HEADER TRANSFERASE/DNA 12-MAR-14 4P4O TITLE CRYSTAL STRUCTURE OF LEISHMANIA INFANTUM POLYMERASE BETA: TERNARY GAP TITLE 2 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*T)-3'); COMPND 7 CHAIN: E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 11 CHAIN: G; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (5'-D(P*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'); COMPND 15 CHAIN: F; 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-DEC-23 4P4O 1 LINK REVDAT 3 25-DEC-19 4P4O 1 REMARK REVDAT 2 06-SEP-17 4P4O 1 REMARK REVDAT 1 06-AUG-14 4P4O 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: 1.7.1_743) 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) : 47.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24157 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.550 REMARK 3 FREE R VALUE TEST SET COUNT : 1822 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 47.0696 - 4.9536 1.00 2426 198 0.2512 0.2463 REMARK 3 2 4.9536 - 3.9325 1.00 2289 186 0.1752 0.1998 REMARK 3 3 3.9325 - 3.4355 1.00 2243 184 0.1768 0.1975 REMARK 3 4 3.4355 - 3.1215 1.00 2230 182 0.1762 0.2332 REMARK 3 5 3.1215 - 2.8978 1.00 2205 181 0.1876 0.2465 REMARK 3 6 2.8978 - 2.7270 1.00 2197 178 0.1779 0.2317 REMARK 3 7 2.7270 - 2.5904 1.00 2186 180 0.1848 0.2359 REMARK 3 8 2.5904 - 2.4777 1.00 2183 178 0.1796 0.2572 REMARK 3 9 2.4777 - 2.3823 1.00 2191 179 0.1960 0.2470 REMARK 3 10 2.3823 - 2.3001 0.99 2162 176 0.1979 0.2609 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 : 0.35 REMARK 3 B_SOL : 34.76 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.620 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.220 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) : 8.82300 REMARK 3 B22 (A**2) : 8.82300 REMARK 3 B33 (A**2) : 6.94450 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 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 : 0.008 2892 REMARK 3 ANGLE : 1.125 3985 REMARK 3 CHIRALITY : 0.063 439 REMARK 3 PLANARITY : 0.005 449 REMARK 3 DIHEDRAL : 17.550 1136 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 1.2942 35.1511 70.7826 REMARK 3 T TENSOR REMARK 3 T11: 0.1401 T22: 0.1921 REMARK 3 T33: 0.1219 T12: -0.0016 REMARK 3 T13: -0.0364 T23: -0.0569 REMARK 3 L TENSOR REMARK 3 L11: 1.6841 L22: 1.9807 REMARK 3 L33: 0.8179 L12: -0.8817 REMARK 3 L13: 0.4758 L23: -0.5261 REMARK 3 S TENSOR REMARK 3 S11: -0.0254 S12: -0.3533 S13: 0.0354 REMARK 3 S21: 0.2359 S22: 0.0838 S23: 0.0250 REMARK 3 S31: 0.0117 S32: -0.1047 S33: -0.0644 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 4P4O 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_1000200691. 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 : 24191 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 94.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.4000 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL 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: 0.1 M MAGNESIUM FORMATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 101.09400 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 50.54700 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 75.82050 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 25.27350 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 126.36750 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 101.09400 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 50.54700 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 25.27350 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 75.82050 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 126.36750 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: 5030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, G, F 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 537 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 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 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 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 DG G 4 REMARK 465 DC F 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 GLN A 20 CG CD OE1 NE2 REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 LEU A 69 CG CD1 CD2 REMARK 470 LYS A 71 CD CE NZ REMARK 470 THR A 89 OG1 CG2 REMARK 470 LYS A 90 CG CD CE NZ REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 327 CG CD OE1 OE2 REMARK 470 ILE A 331 CG1 CG2 CD1 REMARK 470 DT E 6 O3' 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 674 O HOH A 692 2.01 REMARK 500 NZ LYS A 334 O HOH A 501 2.06 REMARK 500 O HOH A 501 O HOH A 540 2.19 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 DG G 1 P DG G 1 OP3 -0.121 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 DA E 2 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DA E 2 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DT E 4 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 DC F 4 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT F 7 O4' - C1' - N1 ANGL. DEV. = 2.8 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 ALA A 23 30.51 -70.51 REMARK 500 ALA A 28 7.30 -58.92 REMARK 500 LEU A 29 41.55 -84.83 REMARK 500 GLU A 31 69.86 -64.23 REMARK 500 LEU A 70 -46.50 89.94 REMARK 500 LYS A 71 -30.43 -37.45 REMARK 500 LYS A 90 153.84 162.29 REMARK 500 CYS A 182 -129.43 -117.14 REMARK 500 LYS A 334 -73.95 -105.14 REMARK 500 ARG A 374 48.33 -108.89 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 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 100 O REMARK 620 2 VAL A 102 O 95.6 REMARK 620 3 PHE A 105 O 87.8 75.6 REMARK 620 4 HOH A 632 O 94.7 88.4 164.0 REMARK 620 5 DA E 5 OP1 176.3 80.7 91.3 85.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 194 OD1 REMARK 620 2 ASP A 196 OD2 81.1 REMARK 620 3 D3T A 401 O1A 100.1 95.5 REMARK 620 4 D3T A 401 O1B 173.5 95.5 85.7 REMARK 620 5 D3T A 401 O1G 95.8 171.1 93.3 86.7 REMARK 620 6 HOH A 578 O 87.0 84.4 172.8 87.1 87.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA F 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 508 O REMARK 620 2 HOH A 509 O 97.1 REMARK 620 3 DT F 10 OP1 77.6 98.0 REMARK 620 4 HOH F 205 O 93.3 97.4 163.0 REMARK 620 5 HOH F 209 O 155.1 103.2 85.5 98.1 REMARK 620 6 HOH F 213 O 78.7 175.7 82.2 81.9 81.1 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 D3T A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA F 101 DBREF 4P4O A 1 376 UNP Q9U6N3 Q9U6N3_LEIIN 1 376 DBREF 4P4O E 1 6 PDB 4P4O 4P4O 1 6 DBREF 4P4O G 1 4 PDB 4P4O 4P4O 1 4 DBREF 4P4O F 1 11 PDB 4P4O 4P4O 1 11 SEQADV 4P4O GLY A -1 UNP Q9U6N3 EXPRESSION TAG SEQADV 4P4O 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 E 6 DC DA DG DT DA DT SEQRES 1 G 4 DG DC DC DG SEQRES 1 F 11 DC DG DG DC DA DA DT DA DC DT DG HET D3T A 401 28 HET NA A 402 1 HET MG A 403 1 HET NA F 101 1 HETNAM D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION FORMUL 5 D3T C10 H17 N2 O13 P3 FORMUL 6 NA 2(NA 1+) FORMUL 7 MG MG 2+ FORMUL 9 HOH *237(H2 O) HELIX 1 AA1 ALA A 23 ALA A 28 1 6 HELIX 2 AA2 GLU A 31 HIS A 39 1 9 HELIX 3 AA3 LYS A 90 THR A 100 1 11 HELIX 4 AA4 GLY A 106 GLY A 118 1 13 HELIX 5 AA5 THR A 121 ALA A 129 1 9 HELIX 6 AA6 ASP A 130 ILE A 132 5 3 HELIX 7 AA7 THR A 136 TYR A 145 1 10 HELIX 8 AA8 TYR A 145 ASN A 150 1 6 HELIX 9 AA9 MET A 155 GLY A 174 1 20 HELIX 10 AB1 CYS A 182 ARG A 187 1 6 HELIX 11 AB2 PRO A 211 THR A 215 5 5 HELIX 12 AB3 GLY A 216 LEU A 228 1 13 HELIX 13 AB4 GLU A 276 LYS A 278 5 3 HELIX 14 AB5 SER A 279 GLY A 289 1 11 HELIX 15 AB6 SER A 290 LYS A 304 1 15 HELIX 16 AB7 THR A 318 ILE A 329 1 12 HELIX 17 AB8 LYS A 344 ASP A 349 1 6 HELIX 18 AB9 SER A 356 LEU A 364 1 9 HELIX 19 AC1 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 SER A 200 N SER A 178 SHEET 3 AA2 5 ARG A 268 ILE A 275 1 O ASP A 271 N VAL A 195 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 3 TYR A 306 ASN A 309 0 SHEET 2 AA3 3 GLY A 312 LYS A 315 -1 O PHE A 314 N LEU A 307 SHEET 3 AA3 3 ARG A 351 VAL A 352 -1 O VAL A 352 N LEU A 313 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 402 1555 1555 2.65 LINK O VAL A 102 NA NA A 402 1555 1555 2.97 LINK O PHE A 105 NA NA A 402 1555 1555 2.81 LINK OD1 ASP A 194 MG MG A 403 1555 1555 2.27 LINK OD2 ASP A 196 MG MG A 403 1555 1555 2.16 LINK O1A D3T A 401 MG MG A 403 1555 1555 2.09 LINK O1B D3T A 401 MG MG A 403 1555 1555 2.23 LINK O1G D3T A 401 MG MG A 403 1555 1555 2.09 LINK NA NA A 402 O HOH A 632 1555 1555 3.18 LINK NA NA A 402 OP1 DA E 5 1555 1555 2.72 LINK MG MG A 403 O HOH A 578 1555 1555 2.42 LINK O HOH A 508 NA NA F 101 1555 1555 2.26 LINK O HOH A 509 NA NA F 101 6554 1555 2.41 LINK OP1 DT F 10 NA NA F 101 1555 1555 2.15 LINK NA NA F 101 O HOH F 205 1555 1555 2.00 LINK NA NA F 101 O HOH F 209 1555 1555 2.23 LINK NA NA F 101 O HOH F 213 1555 1555 2.71 CISPEP 1 LEU A 69 LEU A 70 0 13.56 CISPEP 2 GLY A 289 SER A 290 0 1.90 SITE 1 AC1 19 GLY A 183 SER A 184 ARG A 187 SER A 192 SITE 2 AC1 19 GLY A 193 ASP A 194 ASP A 196 THR A 286 SITE 3 AC1 19 PHE A 287 LYS A 291 ASN A 294 MG A 403 SITE 4 AC1 19 HOH A 586 HOH A 615 HOH A 624 HOH A 702 SITE 5 AC1 19 HOH A 703 DT E 6 DA F 5 SITE 1 AC2 4 THR A 100 VAL A 102 PHE A 105 DA E 5 SITE 1 AC3 4 ASP A 194 ASP A 196 D3T A 401 HOH A 578 SITE 1 AC4 6 HOH A 508 HOH A 509 DT F 10 HOH F 205 SITE 2 AC4 6 HOH F 209 HOH F 213 CRYST1 108.680 108.680 151.641 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 0.009201 0.005312 0.000000 0.00000 SCALE2 0.000000 0.010625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006595 0.00000