HEADER TRANSFERASE/DNA 01-AUG-13 4M04 TITLE HUMAN DNA POLYMERASE MU TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED DNA/RNA POLYMERASE MU; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POLYMERASE MU LOOP2 DELETION VARIANT, UNP RESIDUES 132-494; COMPND 5 SYNONYM: POL MU, TERMINAL TRANSFERASE; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TEMPLATE STRAND; COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: UPSTREAM PRIMER STRAND; COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DOWNSTREAM PRIMER STRAND; COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLM, POLMU; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHESIZED BY OLIGOS ETC; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: SYNTHESIZED BY OLIGOS ETC; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 OTHER_DETAILS: SYNTHESIZED BY OLIGOS ETC KEYWDS POLYMERASE, DNA BREAK REPAIR, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.F.MOON,J.M.PRYOR,D.A.RAMSDEN,T.A.KUNKEL,K.BEBENEK,L.C.PEDERSEN REVDAT 5 20-SEP-23 4M04 1 REMARK SEQADV LINK REVDAT 4 15-NOV-17 4M04 1 REMARK REVDAT 3 19-MAR-14 4M04 1 JRNL REVDAT 2 05-MAR-14 4M04 1 JRNL REVDAT 1 05-FEB-14 4M04 0 JRNL AUTH A.F.MOON,J.M.PRYOR,D.A.RAMSDEN,T.A.KUNKEL,K.BEBENEK, JRNL AUTH 2 L.C.PEDERSEN JRNL TITL SUSTAINED ACTIVE SITE RIGIDITY DURING SYNTHESIS BY HUMAN DNA JRNL TITL 2 POLYMERASE MU. JRNL REF NAT.STRUCT.MOL.BIOL. V. 21 253 2014 JRNL REFN ISSN 1545-9993 JRNL PMID 24487959 JRNL DOI 10.1038/NSMB.2766 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 36188 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1805 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 23.1762 - 4.4539 1.00 2837 149 0.1595 0.1972 REMARK 3 2 4.4539 - 3.5392 1.00 2693 143 0.1331 0.1381 REMARK 3 3 3.5392 - 3.0930 1.00 2687 140 0.1545 0.1574 REMARK 3 4 3.0930 - 2.8108 1.00 2659 140 0.1835 0.2157 REMARK 3 5 2.8108 - 2.6096 1.00 2635 137 0.1793 0.2310 REMARK 3 6 2.6096 - 2.4559 1.00 2634 139 0.1786 0.1908 REMARK 3 7 2.4559 - 2.3330 1.00 2641 139 0.1684 0.2141 REMARK 3 8 2.3330 - 2.2316 1.00 2612 138 0.1683 0.2346 REMARK 3 9 2.2316 - 2.1457 1.00 2637 138 0.1682 0.2191 REMARK 3 10 2.1457 - 2.0717 1.00 2621 137 0.1677 0.2165 REMARK 3 11 2.0717 - 2.0070 1.00 2621 139 0.1845 0.2657 REMARK 3 12 2.0070 - 1.9496 0.99 2589 134 0.2040 0.2531 REMARK 3 13 1.9496 - 1.8983 0.97 2517 132 0.2058 0.2647 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.47 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 : 0.010 3232 REMARK 3 ANGLE : 1.325 4483 REMARK 3 CHIRALITY : 0.085 491 REMARK 3 PLANARITY : 0.006 520 REMARK 3 DIHEDRAL : 12.772 1036 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4M04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081297. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAXHF MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36290 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.898 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 : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.31600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2IHM (MOLECULE B) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY MIXING 1UL OF REMARK 280 PROTEIN/DNA MIXTURE WITH 1UL MOTHER LIQUOR (85-90MM HEPES PH 7.5, REMARK 280 17-18% PEG4000), USING THE SITTING DROP VAPOR DIFFUSION REMARK 280 TECHNIQUE. CRYSTALS WERE THEN TRANSFERRED TO A CRYOPROTECTANT REMARK 280 SOLUTION CONTAINING 0.1M HEPES PH 7.5, 10MM MGCL2, 50MM NACL, 20% REMARK 280 PEG4000, 5% GLYCEROL, 1MM DUMPNPP IN TWO STEPS. , VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 29.94600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.88650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.23350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.88650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.94600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.23350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 127 REMARK 465 SER A 128 REMARK 465 ALA A 129 REMARK 465 ALA A 130 REMARK 465 ALA A 131 REMARK 465 PRO A 132 REMARK 465 LEU A 133 REMARK 465 SER A 134 REMARK 465 PRO A 135 REMARK 465 ALA A 136 REMARK 465 HIS A 365 REMARK 465 GLN A 366 REMARK 465 HIS A 367 REMARK 465 SER A 368 REMARK 465 CYS A 369 REMARK 465 CYS A 370 REMARK 465 GLU A 371 REMARK 465 SER A 372 REMARK 465 PRO A 373 REMARK 465 THR A 374 REMARK 465 ARG A 375 REMARK 465 LEU A 376 REMARK 465 ALA A 377 REMARK 465 GLN A 378 REMARK 465 GLN A 379 REMARK 465 SER A 380 REMARK 465 HIS A 381 REMARK 465 MET A 382 REMARK 465 ASP A 383 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 TRP A 137 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 137 CZ3 CH2 REMARK 470 GLN A 200 CD OE1 NE2 REMARK 470 GLU A 223 CD OE1 OE2 REMARK 470 GLN A 268 CG CD OE1 NE2 REMARK 470 GLN A 270 CG CD OE1 NE2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 GLN A 274 CG CD OE1 NE2 REMARK 470 ASP A 296 OD1 OD2 REMARK 470 GLN A 300 CD OE1 NE2 REMARK 470 LYS A 339 CD CE NZ REMARK 470 GLN A 355 CD OE1 NE2 REMARK 470 GLN A 357 OE1 NE2 REMARK 470 LYS A 467 CD CE NZ REMARK 470 GLN A 471 OE1 NE2 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 1006 O HOH A 1009 2.12 REMARK 500 O HOH A 952 O HOH D 104 2.12 REMARK 500 CL CL A 706 O HOH A 1094 2.12 REMARK 500 NH2 ARG A 145 O HOH A 987 2.12 REMARK 500 O HOH A 1062 O HOH A 1116 2.15 REMARK 500 OE2 GLU A 218 O HOH A 1004 2.16 REMARK 500 NH1 ARG A 253 O HOH A 997 2.17 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 267 CD GLU A 267 OE2 0.075 REMARK 500 DG D 1 P DG D 1 OP3 -0.126 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 DC T 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA T 7 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG T 9 O4' - C1' - N9 ANGL. DEV. = -6.1 DEGREES REMARK 500 DC P 1 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DT P 3 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DG D 1 O4' - C1' - N9 ANGL. DEV. = -6.6 DEGREES REMARK 500 DC D 2 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 DC D 3 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC D 3 O4' - C1' - N1 ANGL. DEV. = -5.7 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 153 38.16 -141.94 REMARK 500 LEU A 310 96.10 -161.91 REMARK 500 THR A 318 -148.46 -125.42 REMARK 500 THR A 318 -153.66 -129.52 REMARK 500 SER A 411 -148.64 -168.12 REMARK 500 ASN A 493 49.84 -85.33 REMARK 500 REMARK 500 REMARK: NULL 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 EPE A 709 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 707 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 97.2 REMARK 620 3 VAL A 246 O 91.1 94.5 REMARK 620 4 HOH A 986 O 84.6 87.0 175.6 REMARK 620 5 DT P 3 OP1 170.3 92.2 90.1 94.0 REMARK 620 6 HOH P 105 O 85.7 175.5 88.8 90.0 84.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 93.8 REMARK 620 3 ASP A 418 OD1 87.5 93.8 REMARK 620 4 DUP A 701 O1A 90.7 92.1 173.9 REMARK 620 5 HOH A 807 O 90.7 173.5 91.2 83.0 REMARK 620 6 DA P 4 O3' 171.7 88.7 84.5 97.1 87.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 91.6 REMARK 620 3 DUP A 701 O2B 169.2 95.5 REMARK 620 4 DUP A 701 O3G 84.8 176.4 88.1 REMARK 620 5 DUP A 701 O1A 97.3 91.9 90.5 88.0 REMARK 620 6 HOH A 821 O 81.4 89.9 90.5 90.2 177.9 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 DUP A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 708 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 709 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IHM RELATED DB: PDB REMARK 900 RELATED ID: 4LZD RELATED DB: PDB REMARK 900 RELATED ID: 4LZG RELATED DB: PDB REMARK 900 RELATED ID: 4M0A RELATED DB: PDB DBREF 4M04 A 132 494 UNP Q9NP87 DPOLM_HUMAN 132 494 DBREF 4M04 T 1 9 PDB 4M04 4M04 1 9 DBREF 4M04 P 1 4 PDB 4M04 4M04 1 4 DBREF 4M04 D 1 4 PDB 4M04 4M04 1 4 SEQADV 4M04 GLY A 127 UNP Q9NP87 EXPRESSION TAG SEQADV 4M04 SER A 128 UNP Q9NP87 EXPRESSION TAG SEQADV 4M04 ALA A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 4M04 ALA A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 4M04 ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 4M04 A UNP Q9NP87 PRO 398 DELETION SEQADV 4M04 A UNP Q9NP87 GLY 399 DELETION SEQADV 4M04 A UNP Q9NP87 ALA 400 DELETION SEQADV 4M04 A UNP Q9NP87 ALA 401 DELETION SEQADV 4M04 A UNP Q9NP87 VAL 402 DELETION SEQADV 4M04 A UNP Q9NP87 GLY 403 DELETION SEQADV 4M04 A UNP Q9NP87 GLY 404 DELETION SEQADV 4M04 A UNP Q9NP87 SER 405 DELETION SEQADV 4M04 A UNP Q9NP87 THR 406 DELETION SEQADV 4M04 A UNP Q9NP87 ARG 407 DELETION SEQADV 4M04 A UNP Q9NP87 PRO 408 DELETION SEQADV 4M04 A UNP Q9NP87 CYS 409 DELETION SEQADV 4M04 A UNP Q9NP87 PRO 410 DELETION SEQADV 4M04 GLY A 410 UNP Q9NP87 INSERTION SEQRES 1 A 356 GLY SER ALA ALA ALA PRO LEU SER PRO ALA TRP MET PRO SEQRES 2 A 356 ALA TYR ALA CYS GLN ARG PRO THR PRO LEU THR HIS HIS SEQRES 3 A 356 ASN THR GLY LEU SER GLU ALA LEU GLU ILE LEU ALA GLU SEQRES 4 A 356 ALA ALA GLY PHE GLU GLY SER GLU GLY ARG LEU LEU THR SEQRES 5 A 356 PHE CYS ARG ALA ALA SER VAL LEU LYS ALA LEU PRO SER SEQRES 6 A 356 PRO VAL THR THR LEU SER GLN LEU GLN GLY LEU PRO HIS SEQRES 7 A 356 PHE GLY GLU HIS SER SER ARG VAL VAL GLN GLU LEU LEU SEQRES 8 A 356 GLU HIS GLY VAL CYS GLU GLU VAL GLU ARG VAL ARG ARG SEQRES 9 A 356 SER GLU ARG TYR GLN THR MET LYS LEU PHE THR GLN ILE SEQRES 10 A 356 PHE GLY VAL GLY VAL LYS THR ALA ASP ARG TRP TYR ARG SEQRES 11 A 356 GLU GLY LEU ARG THR LEU ASP ASP LEU ARG GLU GLN PRO SEQRES 12 A 356 GLN LYS LEU THR GLN GLN GLN LYS ALA GLY LEU GLN HIS SEQRES 13 A 356 HIS GLN ASP LEU SER THR PRO VAL LEU ARG SER ASP VAL SEQRES 14 A 356 ASP ALA LEU GLN GLN VAL VAL GLU GLU ALA VAL GLY GLN SEQRES 15 A 356 ALA LEU PRO GLY ALA THR VAL THR LEU THR GLY GLY PHE SEQRES 16 A 356 ARG ARG GLY LYS LEU GLN GLY HIS ASP VAL ASP PHE LEU SEQRES 17 A 356 ILE THR HIS PRO LYS GLU GLY GLN GLU ALA GLY LEU LEU SEQRES 18 A 356 PRO ARG VAL MET CYS ARG LEU GLN ASP GLN GLY LEU ILE SEQRES 19 A 356 LEU TYR HIS GLN HIS GLN HIS SER CYS CYS GLU SER PRO SEQRES 20 A 356 THR ARG LEU ALA GLN GLN SER HIS MET ASP ALA PHE GLU SEQRES 21 A 356 ARG SER PHE CYS ILE PHE ARG LEU PRO GLN PRO GLY SER SEQRES 22 A 356 TRP LYS ALA VAL ARG VAL ASP LEU VAL VAL ALA PRO VAL SEQRES 23 A 356 SER GLN PHE PRO PHE ALA LEU LEU GLY TRP THR GLY SER SEQRES 24 A 356 LYS LEU PHE GLN ARG GLU LEU ARG ARG PHE SER ARG LYS SEQRES 25 A 356 GLU LYS GLY LEU TRP LEU ASN SER HIS GLY LEU PHE ASP SEQRES 26 A 356 PRO GLU GLN LYS THR PHE PHE GLN ALA ALA SER GLU GLU SEQRES 27 A 356 ASP ILE PHE ARG HIS LEU GLY LEU GLU TYR LEU PRO PRO SEQRES 28 A 356 GLU GLN ARG ASN ALA SEQRES 1 T 9 DC DG DG DC DA DT DA DC DG SEQRES 1 P 4 DC DG DT DA SEQRES 1 D 4 DG DC DC DG HET DUP A 701 28 HET MG A 702 1 HET MG A 703 1 HET EDO A 704 4 HET EDO A 705 4 HET CL A 706 1 HET NA A 707 1 HET EDO A 708 4 HET EPE A 709 12 HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES FORMUL 5 DUP C9 H16 N3 O13 P3 FORMUL 6 MG 2(MG 2+) FORMUL 8 EDO 3(C2 H6 O2) FORMUL 10 CL CL 1- FORMUL 11 NA NA 1+ FORMUL 13 EPE C8 H18 N2 O4 S FORMUL 14 HOH *381(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 SER A 172 ALA A 188 1 17 HELIX 4 4 THR A 195 GLN 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 GLN A 268 1 8 HELIX 10 10 PRO A 269 LEU A 272 5 4 HELIX 11 11 THR A 273 HIS A 282 1 10 HELIX 12 12 HIS A 282 SER A 287 1 6 HELIX 13 13 ARG A 292 LEU A 310 1 19 HELIX 14 14 THR A 318 ARG A 323 1 6 HELIX 15 15 GLY A 345 GLN A 357 1 13 HELIX 16 16 PRO A 423 SER A 425 5 3 HELIX 17 17 GLN A 426 GLY A 436 1 11 HELIX 18 18 SER A 437 GLY A 453 1 17 HELIX 19 19 SER A 474 LEU A 482 1 9 HELIX 20 20 PRO A 488 ARG A 492 5 5 SHEET 1 A 2 VAL A 290 LEU 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 VAL A 331 THR A 336 -1 O LEU A 334 N THR A 316 SHEET 3 B 5 SER A 411 VAL A 421 1 O VAL A 420 N ILE A 335 SHEET 4 B 5 ARG A 387 GLN A 396 -1 N PHE A 392 O VAL A 415 SHEET 5 B 5 ILE A 360 TYR A 362 -1 N LEU A 361 O ILE A 391 SHEET 1 C 3 TRP A 455 LEU A 456 0 SHEET 2 C 3 LEU A 461 ASP A 463 -1 O PHE A 462 N TRP A 455 SHEET 3 C 3 THR A 468 PHE A 469 -1 O THR A 468 N ASP A 463 LINK O THR A 241 NA NA A 707 1555 1555 2.35 LINK O ILE A 243 NA NA A 707 1555 1555 2.38 LINK O VAL A 246 NA NA A 707 1555 1555 2.34 LINK OD2 ASP A 330 MG MG A 702 1555 1555 2.03 LINK OD1 ASP A 330 MG MG A 703 1555 1555 2.03 LINK OD1 ASP A 332 MG MG A 702 1555 1555 2.04 LINK OD2 ASP A 332 MG MG A 703 1555 1555 2.04 LINK OD1 ASP A 418 MG MG A 702 1555 1555 2.05 LINK O1A DUP A 701 MG MG A 702 1555 1555 2.30 LINK O2B DUP A 701 MG MG A 703 1555 1555 2.04 LINK O3G DUP A 701 MG MG A 703 1555 1555 2.08 LINK O1A DUP A 701 MG MG A 703 1555 1555 2.13 LINK MG MG A 702 O HOH A 807 1555 1555 2.07 LINK MG MG A 702 O3' DA P 4 1555 1555 2.13 LINK MG MG A 703 O HOH A 821 1555 1555 2.14 LINK NA NA A 707 O HOH A 986 1555 1555 2.55 LINK NA NA A 707 OP1 DT P 3 1555 1555 2.68 LINK NA NA A 707 O HOH P 105 1555 1555 2.36 CISPEP 1 GLY A 436 SER A 437 0 -3.94 SITE 1 AC1 25 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC1 25 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC1 25 GLY A 433 TRP A 434 GLY A 436 LYS A 438 SITE 4 AC1 25 MG A 702 MG A 703 EDO A 705 HOH A 805 SITE 5 AC1 25 HOH A 807 HOH A 821 HOH A 828 HOH A 853 SITE 6 AC1 25 HOH A 876 HOH A 927 HOH A1007 DA P 4 SITE 7 AC1 25 DA T 5 SITE 1 AC2 7 ASP A 330 ASP A 332 ASP A 418 DUP A 701 SITE 2 AC2 7 MG A 703 HOH A 807 DA P 4 SITE 1 AC3 5 ASP A 330 ASP A 332 DUP A 701 MG A 702 SITE 2 AC3 5 HOH A 821 SITE 1 AC4 4 GLU A 207 HIS A 208 ARG A 211 DG D 1 SITE 1 AC5 7 ARG A 387 GLY A 433 TRP A 434 ARG A 445 SITE 2 AC5 7 DUP A 701 HOH A 993 DA P 4 SITE 1 AC6 5 SER A 172 GLY A 174 ARG A 175 HOH A1094 SITE 2 AC6 5 HOH A1095 SITE 1 AC7 6 THR A 241 ILE A 243 VAL A 246 HOH A 986 SITE 2 AC7 6 DT P 3 HOH P 105 SITE 1 AC8 5 GLN A 426 HIS A 459 PHE A 469 HOH A 989 SITE 2 AC8 5 HOH A1116 SITE 1 AC9 4 LYS A 325 LEU A 326 GLN A 327 HOH A 995 CRYST1 59.892 68.467 109.773 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016697 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014606 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009110 0.00000