PDB Short entry for 4P4P HEADER TRANSFERASE/DNA 12-MAR-14 4P4P TITLE CRYSTAL STRUCTURE OF LEISHMANIA INFANTUM POLYMERASE BETA: NICK COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (5'-D(P*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3'); COMPND 15 CHAIN: B; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA INFANTUM; SOURCE 3 ORGANISM_TAXID: 5671; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 4; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.MEJIA,M.BURAK,A.ALONSO,V.LARRAGA,T.KUNKEL,K.BEBENEK,M.GARCIA-DIAZ REVDAT 4 27-SEP-23 4P4P 1 REMARK LINK REVDAT 3 25-DEC-19 4P4P 1 REMARK REVDAT 2 06-SEP-17 4P4P 1 SOURCE REMARK REVDAT 1 06-AUG-14 4P4P 0 JRNL AUTH E.MEJIA,M.BURAK,A.ALONSO,V.LARRAGA,T.A.KUNKEL,K.BEBENEK, JRNL AUTH 2 M.GARCIA-DIAZ JRNL TITL STRUCTURES OF THE LEISHMANIA INFANTUM POLYMERASE BETA. JRNL REF DNA REPAIR (AMST.) V. 18 1 2014 JRNL REFN ISSN 1568-7856 JRNL PMID 24666693 JRNL DOI 10.1016/J.DNAREP.2014.03.001 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24483 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 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 44.3107 - 5.5335 1.00 1784 156 0.2233 0.2647 REMARK 3 2 5.5335 - 4.3934 1.00 1661 148 0.1766 0.2036 REMARK 3 3 4.3934 - 3.8384 1.00 1626 144 0.1656 0.1981 REMARK 3 4 3.8384 - 3.4876 1.00 1612 144 0.1817 0.2344 REMARK 3 5 3.4876 - 3.2377 1.00 1607 143 0.1822 0.2331 REMARK 3 6 3.2377 - 3.0469 1.00 1593 142 0.2152 0.2475 REMARK 3 7 3.0469 - 2.8943 1.00 1605 142 0.2017 0.2690 REMARK 3 8 2.8943 - 2.7683 1.00 1586 141 0.1915 0.2590 REMARK 3 9 2.7683 - 2.6618 1.00 1561 139 0.1896 0.2178 REMARK 3 10 2.6618 - 2.5699 1.00 1583 141 0.1833 0.2085 REMARK 3 11 2.5699 - 2.4896 1.00 1574 140 0.1773 0.2097 REMARK 3 12 2.4896 - 2.4184 1.00 1567 139 0.1860 0.2696 REMARK 3 13 2.4184 - 2.3548 1.00 1591 141 0.2122 0.2372 REMARK 3 14 2.3548 - 2.2973 0.98 1536 137 0.2131 0.2732 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2705 REMARK 3 ANGLE : 1.045 3730 REMARK 3 CHIRALITY : 0.064 412 REMARK 3 PLANARITY : 0.005 420 REMARK 3 DIHEDRAL : 18.591 1058 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 376 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.9780 -34.8218 -8.3482 REMARK 3 T TENSOR REMARK 3 T11: 0.1832 T22: 0.1342 REMARK 3 T33: 0.1402 T12: 0.0018 REMARK 3 T13: 0.0389 T23: 0.0084 REMARK 3 L TENSOR REMARK 3 L11: 1.2033 L22: 0.9346 REMARK 3 L33: 0.6783 L12: -0.5622 REMARK 3 L13: -0.6819 L23: 0.3895 REMARK 3 S TENSOR REMARK 3 S11: 0.1093 S12: -0.0669 S13: 0.0329 REMARK 3 S21: 0.0630 S22: -0.0528 S23: 0.0153 REMARK 3 S31: -0.0646 S32: 0.0016 S33: -0.0444 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 4P4P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000200693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24544 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.297 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <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: NULL REMARK 200 STARTING MODEL: 1BPY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE, PH 4.6 AND 12.5% PEG 4000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 106.40600 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 53.20300 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.80450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.60150 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 133.00750 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 106.40600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 53.20300 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 26.60150 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 79.80450 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 133.00750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 527 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 542 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 ARG A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 PHE A 6 REMARK 465 LEU A 7 REMARK 465 ARG A 8 REMARK 465 ARG A 9 REMARK 465 ASP A 10 REMARK 465 HIS A 11 REMARK 465 ARG A 12 REMARK 465 GLU A 13 REMARK 465 ASN A 14 REMARK 465 ILE A 15 REMARK 465 ILE A 16 REMARK 465 ARG A 17 REMARK 465 ILE A 18 REMARK 465 PHE A 19 REMARK 465 GLN A 20 REMARK 465 GLU A 21 REMARK 465 MET A 22 REMARK 465 ALA A 23 REMARK 465 ASP A 24 REMARK 465 LEU A 25 REMARK 465 ASN A 26 REMARK 465 ASN A 27 REMARK 465 ALA A 28 REMARK 465 LEU A 29 REMARK 465 GLY A 30 REMARK 465 GLU A 31 REMARK 465 SER A 36 REMARK 465 SER A 37 REMARK 465 TYR A 38 REMARK 465 HIS A 39 REMARK 465 ARG A 40 REMARK 465 SER A 41 REMARK 465 ILE A 42 REMARK 465 GLU A 43 REMARK 465 SER A 44 REMARK 465 LEU A 45 REMARK 465 LYS A 46 REMARK 465 THR A 47 REMARK 465 ASN A 48 REMARK 465 LEU A 49 REMARK 465 ASP A 50 REMARK 465 LYS A 51 REMARK 465 PRO A 52 REMARK 465 LEU A 53 REMARK 465 ASN A 54 REMARK 465 THR A 55 REMARK 465 PRO A 56 REMARK 465 GLN A 57 REMARK 465 ASP A 58 REMARK 465 LEU A 59 REMARK 465 LYS A 60 REMARK 465 ALA A 61 REMARK 465 PHE A 62 REMARK 465 SER A 63 REMARK 465 GLY A 64 REMARK 465 PHE A 65 REMARK 465 GLY A 66 REMARK 465 ALA A 67 REMARK 465 LYS A 68 REMARK 465 LEU A 69 REMARK 465 LEU A 70 REMARK 465 LYS A 71 REMARK 465 LYS A 72 REMARK 465 ALA A 73 REMARK 465 GLU A 74 REMARK 465 GLU A 75 REMARK 465 ILE A 76 REMARK 465 MET A 77 REMARK 465 ALA A 78 REMARK 465 THR A 79 REMARK 465 GLY A 80 REMARK 465 LYS A 81 REMARK 465 LEU A 82 REMARK 465 GLU A 83 REMARK 465 GLU A 84 REMARK 465 LEU A 85 REMARK 465 GLU A 86 REMARK 465 SER A 87 REMARK 465 LYS A 88 REMARK 465 THR A 89 REMARK 465 LYS A 90 REMARK 465 VAL A 253 REMARK 465 ARG A 254 REMARK 465 ASP A 255 REMARK 465 LYS A 256 REMARK 465 ALA A 257 REMARK 465 GLY A 258 REMARK 465 ARG A 259 REMARK 465 GLU A 260 REMARK 465 DC D 3 REMARK 465 DG D 4 REMARK 465 DC B 1 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 LEU A 93 CG CD1 CD2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 ARG A 108 CD NE CZ NH1 NH2 REMARK 470 GLU A 320 CG CD OE1 OE2 REMARK 470 ARG A 332 CG CD NE CZ NH1 NH2 REMARK 470 DG B 2 P OP1 OP2 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 DG D 1 P DG D 1 OP3 -0.129 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 DG C 3 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT C 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC C 6 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DG D 1 OP1 - P - OP2 ANGL. DEV. = -11.9 DEGREES REMARK 500 DC B 4 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DG B 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.3 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 CYS A 182 -131.69 -112.65 REMARK 500 ARG A 332 -66.68 -23.39 REMARK 500 LYS A 334 -84.28 -117.39 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 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 100 O REMARK 620 2 VAL A 102 O 95.8 REMARK 620 3 PHE A 105 O 91.3 76.0 REMARK 620 4 HOH A 646 O 87.7 83.9 159.7 REMARK 620 5 DA C 5 OP1 171.2 82.6 79.9 100.7 REMARK 620 6 HOH C 117 O 79.1 167.1 92.2 107.5 100.6 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 NA A 401 DBREF 4P4P A 1 376 UNP Q9U6N3 Q9U6N3_LEIIN 1 376 DBREF 4P4P C 1 6 PDB 4P4P 4P4P 1 6 DBREF 4P4P D 1 3 PDB 4P4P 4P4P 1 3 DBREF 4P4P B 1 11 PDB 4P4P 4P4P 1 11 SEQADV 4P4P GLY A -1 UNP Q9U6N3 EXPRESSION TAG SEQADV 4P4P HIS A 0 UNP Q9U6N3 EXPRESSION TAG SEQRES 1 A 378 GLY HIS MET LEU ARG ARG LYS PHE LEU ARG ARG ASP HIS SEQRES 2 A 378 ARG GLU ASN ILE ILE ARG ILE PHE GLN GLU MET ALA ASP SEQRES 3 A 378 LEU ASN ASN ALA LEU GLY GLU LYS TYR LYS VAL SER SER SEQRES 4 A 378 TYR HIS ARG SER ILE GLU SER LEU LYS THR ASN LEU ASP SEQRES 5 A 378 LYS PRO LEU ASN THR PRO GLN ASP LEU LYS ALA PHE SER SEQRES 6 A 378 GLY PHE GLY ALA LYS LEU LEU LYS LYS ALA GLU GLU ILE SEQRES 7 A 378 MET ALA THR GLY LYS LEU GLU GLU LEU GLU SER LYS THR SEQRES 8 A 378 LYS PRO LYS LEU LYS ALA ILE GLN GLU LEU THR GLN VAL SEQRES 9 A 378 HIS GLY PHE GLY PRO ARG ALA ALA ALA ALA LEU PHE ASP SEQRES 10 A 378 ARG GLU GLY ILE PHE THR VAL ASP GLU LEU LEU GLN LYS SEQRES 11 A 378 ALA ASP SER ILE PRO SER LEU THR ASP GLN GLN ARG VAL SEQRES 12 A 378 GLY ILE LYS TYR PHE TYR ASP ILE ASN GLU LYS ILE PRO SEQRES 13 A 378 MET GLN GLU SER VAL LEU HIS GLU ASN TYR LEU ARG GLU SEQRES 14 A 378 LYS CYS MET GLU VAL LEU GLY LYS ASP PHE SER ILE LEU SEQRES 15 A 378 ILE CYS GLY SER TYR ARG ARG ARG HIS PRO PHE SER GLY SEQRES 16 A 378 ASP VAL ASP ALA ILE LEU SER ARG THR LEU ASP ALA PRO SEQRES 17 A 378 PRO LEU SER GLU PRO VAL ALA ALA THR GLY VAL LEU GLY SEQRES 18 A 378 HIS PHE VAL GLU PHE LEU GLU SER LEU LYS TYR LEU GLU SEQRES 19 A 378 ALA THR MET ALA GLN GLY PRO LEU LYS TYR MET GLY MET SEQRES 20 A 378 GLY ARG LEU PRO PRO ARG ILE VAL ARG ASP LYS ALA GLY SEQRES 21 A 378 ARG GLU ASN THR LYS VAL TYR LYS ALA ARG ARG VAL ASP SEQRES 22 A 378 ILE ARG LEU ILE GLU THR LYS SER VAL PRO THR ALA MET SEQRES 23 A 378 LEU THR PHE THR GLY SER LYS ASN PHE ASN VAL ILE MET SEQRES 24 A 378 ARG GLN ALA ALA ILE SER LYS GLY TYR LEU LEU ASN GLU SEQRES 25 A 378 TYR GLY LEU PHE LYS LEU GLY THR PRO GLU GLU ALA ARG SEQRES 26 A 378 ALA LEU TYR GLU ARG ILE GLY ILE ARG GLY LYS ASN ALA SEQRES 27 A 378 GLY GLU GLU LEU GLY VAL PRO LYS ASP GLU LEU GLU ASP SEQRES 28 A 378 LYS ARG VAL GLU VAL ARG SER GLU GLN ASP VAL PHE ASP SEQRES 29 A 378 VAL LEU GLY MET PRO TYR ALA LYS PRO GLU ASN ARG ASP SEQRES 30 A 378 PRO SEQRES 1 C 7 DC DA DG DT DA DC DT SEQRES 1 D 4 DG DC DC DG SEQRES 1 B 11 DC DG DG DC DA DG DT DA DC DT DG HET NA A 401 1 HETNAM NA SODIUM ION FORMUL 5 NA NA 1+ FORMUL 6 HOH *250(H2 O) HELIX 1 AA1 LYS A 92 THR A 100 1 9 HELIX 2 AA2 GLY A 106 GLY A 118 1 13 HELIX 3 AA3 THR A 121 ALA A 129 1 9 HELIX 4 AA4 ASP A 130 ILE A 132 5 3 HELIX 5 AA5 THR A 136 TYR A 145 1 10 HELIX 6 AA6 TYR A 145 ASN A 150 1 6 HELIX 7 AA7 MET A 155 LEU A 173 1 19 HELIX 8 AA8 CYS A 182 ARG A 187 1 6 HELIX 9 AA9 PRO A 211 THR A 215 5 5 HELIX 10 AB1 GLY A 216 LEU A 228 1 13 HELIX 11 AB2 GLU A 276 LYS A 278 5 3 HELIX 12 AB3 SER A 279 GLY A 289 1 11 HELIX 13 AB4 SER A 290 LYS A 304 1 15 HELIX 14 AB5 THR A 318 GLY A 330 1 13 HELIX 15 AB6 LYS A 344 ASP A 349 1 6 HELIX 16 AB7 SER A 356 LEU A 364 1 9 HELIX 17 AB8 LYS A 370 ARG A 374 5 5 SHEET 1 AA1 2 ILE A 153 PRO A 154 0 SHEET 2 AA1 2 PHE A 191 SER A 192 -1 O SER A 192 N ILE A 153 SHEET 1 AA2 5 PHE A 177 ILE A 181 0 SHEET 2 AA2 5 VAL A 195 ARG A 201 -1 O ILE A 198 N LEU A 180 SHEET 3 AA2 5 ARG A 268 ILE A 275 1 O ARG A 273 N LEU A 199 SHEET 4 AA2 5 LYS A 241 GLY A 246 -1 N GLY A 246 O ARG A 268 SHEET 5 AA2 5 LEU A 231 GLN A 237 -1 N ALA A 236 O MET A 243 SHEET 1 AA3 2 TYR A 306 ASN A 309 0 SHEET 2 AA3 2 GLY A 312 LYS A 315 -1 O PHE A 314 N LEU A 307 SHEET 1 AA4 2 GLU A 338 GLU A 339 0 SHEET 2 AA4 2 VAL A 342 PRO A 343 -1 O VAL A 342 N GLU A 339 LINK O THR A 100 NA NA A 401 1555 1555 2.47 LINK O VAL A 102 NA NA A 401 1555 1555 2.92 LINK O PHE A 105 NA NA A 401 1555 1555 2.94 LINK NA NA A 401 O HOH A 646 1555 1555 2.85 LINK NA NA A 401 OP1 DA C 5 1555 1555 2.53 LINK NA NA A 401 O HOH C 117 1555 1555 2.16 CISPEP 1 GLY A 289 SER A 290 0 0.76 SITE 1 AC1 6 THR A 100 VAL A 102 PHE A 105 HOH A 646 SITE 2 AC1 6 DA C 5 HOH C 117 CRYST1 106.497 106.497 159.609 90.00 90.00 120.00 P 65 2 2 12 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 0.009390 0.005421 0.000000 0.00000 SCALE2 0.000000 0.010843 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006265 0.00000