22: 0.2971 REMARK 3 T33: 0.3462 T12: -0.1141 REMARK 3 T13: -0.1069 T23: 0.1583 REMARK 3 L TENSOR REMARK 3 L11: 4.7434 L22: 2.1719 REMARK 3 L33: 2.3752 L12: -0.1582 REMARK 3 L13: 0.4011 L23: -0.1312 REMARK 3 S TENSOR REMARK 3 S11: 0.0844 S12: -0.3039 S13: -0.4471 REMARK 3 S21: -0.0939 S22: 0.2454 S23: 0.4013 REMARK 3 S31: 0.3172 S32: -0.2526 S33: -0.1856 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 232 THROUGH 367 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.4522 14.2776 -2.5895 REMARK 3 T TENSOR REMARK 3 T11: 0.3611 T22: 0.2807 REMARK 3 T33: 0.2696 T12: -0.1092 REMARK 3 T13: -0.1224 T23: 0.0952 REMARK 3 L TENSOR REMARK 3 L11: 1.2252 L22: 2.7963 REMARK 3 L33: 1.6179 L12: 0.2989 REMARK 3 L13: 0.0983 L23: -0.2157 REMARK 3 S TENSOR REMARK 3 S11: -0.0326 S12: 0.1196 S13: 0.0257 REMARK 3 S21: -0.5510 S22: 0.2022 S23: 0.2840 REMARK 3 S31: -0.0688 S32: -0.1695 S33: -0.0902 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 368 THROUGH 465 ) REMARK 3 ORIGIN FOR THE GROUP (A): -46.0810 26.9749 6.7984 REMARK 3 T TENSOR REMARK 3 T11: 0.4108 T22: 0.3227 REMARK 3 T33: 0.4633 T12: 0.0368 REMARK 3 T13: -0.0056 T23: 0.1353 REMARK 3 L TENSOR REMARK 3 L11: 3.7315 L22: 3.1442 REMARK 3 L33: 4.1036 L12: -0.3773 REMARK 3 L13: 1.2973 L23: -0.3329 REMARK 3 S TENSOR REMARK 3 S11: -0.0658 S12: 0.0049 S13: 0.5716 REMARK 3 S21: -0.2269 S22: 0.1734 S23: 0.7092 REMARK 3 S31: -0.7566 S32: -0.4457 S33: 0.0580 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 466 THROUGH 540 ) REMARK 3 ORIGIN FOR THE GROUP (A): -44.2444 5.5874 14.4648 REMARK 3 T TENSOR REMARK 3 T11: 0.2944 T22: 0.3972 REMARK 3 T33: 0.4461 T12: -0.0964 REMARK 3 T13: -0.0235 T23: 0.2085 REMARK 3 L TENSOR REMARK 3 L11: 1.5687 L22: 1.7204 REMARK 3 L33: 2.5766 L12: -1.0489 REMARK 3 L13: 1.0341 L23: -0.6313 REMARK 3 S TENSOR REMARK 3 S11: 0.1075 S12: -0.3393 S13: -0.3538 REMARK 3 S21: 0.0909 S22: 0.3006 S23: 0.6769 REMARK 3 S31: 0.1385 S32: -0.5763 S33: -0.3726 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 5DV4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213856. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-11 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54573 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 50.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 1.1M AMMONIUM TARTRATE, REMARK 280 0.2M NDSB-201, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 111.45867 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 55.72933 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 55.72933 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 111.45867 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: 1510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 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 A 945 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 MET A 158 REMARK 465 LEU A 159 REMARK 465 ASP A 160 REMARK 465 ASN A 161 REMARK 465 LEU A 162 REMARK 465 ALA A 163 REMARK 465 VAL A 164 REMARK 465 HIS A 165 REMARK 465 PRO A 166 REMARK 465 GLU A 167 REMARK 465 GLN A 168 REMARK 465 ILE A 183 REMARK 465 LEU A 184 REMARK 465 PRO A 185 REMARK 465 GLY A 340 REMARK 465 ALA A 341 REMARK 465 GLY A 342 REMARK 465 MET A 343 REMARK 465 LYS A 344 REMARK 465 PRO A 345 REMARK 465 ILE A 346 REMARK 465 HIS A 347 REMARK 465 ALA A 348 REMARK 465 ALA A 349 REMARK 465 ASP A 350 REMARK 465 GLY A 394 REMARK 465 SER A 395 REMARK 465 PRO A 396 REMARK 465 THR A 397 REMARK 465 ALA A 398 REMARK 465 ASP A 399 REMARK 465 PRO A 400 REMARK 465 ASN A 450 REMARK 465 GLY A 451 REMARK 465 LYS A 452 REMARK 465 ASN A 453 REMARK 465 GLY A 454 REMARK 465 SER A 455 REMARK 465 SER A 456 REMARK 465 PRO A 541 REMARK 465 LEU A 542 REMARK 465 LEU A 543 REMARK 465 PRO A 544 REMARK 465 LEU A 545 REMARK 465 VAL A 546 REMARK 465 ASN A 547 REMARK 465 GLY A 548 REMARK 465 VAL A 549 REMARK 465 HIS A 550 REMARK 465 LEU A 551 REMARK 465 PRO A 552 REMARK 465 ASN A 553 REMARK 465 ARG A 554 REMARK 465 ARG A 555 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 SER A 448 CB OG REMARK 470 CYS A 449 SG 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 OD2 ASP A 508 O HOH A 701 1.89 REMARK 500 O HOH A 748 O HOH A 859 1.92 REMARK 500 O HOH A 988 O HOH A 1003 1.92 REMARK 500 O HOH A 715 O HOH A 751 1.96 REMARK 500 SD MET A 192 O HOH A 941 1.98 REMARK 500 O HOH A 870 O HOH A 879 1.98 REMARK 500 O HOH A 894 O HOH A 956 1.98 REMARK 500 O HOH A 789 O HOH A 969 2.01 REMARK 500 N9 NMY A 601 O4 SO4 A 602 2.01 REMARK 500 OE2 GLU A 514 O HOH A 702 2.02 REMARK 500 O HOH A 869 O HOH A 870 2.02 REMARK 500 ND2 ASN A 230 O HOH A 703 2.10 REMARK 500 OE2 GLU A 333 O HOH A 704 2.10 REMARK 500 O LYS A 178 O HOH A 705 2.10 REMARK 500 OE1 GLU A 421 O HOH A 706 2.12 REMARK 500 O HOH A 959 O HOH A 961 2.13 REMARK 500 O HOH A 720 O HOH A 943 2.13 REMARK 500 OE2 GLU A 226 O HOH A 707 2.13 REMARK 500 CD GLU A 514 O HOH A 702 2.15 REMARK 500 NZ LYS A 388 O HOH A 708 2.15 REMARK 500 ND2 ASN A 412 O4 NMY A 601 2.16 REMARK 500 O HOH A 993 O HOH A 1000 2.16 REMARK 500 O LEU A 294 O HOH A 709 2.17 REMARK 500 C9 NMY A 601 O4 SO4 A 602 2.18 REMARK 500 O HOH A 915 O HOH A 997 2.18 REMARK 500 O HOH A 970 O HOH A 1002 2.19 REMARK 500 O SER A 188 O HOH A 710 2.19 REMARK 500 O HOH A 933 O HOH A 999 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 982 O HOH A 986 4465 1.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 240 CD GLU A 240 OE2 -0.084 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 192 CG - SD - CE ANGL. DEV. = 16.5 DEGREES REMARK 500 GLU A 240 OE1 - CD - OE2 ANGL. DEV. = 9.4 DEGREES REMARK 500 GLU A 240 CG - CD - OE1 ANGL. DEV. = -13.3 DEGREES REMARK 500 ASP A 508 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES 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 LEU A 197 103.65 63.53 REMARK 500 LEU A 249 -67.51 -121.70 REMARK 500 LYS A 436 19.68 50.87 REMARK 500 GLU A 437 129.22 59.28 REMARK 500 ARG A 439 -71.84 -69.78 REMARK 500 TYR A 440 25.02 -73.46 REMARK 500 ASN A 472 43.52 74.42 REMARK 500 ASN A 473 46.92 39.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 447 SER A 448 -149.75 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 A1004 DISTANCE = 7.17 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NMY A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DV2 RELATED DB: PDB DBREF 5DV4 A 158 555 UNP Q96LI5 CNO6L_HUMAN 158 555 SEQRES 1 A 398 MET LEU ASP ASN LEU ALA VAL HIS PRO GLU GLN LEU PRO SEQRES 2 A 398 PRO ARG PRO TRP ILE THR LEU LYS GLU ARG ASP GLN ILE SEQRES 3 A 398 LEU PRO SER ALA SER PHE THR VAL MET CYS TYR ASN VAL SEQRES 4 A 398 LEU CYS ASP LYS TYR ALA THR ARG GLN LEU TYR GLY TYR SEQRES 5 A 398 CYS PRO SER TRP ALA LEU ASN TRP GLU TYR ARG LYS LYS SEQRES 6 A 398 GLY ILE MET GLU GLU ILE VAL ASN CYS ASP ALA ASP ILE SEQRES 7 A 398 ILE SER LEU GLN GLU VAL GLU THR GLU GLN TYR PHE THR SEQRES 8 A 398 LEU PHE LEU PRO ALA LEU LYS GLU ARG GLY TYR ASP GLY SEQRES 9 A 398 PHE PHE SER PRO LYS SER ARG ALA LYS ILE MET SER GLU SEQRES 10 A 398 GLN GLU ARG LYS HIS VAL ASP GLY CYS ALA ILE PHE PHE SEQRES 11 A 398 LYS THR GLU LYS PHE THR LEU VAL GLN LYS HIS THR VAL SEQRES 12 A 398 GLU PHE ASN GLN VAL ALA MET ALA ASN SER ASP GLY SER SEQRES 13 A 398 GLU ALA MET LEU ASN ARG VAL MET THR LYS ASP ASN ILE SEQRES 14 A 398 GLY VAL ALA VAL VAL LEU GLU VAL HIS LYS GLU LEU PHE SEQRES 15 A 398 GLY ALA GLY MET LYS PRO ILE HIS ALA ALA ASP LYS GLN SEQRES 16 A 398 LEU LEU ILE VAL ALA ASN ALA HIS MET HIS TRP ASP PRO SEQRES 17 A 398 GLU TYR SER ASP VAL LYS LEU ILE GLN THR MET MET PHE SEQRES 18 A 398 VAL SER GLU VAL LYS ASN ILE LEU GLU LYS ALA SER SER SEQRES 19 A 398 ARG PRO GLY SER PRO THR ALA ASP PRO ASN SER ILE PRO SEQRES 20 A 398 LEU VAL LEU CYS ALA ASP LEU ASN SER LEU PRO ASP SER SEQRES 21 A 398 GLY VAL VAL GLU TYR LEU SER ASN GLY GLY VAL ALA ASP SEQRES 22 A 398 ASN HIS LYS ASP PHE LYS GLU LEU ARG TYR ASN GLU CYS SEQRES 23 A 398 LEU MET ASN PHE SER CYS ASN GLY LYS ASN GLY SER SER SEQRES 24 A 398 GLU GLY ARG ILE THR HIS GLY PHE GLN LEU LYS SER ALA SEQRES 25 A 398 TYR GLU ASN ASN LEU MET PRO TYR THR ASN TYR THR PHE SEQRES 26 A 398 ASP PHE LYS GLY VAL ILE ASP TYR ILE PHE TYR SER LYS SEQRES 27 A 398 THR HIS MET ASN VAL LEU GLY VAL LEU GLY PRO LEU ASP SEQRES 28 A 398 PRO GLN TRP LEU VAL GLU ASN ASN ILE THR GLY CYS PRO SEQRES 29 A 398 HIS PRO HIS ILE PRO SER ASP HIS PHE SER LEU LEU THR SEQRES 30 A 398 GLN LEU GLU LEU HIS PRO PRO LEU LEU PRO LEU VAL ASN SEQRES 31 A 398 GLY VAL HIS LEU PRO ASN ARG ARG HET NMY A 601 42 HET SO4 A 602 5 HET SO4 A 603 5 HETNAM NMY NEOMYCIN HETNAM SO4 SULFATE ION HETSYN NMY MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN FORMUL 2 NMY C23 H46 N6 O13 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *304(H2 O) HELIX 1 AA1 CYS A 198 ALA A 202 5 5 HELIX 2 AA2 THR A 203 GLY A 208 1 6 HELIX 3 AA3 PRO A 211 ASN A 216 1 6 HELIX 4 AA4 ASN A 216 ASP A 232 1 17 HELIX 5 AA5 THR A 243 LEU A 249 1 7 HELIX 6 AA6 LEU A 249 ARG A 257 1 9 HELIX 7 AA7 SER A 273 HIS A 279 1 7 HELIX 8 AA8 PHE A 302 ASN A 309 1 8 HELIX 9 AA9 SER A 313 ARG A 319 1 7 HELIX 10 AB1 LYS A 336 PHE A 339 5 4 HELIX 11 AB2 TYR A 367 SER A 391 1 25 HELIX 12 AB3 SER A 417 GLY A 426 1 10 HELIX 13 AB4 HIS A 432 LYS A 436 5 5 HELIX 14 AB5 ASN A 441 SER A 448 5 8 HELIX 15 AB6 ASP A 508 ASN A 515 1 8 SHEET 1 AA1 7 TRP A 174 THR A 176 0 SHEET 2 AA1 7 MET A 498 LEU A 504 -1 O VAL A 503 N ILE A 175 SHEET 3 AA1 7 LEU A 532 LEU A 538 -1 O GLN A 535 N LEU A 501 SHEET 4 AA1 7 ALA A 187 ASN A 195 -1 N ALA A 187 O LEU A 538 SHEET 5 AA1 7 ILE A 235 GLU A 242 1 O ILE A 235 N MET A 192 SHEET 6 AA1 7 ASP A 281 LYS A 288 -1 O PHE A 286 N ILE A 236 SHEET 7 AA1 7 TYR A 259 PRO A 265 -1 N PHE A 262 O ILE A 285 SHEET 1 AA2 6 PHE A 292 GLU A 301 0 SHEET 2 AA2 6 ILE A 326 VAL A 334 -1 O VAL A 331 N VAL A 295 SHEET 3 AA2 6 GLN A 352 HIS A 360 -1 O LEU A 354 N LEU A 332 SHEET 4 AA2 6 LEU A 405 ASP A 410 1 O CYS A 408 N ALA A 357 SHEET 5 AA2 6 ASP A 489 SER A 494 -1 O PHE A 492 N LEU A 407 SHEET 6 AA2 6 LEU A 466 SER A 468 -1 N LYS A 467 O TYR A 493 SHEET 1 AA3 2 GLY A 427 ALA A 429 0 SHEET 2 AA3 2 ARG A 459 THR A 461 -1 O ILE A 460 N VAL A 428 SHEET 1 AA4 2 ASN A 479 TYR A 480 0 SHEET 2 AA4 2 LYS A 485 GLY A 486 -1 O GLY A 486 N ASN A 479 CISPEP 1 ASP A 181 GLN A 182 0 9.85 CISPEP 2 GLU A 437 LEU A 438 0 -7.16 CISPEP 3 CYS A 520 PRO A 521 0 -1.79 SITE 1 AC1 21 LEU A 206 TYR A 207 GLU A 240 HIS A 360 SITE 2 AC1 21 MET A 361 TRP A 363 PRO A 365 LYS A 371 SITE 3 AC1 21 ASP A 410 ASN A 412 LEU A 414 ASN A 479 SITE 4 AC1 21 PHE A 484 ILE A 488 SO4 A 602 HOH A 724 SITE 5 AC1 21 HOH A 742 HOH A 754 HOH A 816 HOH A 844 SITE 6 AC1 21 HOH A 901 SITE 1 AC2 3 TYR A 201 TRP A 363 NMY A 601 SITE 1 AC3 6 THR A 243 GLU A 244 LYS A 278 HOH A 800 SITE 2 AC3 6 HOH A 826 HOH A 883 CRYST1 77.388 77.388 167.188 90.00 90.00 120.00 P 32 2 1 6 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 0.012922 0.007460 0.000000 0.00000 SCALE2 0.000000 0.014921 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005981 0.00000 MASTER 514 0 3 15 17 0 9 6 0 0 0 31 END