HEADER TRANSFERASE/DNA 26-SEP-06 2IHM TITLE POLYMERASE MU IN TERNARY COMPLEX WITH GAPPED 11MER DNA DUPLEX AND TITLE 2 BOUND INCOMING NUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'; COMPND 3 CHAIN: T, U; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*AP*GP*TP*AP*T)-3'; COMPND 7 CHAIN: P, Q; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(P*GP*CP*CP*G)-3'; COMPND 11 CHAIN: D, E; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA POLYMERASE MU; COMPND 15 CHAIN: A, B; COMPND 16 FRAGMENT: CATALYTIC DOMAIN; COMPND 17 SYNONYM: POL MU; COMPND 18 EC: 2.7.7.7; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 9 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 GENE: POLM; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) - RIL; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PGEX4T3 KEYWDS POLYMERASE, HELIX-TURN-HELIX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.F.MOON,L.C.PEDERSEN,T.A.KUNKEL REVDAT 9 20-SEP-23 2IHM 1 REMARK REVDAT 8 21-DEC-22 2IHM 1 REMARK SEQADV LINK REVDAT 7 24-JAN-18 2IHM 1 AUTHOR REVDAT 6 18-OCT-17 2IHM 1 REMARK REVDAT 5 24-FEB-09 2IHM 1 VERSN REVDAT 4 03-JUL-07 2IHM 1 REMARK REVDAT 3 22-MAY-07 2IHM 1 REMARK REVDAT 2 23-JAN-07 2IHM 1 JRNL REVDAT 1 12-DEC-06 2IHM 0 JRNL AUTH A.F.MOON,M.GARCIA-DIAZ,K.BEBENEK,B.J.DAVIS,X.ZHONG, JRNL AUTH 2 D.A.RAMSDEN,T.A.KUNKEL,L.C.PEDERSEN JRNL TITL STRUCTURAL INSIGHT INTO THE SUBSTRATE SPECIFICITY OF DNA JRNL TITL 2 POLYMERASE MU. JRNL REF NAT.STRUCT.MOL.BIOL. V. 14 45 2007 JRNL REFN ISSN 1545-9993 JRNL PMID 17159995 JRNL DOI 10.1038/NSMB1180 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 35276 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 SET) : 0.230 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1653 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3790 REMARK 3 BIN FREE R VALUE : 0.4080 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 229 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5230 REMARK 3 NUCLEIC ACID ATOMS : 850 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : 5.79000 REMARK 3 B33 (A**2) : -6.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.39000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.39 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.49 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.170 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2IHM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36737 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : 0.10600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.50500 REMARK 200 R SYM FOR SHELL (I) : 0.50500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: MURINE TDT - 1JMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.095M NA CITRATE PH 5.6, 19% REMARK 280 ISPROPANOL, 19% PEG4000, AND 5% GLYCEROL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 48.04250 REMARK 290 SMTRY3 2 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 300 REMARK: EACH ASYMMETRIC UNIT CONTAINS TWO MONOMERS OF POLYMERASE REMARK 300 MU. HOWEVER, THE MONOMERIC FORM OF POLYMERASE MU IS THE BIOLOGICAL REMARK 300 UNIT. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, D, 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: U, Q, E, 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 LEU A 370 REMARK 465 ALA A 371 REMARK 465 ASP A 372 REMARK 465 SER A 373 REMARK 465 ALA A 374 REMARK 465 HIS A 375 REMARK 465 ASN A 376 REMARK 465 LEU A 377 REMARK 465 ARG A 378 REMARK 465 GLN A 379 REMARK 465 ARG A 380 REMARK 465 SER A 381 REMARK 465 SER A 382 REMARK 465 THR A 383 REMARK 465 MET A 384 REMARK 465 PRO A 399 REMARK 465 GLN A 400 REMARK 465 GLN A 401 REMARK 465 ALA A 402 REMARK 465 ALA A 403 REMARK 465 LEU A 404 REMARK 465 ALA A 405 REMARK 465 GLY A 406 REMARK 465 ALA A 407 REMARK 465 LEU A 408 REMARK 465 PRO A 409 REMARK 465 PRO A 410 REMARK 465 CYS A 411 REMARK 465 HIS B 366 REMARK 465 ARG B 367 REMARK 465 SER B 368 REMARK 465 HIS B 369 REMARK 465 LEU B 370 REMARK 465 ALA B 371 REMARK 465 ASP B 372 REMARK 465 SER B 373 REMARK 465 ALA B 374 REMARK 465 HIS B 375 REMARK 465 ASN B 376 REMARK 465 LEU B 377 REMARK 465 ARG B 378 REMARK 465 GLN B 379 REMARK 465 ARG B 380 REMARK 465 SER B 381 REMARK 465 SER B 382 REMARK 465 THR B 383 REMARK 465 MET B 384 REMARK 465 ASP B 385 REMARK 465 VAL B 386 REMARK 465 ALA B 403 REMARK 465 LEU B 404 REMARK 465 ALA B 405 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 DT P 6 O3' REMARK 470 DT Q 6 O3' REMARK 470 SER A 137 OG REMARK 470 SER A 195 OG REMARK 470 GLN A 214 CG CD OE1 NE2 REMARK 470 GLN A 270 CG CD OE1 NE2 REMARK 470 VAL A 344 CG1 CG2 REMARK 470 ARG A 367 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 385 CG OD1 OD2 REMARK 470 VAL A 386 CG1 CG2 REMARK 470 PRO A 412 CG CD REMARK 470 LYS A 469 CG CD CE NZ REMARK 470 ARG A 470 CG CD NE CZ NH1 NH2 REMARK 470 SER B 195 OG REMARK 470 LYS B 226 CG CD CE NZ REMARK 470 GLN B 270 CG CD OE1 NE2 REMARK 470 GLN B 274 CG CD OE1 NE2 REMARK 470 GLU B 339 CG CD OE1 OE2 REMARK 470 GLU B 340 CG CD OE1 OE2 REMARK 470 LYS B 349 CG CD CE NZ REMARK 470 GLN B 364 CG CD OE1 NE2 REMARK 470 GLN B 400 CG CD OE1 NE2 REMARK 470 GLN B 401 CG CD OE1 NE2 REMARK 470 LEU B 408 CG CD1 CD2 REMARK 470 ASP B 465 CG OD1 OD2 REMARK 470 GLU B 467 CG CD OE1 OE2 REMARK 470 LYS B 469 CG CD CE NZ REMARK 470 ARG B 470 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 471 CG1 CG2 REMARK 470 ARG B 482 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 484 CG CD1 CD2 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 DT P 4 O4' DT P 4 C1' 0.169 REMARK 500 DT P 4 O4' DT P 4 C4' 0.200 REMARK 500 DG D 1 P DG D 1 OP3 -0.087 REMARK 500 DT Q 4 O4' DT Q 4 C1' 0.091 REMARK 500 DT Q 4 O4' DT Q 4 C4' 0.233 REMARK 500 DG E 1 P DG E 1 OP3 -0.086 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 DT P 4 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 DT P 4 C5' - C4' - O4' ANGL. DEV. = 15.2 DEGREES REMARK 500 DT P 4 C1' - O4' - C4' ANGL. DEV. = -17.6 DEGREES REMARK 500 DT P 4 O4' - C1' - C2' ANGL. DEV. = 11.1 DEGREES REMARK 500 DT P 4 O4' - C1' - N1 ANGL. DEV. = 8.4 DEGREES REMARK 500 DG Q 3 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT Q 4 C5' - C4' - O4' ANGL. DEV. = 20.8 DEGREES REMARK 500 DT Q 4 C1' - O4' - C4' ANGL. DEV. = -15.2 DEGREES REMARK 500 DT Q 4 O4' - C1' - C2' ANGL. DEV. = 9.9 DEGREES REMARK 500 DT Q 4 O4' - C1' - N1 ANGL. DEV. = 18.5 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 HIS A 151 -159.23 -128.40 REMARK 500 ASN A 153 43.46 -145.68 REMARK 500 TYR A 204 21.42 48.19 REMARK 500 GLN A 268 69.06 -108.91 REMARK 500 GLN A 270 48.77 -74.05 REMARK 500 ARG A 271 -29.38 -150.50 REMARK 500 THR A 309 -52.59 -126.19 REMARK 500 THR A 318 -153.90 -113.38 REMARK 500 GLN A 342 0.80 -68.52 REMARK 500 VAL A 386 32.28 83.39 REMARK 500 ARG A 451 -75.06 -76.36 REMARK 500 GLN A 468 37.90 -62.15 REMARK 500 ARG B 260 -21.11 -148.26 REMARK 500 PRO B 269 -9.07 -53.96 REMARK 500 THR B 318 -154.23 -114.60 REMARK 500 ARG B 323 3.06 -69.42 REMARK 500 GLU B 339 109.06 -58.88 REMARK 500 GLU B 340 7.73 -44.16 REMARK 500 VAL B 344 93.51 -64.47 REMARK 500 ALA B 407 -140.46 -125.54 REMARK 500 CYS B 411 171.21 178.80 REMARK 500 SER B 426 -29.79 -39.06 REMARK 500 ARG B 451 -69.68 -90.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA P 5 0.06 SIDE CHAIN REMARK 500 DT U 7 0.07 SIDE CHAIN REMARK 500 DG Q 3 0.11 SIDE CHAIN REMARK 500 DT Q 4 0.07 SIDE CHAIN REMARK 500 DA Q 5 0.10 SIDE CHAIN REMARK 500 DG E 1 0.07 SIDE CHAIN 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 NA A 900 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA P 5 OP1 REMARK 620 2 THR A 241 O 154.7 REMARK 620 3 VAL A 243 O 105.1 96.4 REMARK 620 4 VAL A 246 O 96.2 92.4 101.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 901 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA Q 5 OP1 REMARK 620 2 VAL B 246 O 99.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 700 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 81.1 REMARK 620 3 D3T A 538 O1A 87.1 91.0 REMARK 620 4 D3T A 538 O3G 97.5 178.5 89.3 REMARK 620 5 D3T A 538 O1B 172.5 98.3 85.4 83.2 REMARK 620 6 HOH A 903 O 89.9 89.1 177.0 90.6 97.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 800 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 D3T A 638 O1B REMARK 620 2 D3T A 638 O3G 87.2 REMARK 620 3 D3T A 638 O1A 87.7 78.9 REMARK 620 4 ASP B 330 OD1 164.5 79.8 81.6 REMARK 620 5 ASP B 332 OD2 104.1 165.0 91.6 87.5 REMARK 620 6 HOH B 902 O 99.3 102.8 172.9 91.9 85.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D3T A 538 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D3T A 638 DBREF 2IHM A 137 496 UNP Q9JIW4 DPOLM_MOUSE 137 496 DBREF 2IHM B 137 496 UNP Q9JIW4 DPOLM_MOUSE 137 496 DBREF 2IHM T 1 11 PDB 2IHM 2IHM 1 11 DBREF 2IHM P 1 6 PDB 2IHM 2IHM 1 6 DBREF 2IHM D 1 4 PDB 2IHM 2IHM 1 4 DBREF 2IHM U 1 11 PDB 2IHM 2IHM 1 11 DBREF 2IHM Q 1 6 PDB 2IHM 2IHM 1 6 DBREF 2IHM E 1 4 PDB 2IHM 2IHM 1 4 SEQADV 2IHM VAL A 386 UNP Q9JIW4 ALA 386 VARIANT SEQADV 2IHM VAL B 386 UNP Q9JIW4 ALA 386 VARIANT SEQRES 1 T 11 DC DG DG DC DA DA DT DA DC DT DG SEQRES 1 P 6 DC DA DG DT DA DT SEQRES 1 D 4 DG DC DC DG SEQRES 1 U 11 DC DG DG DC DA DA DT DA DC DT DG SEQRES 1 Q 6 DC DA DG DT DA DT SEQRES 1 E 4 DG DC DC DG SEQRES 1 A 360 SER MET PRO ALA TYR ALA CYS GLN ARG PRO SER PRO LEU SEQRES 2 A 360 THR HIS HIS ASN THR LEU LEU SER GLU ALA LEU GLU THR SEQRES 3 A 360 LEU ALA GLU ALA ALA GLY PHE GLU ALA ASN GLU GLY ARG SEQRES 4 A 360 LEU LEU SER PHE SER ARG ALA ALA SER VAL LEU LYS SER SEQRES 5 A 360 LEU PRO CYS PRO VAL ALA SER LEU SER GLN LEU HIS GLY SEQRES 6 A 360 LEU PRO TYR PHE GLY GLU HIS SER THR ARG VAL ILE GLN SEQRES 7 A 360 GLU LEU LEU GLU HIS GLY THR CYS GLU GLU VAL LYS GLN SEQRES 8 A 360 VAL ARG CYS SER GLU ARG TYR GLN THR MET LYS LEU PHE SEQRES 9 A 360 THR GLN VAL PHE GLY VAL GLY VAL LYS THR ALA ASN ARG SEQRES 10 A 360 TRP TYR GLN GLU GLY LEU ARG THR LEU ASP GLU LEU ARG SEQRES 11 A 360 GLU GLN PRO GLN ARG LEU THR GLN GLN GLN LYS ALA GLY SEQRES 12 A 360 LEU GLN TYR TYR GLN ASP LEU SER THR PRO VAL ARG ARG SEQRES 13 A 360 ALA ASP ALA GLU ALA LEU GLN GLN LEU ILE GLU ALA ALA SEQRES 14 A 360 VAL ARG GLN THR LEU PRO GLY ALA THR VAL THR LEU THR SEQRES 15 A 360 GLY GLY PHE ARG ARG GLY LYS LEU GLN GLY HIS ASP VAL SEQRES 16 A 360 ASP PHE LEU ILE THR HIS PRO GLU GLU GLY GLN GLU VAL SEQRES 17 A 360 GLY LEU LEU PRO LYS VAL MET SER CYS LEU GLN SER GLN SEQRES 18 A 360 GLY LEU VAL LEU TYR HIS GLN TYR HIS ARG SER HIS LEU SEQRES 19 A 360 ALA ASP SER ALA HIS ASN LEU ARG GLN ARG SER SER THR SEQRES 20 A 360 MET ASP VAL PHE GLU ARG SER PHE CYS ILE LEU GLY LEU SEQRES 21 A 360 PRO GLN PRO GLN GLN ALA ALA LEU ALA GLY ALA LEU PRO SEQRES 22 A 360 PRO CYS PRO THR TRP LYS ALA VAL ARG VAL ASP LEU VAL SEQRES 23 A 360 VAL THR PRO SER SER GLN PHE PRO PHE ALA LEU LEU GLY SEQRES 24 A 360 TRP THR GLY SER GLN PHE PHE GLU ARG GLU LEU ARG ARG SEQRES 25 A 360 PHE SER ARG GLN GLU LYS GLY LEU TRP LEU ASN SER HIS SEQRES 26 A 360 GLY LEU PHE ASP PRO GLU GLN LYS ARG VAL PHE HIS ALA SEQRES 27 A 360 THR SER GLU GLU ASP VAL PHE ARG LEU LEU GLY LEU LYS SEQRES 28 A 360 TYR LEU PRO PRO GLU GLN ARG ASN ALA SEQRES 1 B 360 SER MET PRO ALA TYR ALA CYS GLN ARG PRO SER PRO LEU SEQRES 2 B 360 THR HIS HIS ASN THR LEU LEU SER GLU ALA LEU GLU THR SEQRES 3 B 360 LEU ALA GLU ALA ALA GLY PHE GLU ALA ASN GLU GLY ARG SEQRES 4 B 360 LEU LEU SER PHE SER ARG ALA ALA SER VAL LEU LYS SER SEQRES 5 B 360 LEU PRO CYS PRO VAL ALA SER LEU SER GLN LEU HIS GLY SEQRES 6 B 360 LEU PRO TYR PHE GLY GLU HIS SER THR ARG VAL ILE GLN SEQRES 7 B 360 GLU LEU LEU GLU HIS GLY THR CYS GLU GLU VAL LYS GLN SEQRES 8 B 360 VAL ARG CYS SER GLU ARG TYR GLN THR MET LYS LEU PHE SEQRES 9 B 360 THR GLN VAL PHE GLY VAL GLY VAL LYS THR ALA ASN ARG SEQRES 10 B 360 TRP TYR GLN GLU GLY LEU ARG THR LEU ASP GLU LEU ARG SEQRES 11 B 360 GLU GLN PRO GLN ARG LEU THR GLN GLN GLN LYS ALA GLY SEQRES 12 B 360 LEU GLN TYR TYR GLN ASP LEU SER THR PRO VAL ARG ARG SEQRES 13 B 360 ALA ASP ALA GLU ALA LEU GLN GLN LEU ILE GLU ALA ALA SEQRES 14 B 360 VAL ARG GLN THR LEU PRO GLY ALA THR VAL THR LEU THR SEQRES 15 B 360 GLY GLY PHE ARG ARG GLY LYS LEU GLN GLY HIS ASP VAL SEQRES 16 B 360 ASP PHE LEU ILE THR HIS PRO GLU GLU GLY GLN GLU VAL SEQRES 17 B 360 GLY LEU LEU PRO LYS VAL MET SER CYS LEU GLN SER GLN SEQRES 18 B 360 GLY LEU VAL LEU TYR HIS GLN TYR HIS ARG SER HIS LEU SEQRES 19 B 360 ALA ASP SER ALA HIS ASN LEU ARG GLN ARG SER SER THR SEQRES 20 B 360 MET ASP VAL PHE GLU ARG SER PHE CYS ILE LEU GLY LEU SEQRES 21 B 360 PRO GLN PRO GLN GLN ALA ALA LEU ALA GLY ALA LEU PRO SEQRES 22 B 360 PRO CYS PRO THR TRP LYS ALA VAL ARG VAL ASP LEU VAL SEQRES 23 B 360 VAL THR PRO SER SER GLN PHE PRO PHE ALA LEU LEU GLY SEQRES 24 B 360 TRP THR GLY SER GLN PHE PHE GLU ARG GLU LEU ARG ARG SEQRES 25 B 360 PHE SER ARG GLN GLU LYS GLY LEU TRP LEU ASN SER HIS SEQRES 26 B 360 GLY LEU PHE ASP PRO GLU GLN LYS ARG VAL PHE HIS ALA SEQRES 27 B 360 THR SER GLU GLU ASP VAL PHE ARG LEU LEU GLY LEU LYS SEQRES 28 B 360 TYR LEU PRO PRO GLU GLN ARG ASN ALA HET MG A 700 1 HET NA A 900 1 HET NA A 902 1 HET D3T A 538 28 HET D3T A 638 28 HET MG B 800 1 HET NA B 901 1 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE FORMUL 9 MG 2(MG 2+) FORMUL 10 NA 3(NA 1+) FORMUL 12 D3T 2(C10 H17 N2 O13 P3) FORMUL 16 HOH *183(H2 O) HELIX 1 1 TYR A 141 ARG A 145 5 5 HELIX 2 2 ASN A 153 GLU A 170 1 18 HELIX 3 3 ASN A 172 LEU A 189 1 18 HELIX 4 4 SER A 195 HIS A 200 5 6 HELIX 5 5 GLY A 206 GLY A 220 1 15 HELIX 6 6 CYS A 222 SER A 231 1 10 HELIX 7 7 SER A 231 GLN A 242 1 12 HELIX 8 8 GLY A 247 GLU A 257 1 11 HELIX 9 9 THR A 261 GLU A 267 1 7 HELIX 10 10 THR A 273 TYR A 282 1 10 HELIX 11 11 TYR A 282 THR A 288 1 7 HELIX 12 12 ARG A 292 GLN A 308 1 17 HELIX 13 13 THR A 318 ARG A 323 1 6 HELIX 14 14 GLY A 345 GLN A 357 1 13 HELIX 15 15 GLN A 428 GLY A 438 1 11 HELIX 16 16 SER A 439 GLY A 455 1 17 HELIX 17 17 SER A 476 LEU A 484 1 9 HELIX 18 18 PRO A 490 ARG A 494 5 5 HELIX 19 19 TYR B 141 ARG B 145 5 5 HELIX 20 20 ASN B 153 GLU B 170 1 18 HELIX 21 21 ASN B 172 SER B 188 1 17 HELIX 22 22 SER B 195 LEU B 199 5 5 HELIX 23 23 GLY B 206 GLY B 220 1 15 HELIX 24 24 CYS B 222 SER B 231 1 10 HELIX 25 25 SER B 231 GLN B 242 1 12 HELIX 26 26 GLY B 247 GLY B 258 1 12 HELIX 27 27 LEU B 262 ARG B 266 5 5 HELIX 28 28 GLN B 268 LEU B 272 5 5 HELIX 29 29 THR B 273 TYR B 282 1 10 HELIX 30 30 TYR B 282 SER B 287 1 6 HELIX 31 31 ARG B 292 GLN B 308 1 17 HELIX 32 32 THR B 318 ARG B 323 1 6 HELIX 33 33 GLY B 345 SER B 356 1 12 HELIX 34 34 PRO B 425 SER B 427 5 3 HELIX 35 35 GLN B 428 GLY B 438 1 11 HELIX 36 36 SER B 439 GLU B 453 1 15 HELIX 37 37 SER B 476 GLY B 485 1 10 HELIX 38 38 PRO B 490 ARG B 494 5 5 SHEET 1 A 2 VAL A 290 ARG A 291 0 SHEET 2 A 2 GLN A 327 GLY A 328 -1 O GLY A 328 N VAL A 290 SHEET 1 B 5 THR A 314 LEU A 317 0 SHEET 2 B 5 ASP A 330 THR A 336 -1 O LEU A 334 N THR A 316 SHEET 3 B 5 TRP A 414 VAL A 423 1 O VAL A 422 N ILE A 335 SHEET 4 B 5 ARG A 389 PRO A 397 -1 N CYS A 392 O VAL A 419 SHEET 5 B 5 VAL A 360 HIS A 366 -1 N HIS A 366 O ARG A 389 SHEET 1 C 2 TRP A 457 LEU A 458 0 SHEET 2 C 2 LEU A 463 PHE A 464 -1 O PHE A 464 N TRP A 457 SHEET 1 D 2 VAL B 290 ARG B 291 0 SHEET 2 D 2 GLN B 327 GLY B 328 -1 O GLY B 328 N VAL B 290 SHEET 1 E 5 THR B 314 LEU B 317 0 SHEET 2 E 5 VAL B 331 THR B 336 -1 O THR B 336 N THR B 314 SHEET 3 E 5 TRP B 414 VAL B 423 1 O VAL B 422 N ILE B 335 SHEET 4 E 5 ARG B 389 PRO B 397 -1 N CYS B 392 O VAL B 419 SHEET 5 E 5 VAL B 360 TYR B 362 -1 N LEU B 361 O ILE B 393 SHEET 1 F 2 TRP B 457 LEU B 458 0 SHEET 2 F 2 LEU B 463 PHE B 464 -1 O PHE B 464 N TRP B 457 LINK OP1 DA P 5 NA NA A 900 1555 1555 2.54 LINK OP1 DA Q 5 NA NA B 901 1555 1555 2.37 LINK O THR A 241 NA NA A 900 1555 1555 2.48 LINK O VAL A 243 NA NA A 900 1555 1555 2.48 LINK O VAL A 246 NA NA A 900 1555 1555 2.36 LINK OD1 ASP A 330 MG MG A 700 1555 1555 2.36 LINK OD2 ASP A 330 NA NA A 902 1555 1555 2.12 LINK OD2 ASP A 332 MG MG A 700 1555 1555 2.83 LINK O1A D3T A 538 MG MG A 700 1555 1555 2.24 LINK O3G D3T A 538 MG MG A 700 1555 1555 2.51 LINK O1B D3T A 538 MG MG A 700 1555 1555 2.11 LINK O1B D3T A 638 MG MG B 800 1555 1555 1.98 LINK O3G D3T A 638 MG MG B 800 1555 1555 2.75 LINK O1A D3T A 638 MG MG B 800 1555 1555 2.44 LINK MG MG A 700 O HOH A 903 1555 1555 2.28 LINK O VAL B 246 NA NA B 901 1555 1555 2.32 LINK OD1 ASP B 330 MG MG B 800 1555 1555 2.26 LINK OD2 ASP B 332 MG MG B 800 1555 1555 2.44 LINK MG MG B 800 O HOH B 902 1555 1555 2.41 CISPEP 1 GLY A 438 SER A 439 0 0.94 CISPEP 2 GLY B 438 SER B 439 0 -0.01 SITE 1 AC1 4 ASP A 330 ASP A 332 D3T A 538 HOH A 903 SITE 1 AC2 4 D3T A 638 ASP B 330 ASP B 332 HOH B 902 SITE 1 AC3 4 THR A 241 VAL A 243 VAL A 246 DA P 5 SITE 1 AC4 4 THR B 241 VAL B 243 VAL B 246 DA Q 5 SITE 1 AC5 5 ASP A 330 ASP A 332 ASP A 420 D3T A 538 SITE 2 AC5 5 DT P 6 SITE 1 AC6 22 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC6 22 GLN A 327 GLY A 328 HIS A 329 ASP A 330 SITE 3 AC6 22 ASP A 332 GLY A 435 TRP A 436 GLY A 438 SITE 4 AC6 22 GLN A 440 GLU A 443 MG A 700 NA A 902 SITE 5 AC6 22 HOH A 905 HOH A 910 HOH A 924 HOH A 926 SITE 6 AC6 22 DT P 6 DA T 5 SITE 1 AC7 19 HOH A 953 HOH A 983 HOH A 984 GLY B 319 SITE 2 AC7 19 GLY B 320 ARG B 323 LYS B 325 GLY B 328 SITE 3 AC7 19 HIS B 329 ASP B 330 ASP B 332 GLY B 435 SITE 4 AC7 19 TRP B 436 GLY B 438 GLN B 440 GLU B 443 SITE 5 AC7 19 MG B 800 DT Q 6 DA U 5 CRYST1 71.028 96.085 73.090 90.00 106.55 90.00 P 1 21 1 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 0.014079 0.000000 0.004184 0.00000 SCALE2 0.000000 0.010407 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014273 0.00000