HEADER HYDROLASE 13-JUN-10 3NGQ TITLE CRYSTAL STRUCTURE OF THE HUMAN CNOT6L NUCLEASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 6-LIKE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUCLEASE DOMAIN (UNP RESIDUES 158-555); COMPND 5 SYNONYM: CNOT6L, CARBON CATABOLITE REPRESSOR PROTEIN 4 HOMOLOG B; COMPND 6 EC: 3.1.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 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; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS ALPHA/BETA SANDWICH FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,M.MORITA,W.YANG,M.BARTLAM,T.YAMAMOTO,Z.RAO REVDAT 2 20-MAR-24 3NGQ 1 REMARK SEQADV HETSYN LINK REVDAT 1 28-JUL-10 3NGQ 0 JRNL AUTH H.WANG,M.MORITA,X.YANG,T.SUZUKI,W.YANG,J.WANG,K.ITO,Q.WANG, JRNL AUTH 2 C.ZHAO,M.BARTLAM,T.YAMAMOTO,Z.RAO JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN CNOT6L NUCLEASE DOMAIN JRNL TITL 2 REVEALS STRICT POLY(A) SUBSTRATE SPECIFICITY. JRNL REF EMBO J. 2010 JRNL REFN ESSN 1460-2075 JRNL PMID 20628353 JRNL DOI 10.1038/EMBOJ.2010.152 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0044 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 38342 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2050 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) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1945 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2696 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.55000 REMARK 3 B22 (A**2) : -1.55000 REMARK 3 B33 (A**2) : 2.32000 REMARK 3 B12 (A**2) : -0.77000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.075 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2775 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3756 ; 1.793 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 329 ; 7.137 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;35.628 ;24.846 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 477 ;17.905 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;15.709 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 411 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2088 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1671 ; 1.102 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2709 ; 1.959 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1104 ; 2.941 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1047 ; 4.595 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 3NGQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059807. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-07 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) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45797 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 (%) : 85.1 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.46300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, PH 7.5, 1.1M AMMONIUM REMARK 280 TARTRATE, 0.2M NDSB-201, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 110.59800 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 55.29900 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 55.29900 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 110.59800 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 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 GLN A 182 REMARK 465 ILE A 183 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 ALA A 389 REMARK 465 SER A 390 REMARK 465 SER A 391 REMARK 465 ARG A 392 REMARK 465 PRO A 393 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 401 REMARK 465 GLU A 437 REMARK 465 LEU A 438 REMARK 465 ARG A 439 REMARK 465 TYR A 440 REMARK 465 ASN A 441 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 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 GLU A 442 CG CD OE1 OE2 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 650 O HOH A 769 1.91 REMARK 500 O HOH A 562 O HOH A 770 2.09 REMARK 500 O HOH A 736 O HOH A 793 2.10 REMARK 500 CE MET A 321 O HOH A 733 2.15 REMARK 500 OG SER A 402 O HOH A 687 2.15 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 ARG A 172 NE - CZ - NH2 ANGL. DEV. = -3.4 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 LYS A 178 141.21 -171.17 REMARK 500 LEU A 197 101.17 64.12 REMARK 500 LEU A 249 -68.27 -124.84 REMARK 500 ASP A 311 72.37 18.58 REMARK 500 GLU A 337 10.64 -67.20 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 MG A 557 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 240 OE2 REMARK 620 2 HOH A 567 O 147.9 REMARK 620 3 HOH A 570 O 84.3 125.7 REMARK 620 4 HOH A 576 O 86.3 79.4 97.5 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 1PS A 556 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 557 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 558 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NGN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN CNOT6L NUCLEASE DOMAIN IN COMPLEX REMARK 900 WITH AMP REMARK 900 RELATED ID: 3NGO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN CNOT6L NUCLEASE DOMAIN IN COMPLEX REMARK 900 WITH POLY(A) DNA DBREF 3NGQ A 158 555 UNP Q96LI5 CNO6L_HUMAN 158 555 SEQADV 3NGQ GLU A 501 UNP Q96LI5 LEU 501 ENGINEERED MUTATION 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 GLU 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 1PS A 556 13 HET MG A 557 1 HET MG A 558 1 HETNAM 1PS 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE HETNAM MG MAGNESIUM ION HETSYN 1PS 1-(3-SULFOPROPYL) PYRIDINIUM; PPS FORMUL 2 1PS C8 H11 N O3 S FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *256(H2 O) HELIX 1 1 CYS A 198 ALA A 202 5 5 HELIX 2 2 PRO A 211 ASN A 216 1 6 HELIX 3 3 ASN A 216 ASP A 232 1 17 HELIX 4 4 THR A 243 LEU A 249 1 7 HELIX 5 5 LEU A 249 ARG A 257 1 9 HELIX 6 6 SER A 273 HIS A 279 1 7 HELIX 7 7 PHE A 302 ASN A 309 1 8 HELIX 8 8 SER A 313 ARG A 319 1 7 HELIX 9 9 LYS A 336 PHE A 339 5 4 HELIX 10 10 TYR A 367 GLU A 387 1 21 HELIX 11 11 SER A 417 GLY A 426 1 10 HELIX 12 12 HIS A 432 LYS A 436 5 5 HELIX 13 13 GLU A 442 SER A 448 5 7 HELIX 14 14 ASP A 508 ASN A 515 1 8 SHEET 1 A 7 TRP A 174 THR A 176 0 SHEET 2 A 7 MET A 498 LEU A 504 -1 O VAL A 503 N ILE A 175 SHEET 3 A 7 LEU A 532 LEU A 538 -1 O GLN A 535 N GLY A 502 SHEET 4 A 7 ALA A 187 ASN A 195 -1 N PHE A 189 O LEU A 536 SHEET 5 A 7 ILE A 235 GLU A 242 1 O SER A 237 N MET A 192 SHEET 6 A 7 ASP A 281 LYS A 288 -1 O PHE A 286 N ILE A 236 SHEET 7 A 7 TYR A 259 PRO A 265 -1 N PHE A 262 O ILE A 285 SHEET 1 B 6 PHE A 292 GLU A 301 0 SHEET 2 B 6 ILE A 326 VAL A 334 -1 O VAL A 331 N VAL A 295 SHEET 3 B 6 LEU A 353 HIS A 360 -1 O LEU A 354 N LEU A 332 SHEET 4 B 6 LEU A 405 ASP A 410 1 O CYS A 408 N ALA A 357 SHEET 5 B 6 ASP A 489 SER A 494 -1 O PHE A 492 N LEU A 407 SHEET 6 B 6 LEU A 466 SER A 468 -1 N LYS A 467 O TYR A 493 SHEET 1 C 2 GLY A 427 ALA A 429 0 SHEET 2 C 2 ARG A 459 THR A 461 -1 O ILE A 460 N VAL A 428 SHEET 1 D 2 ASN A 479 TYR A 480 0 SHEET 2 D 2 LYS A 485 GLY A 486 -1 O GLY A 486 N ASN A 479 LINK OE2 GLU A 240 MG MG A 557 1555 1555 2.21 LINK OD2 ASP A 410 MG MG A 558 1555 1555 2.42 LINK MG MG A 557 O HOH A 567 1555 1555 2.56 LINK MG MG A 557 O HOH A 570 1555 1555 2.38 LINK MG MG A 557 O HOH A 576 1555 1555 2.31 CISPEP 1 CYS A 520 PRO A 521 0 1.96 SITE 1 AC1 6 TRP A 363 PRO A 365 LYS A 371 ASN A 412 SITE 2 AC1 6 ASN A 479 PHE A 484 SITE 1 AC2 4 GLU A 240 HOH A 567 HOH A 570 HOH A 576 SITE 1 AC3 4 ASP A 410 ASN A 412 ILE A 488 HIS A 529 CRYST1 77.152 77.152 165.897 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 0.012961 0.007483 0.000000 0.00000 SCALE2 0.000000 0.014967 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006028 0.00000