HEADER TRANSCRIPTION 15-FEB-15 5AIL TITLE HUMAN PARP9 2ND MACRODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY [ADP-RIBOSE] POLYMERASE 9; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: 2ND MACRODOMAIN, UNP RESIDUES 310-493; COMPND 5 SYNONYM: PARP-9, ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 9, COMPND 6 ARTD9, B AGGRESSIVE LYMPHOMA PROTEIN, PARP9; COMPND 7 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR C.SIEG,L.SHRESTHA,R.TALON,F.SORRELL,E.WILLIAMS,F.VON DELFT,C.BOUNTRA, AUTHOR 2 C.ARROWSMITH,A.M.EDWARDS,S.KNAPP,J.M.ELKINS REVDAT 3 10-JAN-24 5AIL 1 REMARK REVDAT 2 13-SEP-17 5AIL 1 REMARK REVDAT 1 25-FEB-15 5AIL 0 JRNL AUTH J.M.ELKINS JRNL TITL STRUCTURE OF PARP9 2ND MACRODOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 55395 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2908 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4054 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 211 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2838 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 117 REMARK 3 SOLVENT ATOMS : 377 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -1.08000 REMARK 3 B33 (A**2) : 1.28000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.100 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.211 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3084 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3058 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4158 ; 1.539 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7079 ; 1.053 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 384 ; 5.733 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;37.239 ;25.826 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 549 ;11.091 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;41.107 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 487 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3326 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 644 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1490 ; 1.753 ; 1.598 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1489 ; 1.746 ; 1.595 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1870 ; 2.217 ; 2.388 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1594 ; 2.766 ; 2.090 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6139 ; 2.745 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 107 ;34.258 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6351 ; 9.435 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 273 455 B 273 455 22872 0.06 0.05 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 5AIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1290063053. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9181 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58370 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 22.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.74000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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 3Q71 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG1000, 0.1M SPG PH 6.0 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 29.24450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.18450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.00500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.18450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.24450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.00500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 PHE A 337 REMARK 465 GLN A 338 REMARK 465 ARG A 339 REMARK 465 SER A 340 REMARK 465 LEU A 457 REMARK 465 ASN A 458 REMARK 465 PHE B 337 REMARK 465 GLN B 338 REMARK 465 ARG B 339 REMARK 465 SER B 340 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 GLN A 336 CD OE1 NE2 REMARK 470 GLN A 341 CG CD OE1 NE2 REMARK 470 LYS A 403 CE NZ REMARK 470 LYS A 420 NZ REMARK 470 LYS A 442 CE NZ REMARK 470 LYS A 453 CE NZ REMARK 470 GLN B 336 CD OE1 NE2 REMARK 470 GLN B 341 CG CD OE1 NE2 REMARK 470 LYS B 372 NZ REMARK 470 LYS B 403 CE NZ REMARK 470 LYS B 420 CD CE NZ REMARK 470 LYS B 442 CD CE NZ REMARK 470 LYS B 450 CD CE NZ REMARK 470 LYS B 453 CE NZ 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 OD1 ASN A 275 OH TYR A 441 2.11 REMARK 500 OD1 ASN B 275 OH TYR B 441 2.11 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 2018 O HOH B 2153 2865 1.88 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 325 CG - SD - CE ANGL. DEV. = -12.3 DEGREES REMARK 500 GLU A 328 OE1 - CD - OE2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ARG A 451 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 MET B 325 CG - SD - CE ANGL. DEV. = -12.4 DEGREES REMARK 500 GLU B 328 OE1 - CD - OE2 ANGL. DEV. = -7.7 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 ASN A 280 -111.54 49.80 REMARK 500 ASP A 307 97.59 -162.86 REMARK 500 PHE A 349 -123.03 53.13 REMARK 500 PRO A 393 -167.79 -76.70 REMARK 500 ASN B 280 -111.32 49.42 REMARK 500 ASP B 307 98.54 -163.00 REMARK 500 PHE B 349 -124.27 53.28 REMARK 500 PRO B 393 -169.59 -78.45 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 A2128 DISTANCE = 6.54 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 15P A 1459 REMARK 610 15P A 1460 REMARK 610 15P B 1463 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1457 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1459 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1460 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1461 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1458 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 15P A 1459 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 15P B 1463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 15P A 1460 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1461 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1464 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1465 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AIK RELATED DB: PDB REMARK 900 HUMAN DYRK1A IN COMPLEX WITH LDN-211898 DBREF 5AIL A 275 458 UNP Q8IXQ6 PARP9_HUMAN 310 493 DBREF 5AIL B 275 458 UNP Q8IXQ6 PARP9_HUMAN 310 493 SEQADV 5AIL SER A 273 UNP Q8IXQ6 EXPRESSION TAG SEQADV 5AIL MET A 274 UNP Q8IXQ6 EXPRESSION TAG SEQADV 5AIL SER B 273 UNP Q8IXQ6 EXPRESSION TAG SEQADV 5AIL MET B 274 UNP Q8IXQ6 EXPRESSION TAG SEQRES 1 A 186 SER MET ASN ALA MET VAL VAL ASN ASN LEU THR LEU GLN SEQRES 2 A 186 ILE VAL GLN GLY HIS ILE GLU TRP GLN THR ALA ASP VAL SEQRES 3 A 186 ILE VAL ASN SER VAL ASN PRO HIS ASP ILE THR VAL GLY SEQRES 4 A 186 PRO VAL ALA LYS SER ILE LEU GLN GLN ALA GLY VAL GLU SEQRES 5 A 186 MET LYS SER GLU PHE LEU ALA THR LYS ALA LYS GLN PHE SEQRES 6 A 186 GLN ARG SER GLN LEU VAL LEU VAL THR LYS GLY PHE ASN SEQRES 7 A 186 LEU PHE CYS LYS TYR ILE TYR HIS VAL LEU TRP HIS SER SEQRES 8 A 186 GLU PHE PRO LYS PRO GLN ILE LEU LYS HIS ALA MET LYS SEQRES 9 A 186 GLU CYS LEU GLU LYS CYS ILE GLU GLN ASN ILE THR SER SEQRES 10 A 186 ILE SER PHE PRO ALA LEU GLY THR GLY ASN MET GLU ILE SEQRES 11 A 186 LYS LYS GLU THR ALA ALA GLU ILE LEU PHE ASP GLU VAL SEQRES 12 A 186 LEU THR PHE ALA LYS ASP HIS VAL LYS HIS GLN LEU THR SEQRES 13 A 186 VAL LYS PHE VAL ILE PHE PRO THR ASP LEU GLU ILE TYR SEQRES 14 A 186 LYS ALA PHE SER SER GLU MET ALA LYS ARG SER LYS MET SEQRES 15 A 186 LEU SER LEU ASN SEQRES 1 B 186 SER MET ASN ALA MET VAL VAL ASN ASN LEU THR LEU GLN SEQRES 2 B 186 ILE VAL GLN GLY HIS ILE GLU TRP GLN THR ALA ASP VAL SEQRES 3 B 186 ILE VAL ASN SER VAL ASN PRO HIS ASP ILE THR VAL GLY SEQRES 4 B 186 PRO VAL ALA LYS SER ILE LEU GLN GLN ALA GLY VAL GLU SEQRES 5 B 186 MET LYS SER GLU PHE LEU ALA THR LYS ALA LYS GLN PHE SEQRES 6 B 186 GLN ARG SER GLN LEU VAL LEU VAL THR LYS GLY PHE ASN SEQRES 7 B 186 LEU PHE CYS LYS TYR ILE TYR HIS VAL LEU TRP HIS SER SEQRES 8 B 186 GLU PHE PRO LYS PRO GLN ILE LEU LYS HIS ALA MET LYS SEQRES 9 B 186 GLU CYS LEU GLU LYS CYS ILE GLU GLN ASN ILE THR SER SEQRES 10 B 186 ILE SER PHE PRO ALA LEU GLY THR GLY ASN MET GLU ILE SEQRES 11 B 186 LYS LYS GLU THR ALA ALA GLU ILE LEU PHE ASP GLU VAL SEQRES 12 B 186 LEU THR PHE ALA LYS ASP HIS VAL LYS HIS GLN LEU THR SEQRES 13 B 186 VAL LYS PHE VAL ILE PHE PRO THR ASP LEU GLU ILE TYR SEQRES 14 B 186 LYS ALA PHE SER SER GLU MET ALA LYS ARG SER LYS MET SEQRES 15 B 186 LEU SER LEU ASN HET EDO A1457 4 HET EDO A1458 4 HET 15P A1459 34 HET 15P A1460 10 HET PO4 A1461 5 HET EDO B1459 4 HET EDO B1460 4 HET EDO B1461 4 HET EDO B1462 4 HET 15P B1463 34 HET PO4 B1464 5 HET PO4 B1465 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM 15P POLYETHYLENE GLYCOL (N=34) HETNAM PO4 PHOSPHATE ION HETSYN EDO ETHYLENE GLYCOL HETSYN 15P PEG 1500 FORMUL 3 EDO 6(C2 H6 O2) FORMUL 5 15P 3(C69 H140 O35) FORMUL 7 PO4 3(O4 P 3-) FORMUL 15 HOH *377(H2 O) HELIX 1 1 HIS A 290 GLN A 294 5 5 HELIX 2 2 GLY A 311 GLY A 322 1 12 HELIX 3 3 GLY A 322 GLN A 336 1 15 HELIX 4 4 PRO A 366 GLN A 385 1 20 HELIX 5 5 LYS A 403 HIS A 422 1 20 HELIX 6 6 ASP A 437 SER A 456 1 20 HELIX 7 7 HIS B 290 GLN B 294 5 5 HELIX 8 8 GLY B 311 GLY B 322 1 12 HELIX 9 9 GLY B 322 GLN B 336 1 15 HELIX 10 10 PRO B 366 GLN B 385 1 20 HELIX 11 11 LYS B 403 HIS B 422 1 20 HELIX 12 12 ASP B 437 SER B 456 1 20 SHEET 1 AA 7 ALA A 276 VAL A 279 0 SHEET 2 AA 7 LEU A 282 GLN A 288 -1 O LEU A 282 N VAL A 279 SHEET 3 AA 7 LEU A 427 ILE A 433 1 O LEU A 427 N THR A 283 SHEET 4 AA 7 SER A 389 PHE A 392 1 O ILE A 390 N LYS A 430 SHEET 5 AA 7 VAL A 298 VAL A 303 1 O VAL A 298 N SER A 391 SHEET 6 AA 7 TYR A 355 LEU A 360 1 O TYR A 355 N ILE A 299 SHEET 7 AA 7 VAL A 343 LYS A 347 -1 O LEU A 344 N HIS A 358 SHEET 1 BA 7 ALA B 276 VAL B 279 0 SHEET 2 BA 7 LEU B 282 GLN B 288 -1 O LEU B 282 N VAL B 279 SHEET 3 BA 7 LEU B 427 ILE B 433 1 O LEU B 427 N THR B 283 SHEET 4 BA 7 SER B 389 PHE B 392 1 O ILE B 390 N LYS B 430 SHEET 5 BA 7 VAL B 298 VAL B 303 1 O VAL B 298 N SER B 391 SHEET 6 BA 7 TYR B 355 LEU B 360 1 O TYR B 355 N ILE B 299 SHEET 7 BA 7 VAL B 343 LYS B 347 -1 O LEU B 344 N HIS B 358 SITE 1 AC1 5 THR A 388 GLN A 426 LEU A 427 THR A 428 SITE 2 AC1 5 HOH A2014 SITE 1 AC2 5 THR B 388 GLN B 426 LEU B 427 THR B 428 SITE 2 AC2 5 HOH B2007 SITE 1 AC3 7 SER B 302 VAL B 313 ALA B 394 LEU B 395 SITE 2 AC3 7 GLY B 396 THR B 397 HOH B2115 SITE 1 AC4 3 LYS B 335 LYS B 404 GLU B 405 SITE 1 AC5 3 THR B 295 LYS B 430 HOH B2111 SITE 1 AC6 3 LYS A 403 LYS A 404 GLU A 405 SITE 1 AC7 9 ASP A 297 LYS A 354 TYR A 355 SER A 363 SITE 2 AC7 9 GLU A 364 GLN A 385 ASN A 386 15P A1460 SITE 3 AC7 9 HOH A2142 SITE 1 AC8 10 ASP B 297 LYS B 354 TYR B 355 SER B 363 SITE 2 AC8 10 GLU B 364 GLN B 385 ASN B 386 GLU B 401 SITE 3 AC8 10 HOH B2080 HOH B2126 SITE 1 AC9 4 LEU A 351 15P A1459 HOH A2197 HOH A2199 SITE 1 BC1 5 HIS A 306 LYS A 333 LYS A 424 HOH A2168 SITE 2 BC1 5 HOH A2201 SITE 1 BC2 4 HIS B 306 LYS B 333 LYS B 424 HOH B2175 SITE 1 BC3 3 LYS A 453 GLN B 369 HIS B 373 CRYST1 58.489 74.010 94.369 90.00 90.00 90.00 P 21 21 21 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 0.017097 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010597 0.00000 MTRIX1 1 1.000000 0.001250 0.001190 23.46435 1 MTRIX2 1 -0.001250 0.999990 0.003700 0.11643 1 MTRIX3 1 -0.001190 -0.003700 0.999990 -46.97213 1