HEADER REPLICATION/DNA 15-APR-19 6JUN TITLE MSDPO4-DNA COMPLEX 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: F, A; COMPND 4 SYNONYM: POL IV; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3'); COMPND 10 CHAIN: H, G, C, B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA PRIMER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS STR. MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 VARIANT: ATCC 700084 / MC(2)155; SOURCE 5 GENE: MSMEG_1014, MSMEG_2294; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS; SOURCE 11 ORGANISM_TAXID: 1772 KEYWDS DNA POLYMERASE, REPLICATION, REPLICATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.T.NAIR,M.K.JOHNSON REVDAT 2 22-NOV-23 6JUN 1 REMARK LINK REVDAT 1 19-FEB-20 6JUN 0 JRNL AUTH M.K.JOHNSON,J.KOTTUR,D.T.NAIR JRNL TITL A POLAR FILTER IN DNA POLYMERASES PREVENTS RIBONUCLEOTIDE JRNL TITL 2 INCORPORATION. JRNL REF NUCLEIC ACIDS RES. V. 47 10693 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 31544946 JRNL DOI 10.1093/NAR/GKZ792 REMARK 2 REMARK 2 RESOLUTION. 2.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 32341 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1618 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 75.8773 - 5.7457 1.00 2768 148 0.1980 0.1863 REMARK 3 2 5.7457 - 4.5607 1.00 2621 140 0.1909 0.2400 REMARK 3 3 4.5607 - 3.9843 1.00 2631 109 0.1720 0.2030 REMARK 3 4 3.9843 - 3.6200 1.00 2547 137 0.2044 0.2217 REMARK 3 5 3.6200 - 3.3605 1.00 2565 131 0.2310 0.2780 REMARK 3 6 3.3605 - 3.1624 1.00 2526 165 0.2516 0.3272 REMARK 3 7 3.1624 - 3.0040 1.00 2518 148 0.2605 0.3279 REMARK 3 8 3.0040 - 2.8732 1.00 2549 130 0.2695 0.3356 REMARK 3 9 2.8732 - 2.7626 0.99 2524 143 0.3106 0.3153 REMARK 3 10 2.7626 - 2.6673 0.99 2494 132 0.3095 0.4069 REMARK 3 11 2.6673 - 2.5839 0.99 2488 123 0.3002 0.3561 REMARK 3 12 2.5839 - 2.5100 0.98 2492 112 0.3183 0.3787 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.710 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 : 0.004 6334 REMARK 3 ANGLE : 0.665 8798 REMARK 3 CHIRALITY : 0.043 1020 REMARK 3 PLANARITY : 0.005 1000 REMARK 3 DIHEDRAL : 12.974 3652 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 6JUN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-APR-19. REMARK 100 THE DEPOSITION ID IS D_1300011773. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1272 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32439 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.510 REMARK 200 RESOLUTION RANGE LOW (A) : 81.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 6JUL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2KMME, BIS TRIS PROPANE PH 6.0, REMARK 280 NACL, VAPOR DIFFUSION, HANGING 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 26.96000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 105.10500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.66000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 105.10500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.66000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, H, G 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, 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 PRO F 348 REMARK 465 ARG F 349 REMARK 465 PRO F 350 REMARK 465 ALA F 351 REMARK 465 VAL F 352 REMARK 465 THR F 353 REMARK 465 ALA F 354 REMARK 465 GLY F 355 REMARK 465 THR F 356 REMARK 465 DT H 856 REMARK 465 DC H 857 REMARK 465 DT H 858 REMARK 465 DG H 859 REMARK 465 DG H 860 REMARK 465 DG H 861 REMARK 465 DG H 862 REMARK 465 DT H 863 REMARK 465 DC H 864 REMARK 465 DC H 865 REMARK 465 DT G 837 REMARK 465 DG G 849 REMARK 465 DG G 850 REMARK 465 DA G 851 REMARK 465 DC G 852 REMARK 465 DC G 853 REMARK 465 DC G 854 REMARK 465 PRO A 348 REMARK 465 ARG A 349 REMARK 465 PRO A 350 REMARK 465 ALA A 351 REMARK 465 VAL A 352 REMARK 465 THR A 353 REMARK 465 ALA A 354 REMARK 465 GLY A 355 REMARK 465 THR A 356 REMARK 465 DT C 856 REMARK 465 DC C 857 REMARK 465 DT C 858 REMARK 465 DG C 859 REMARK 465 DG C 860 REMARK 465 DG C 861 REMARK 465 DG C 862 REMARK 465 DT C 863 REMARK 465 DC C 864 REMARK 465 DC C 865 REMARK 465 DT B 837 REMARK 465 DG B 849 REMARK 465 DG B 850 REMARK 465 DA B 851 REMARK 465 DC B 852 REMARK 465 DC B 853 REMARK 465 DC B 854 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS F 189 CG CD CE 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 OD2 ASP F 9 OD2 ASP F 107 2.02 REMARK 500 NH2 ARG F 53 O3B 0KX F 401 2.10 REMARK 500 O ARG A 300 O HOH A 1001 2.14 REMARK 500 OG1 THR A 2 O HOH A 1002 2.15 REMARK 500 O VAL A 186 O HOH A 1003 2.18 REMARK 500 O VAL A 132 OG1 THR A 136 2.19 REMARK 500 N2 DG C 868 O2 DC B 846 2.19 REMARK 500 O VAL F 186 O HOH F 501 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 THR F 47 CB THR F 47 OG1 -0.135 REMARK 500 THR F 47 C THR F 47 O -0.175 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 H 869 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC G 838 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 ASP A 117 CB - CG - OD2 ANGL. DEV. = -9.2 DEGREES REMARK 500 DC B 838 O4' - C1' - N1 ANGL. DEV. = 1.8 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 GLN F 12 62.44 31.36 REMARK 500 SER F 145 -159.90 -166.18 REMARK 500 ASP F 181 2.23 -65.74 REMARK 500 SER F 211 34.26 -77.42 REMARK 500 ALA F 216 -25.44 -171.65 REMARK 500 THR F 258 -40.48 -141.06 REMARK 500 THR F 294 160.15 62.85 REMARK 500 ARG F 300 -46.23 -133.20 REMARK 500 THR F 301 128.36 71.01 REMARK 500 ASP F 345 -159.55 59.20 REMARK 500 ASP F 346 -70.39 175.70 REMARK 500 GLN A 12 62.35 32.30 REMARK 500 ARG A 22 79.15 -118.78 REMARK 500 ASP A 72 32.35 -96.74 REMARK 500 THR A 74 114.09 61.35 REMARK 500 TRP A 106 -60.72 75.42 REMARK 500 ASP A 117 5.02 -45.64 REMARK 500 SER A 119 -166.36 -109.87 REMARK 500 SER A 145 -161.38 -165.34 REMARK 500 ALA A 216 -42.96 -166.20 REMARK 500 THR A 258 -9.86 58.77 REMARK 500 ARG A 331 161.60 66.23 REMARK 500 VAL A 333 120.40 68.35 REMARK 500 ASP A 345 139.45 -170.53 REMARK 500 ASP A 346 75.14 -167.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH F 518 DISTANCE = 5.88 ANGSTROMS 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 MG F 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 9 OD2 REMARK 620 2 ASP F 107 OD2 57.4 REMARK 620 3 GLU F 108 OE2 83.8 125.4 REMARK 620 4 0KX F 401 O1A 90.4 77.2 145.6 REMARK 620 5 DC H 873 O3' 168.6 117.3 93.0 98.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 9 OD1 REMARK 620 2 LEU F 10 O 77.9 REMARK 620 3 ASP F 107 OD1 102.1 79.9 REMARK 620 4 ASP F 107 OD2 70.7 113.7 53.5 REMARK 620 5 0KX F 401 O1G 92.1 91.1 161.1 144.8 REMARK 620 6 0KX F 401 O2B 155.5 92.0 97.9 133.5 65.6 REMARK 620 7 0KX F 401 O1A 111.9 162.3 110.9 83.8 74.3 73.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD1 REMARK 620 2 LEU A 10 O 77.4 REMARK 620 3 ASP A 107 OD1 77.1 73.1 REMARK 620 4 ASP A 107 OD2 124.5 97.8 49.6 REMARK 620 5 0KX A 902 O1G 86.2 95.7 161.5 148.6 REMARK 620 6 0KX A 902 O2B 155.5 95.8 123.9 79.6 70.9 REMARK 620 7 0KX A 902 O1A 112.2 167.2 116.6 84.0 76.9 72.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD2 REMARK 620 2 GLU A 108 OE2 98.8 REMARK 620 3 0KX A 902 O1A 84.2 147.8 REMARK 620 4 HOH A1007 O 89.7 72.0 76.0 REMARK 620 5 DC C 873 O3' 178.8 80.1 96.9 90.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0KX F 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG F 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG F 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0KX A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 903 DBREF 6JUN F 1 356 UNP A0QR77 A0QR77_MYCS2 1 356 DBREF 6JUN H 856 873 PDB 6JUN 6JUN 856 873 DBREF 6JUN G 837 854 PDB 6JUN 6JUN 837 854 DBREF 6JUN A 1 356 UNP A0QR77 A0QR77_MYCS2 1 356 DBREF 6JUN C 856 873 PDB 6JUN 6JUN 856 873 DBREF 6JUN B 837 854 PDB 6JUN 6JUN 837 854 SEQADV 6JUN TYR F 14 UNP A0QR77 LEU 14 ENGINEERED MUTATION SEQADV 6JUN THR F 47 UNP A0QR77 CYS 47 ENGINEERED MUTATION SEQADV 6JUN TYR A 14 UNP A0QR77 LEU 14 ENGINEERED MUTATION SEQADV 6JUN THR A 47 UNP A0QR77 CYS 47 ENGINEERED MUTATION SEQRES 1 F 356 MET THR LYS TRP VAL LEU HIS VAL ASP LEU ASP GLN PHE SEQRES 2 F 356 TYR ALA SER VAL GLU LEU ARG ARG ARG PRO ASP LEU ARG SEQRES 3 F 356 GLY GLN PRO VAL ILE VAL GLY GLY SER GLY ASP PRO SER SEQRES 4 F 356 GLU PRO ARG LYS VAL VAL THR THR ALA SER TYR GLU ALA SEQRES 5 F 356 ARG GLU PHE GLY VAL HIS ALA GLY MET PRO LEU ARG ALA SEQRES 6 F 356 ALA ALA ARG ARG CYS PRO ASP ALA THR PHE LEU PRO SER SEQRES 7 F 356 ASP PRO ALA ALA TYR ASP GLU ALA SER GLU GLN VAL MET SEQRES 8 F 356 GLY LEU LEU ARG ASP LEU GLY HIS PRO LEU GLU VAL TRP SEQRES 9 F 356 GLY TRP ASP GLU ALA TYR LEU GLY ALA ASP LEU PRO ASP SEQRES 10 F 356 GLU SER ASP PRO VAL GLU VAL ALA GLU ARG ILE ARG THR SEQRES 11 F 356 VAL VAL ALA ALA GLU THR GLY LEU SER CYS SER VAL GLY SEQRES 12 F 356 ILE SER ASP ASN LYS GLN ARG ALA LYS VAL ALA THR GLY SEQRES 13 F 356 PHE ALA LYS PRO ALA GLY ILE TYR VAL LEU THR GLU ALA SEQRES 14 F 356 ASN TRP MET THR VAL MET GLY ASP ARG PRO PRO ASP ALA SEQRES 15 F 356 LEU TRP GLY VAL GLY PRO LYS THR THR LYS LYS LEU ALA SEQRES 16 F 356 ALA MET GLY ILE THR THR VAL ALA ASP LEU ALA VAL THR SEQRES 17 F 356 ASP PRO SER VAL LEU THR THR ALA PHE GLY PRO SER THR SEQRES 18 F 356 GLY LEU TRP LEU LEU LEU LEU ALA LYS GLY GLY GLY ASP SEQRES 19 F 356 THR GLU VAL SER SER GLU PRO TRP VAL PRO ARG SER ARG SEQRES 20 F 356 SER HIS VAL VAL THR PHE PRO GLN ASP LEU THR GLU ARG SEQRES 21 F 356 ARG GLU MET ASP SER ALA VAL ARG ASP LEU ALA LEU GLN SEQRES 22 F 356 THR LEU ALA GLU ILE VAL GLU GLN GLY ARG ILE VAL THR SEQRES 23 F 356 ARG VAL ALA VAL THR VAL ARG THR SER THR PHE TYR THR SEQRES 24 F 356 ARG THR LYS ILE ARG LYS LEU PRO ALA PRO SER THR ASP SEQRES 25 F 356 ALA GLY GLN ILE VAL ASP THR ALA LEU ALA VAL LEU ASP SEQRES 26 F 356 GLN PHE GLU LEU ASP ARG PRO VAL ARG LEU LEU GLY VAL SEQRES 27 F 356 ARG LEU GLU LEU ALA MET ASP ASP VAL PRO ARG PRO ALA SEQRES 28 F 356 VAL THR ALA GLY THR SEQRES 1 H 18 DT DC DT DG DG DG DG DT DC DC DT DA DG SEQRES 2 H 18 DG DA DC DC DC SEQRES 1 G 18 DT DC DT DG DG DG DG DT DC DC DT DA DG SEQRES 2 G 18 DG DA DC DC DC SEQRES 1 A 356 MET THR LYS TRP VAL LEU HIS VAL ASP LEU ASP GLN PHE SEQRES 2 A 356 TYR ALA SER VAL GLU LEU ARG ARG ARG PRO ASP LEU ARG SEQRES 3 A 356 GLY GLN PRO VAL ILE VAL GLY GLY SER GLY ASP PRO SER SEQRES 4 A 356 GLU PRO ARG LYS VAL VAL THR THR ALA SER TYR GLU ALA SEQRES 5 A 356 ARG GLU PHE GLY VAL HIS ALA GLY MET PRO LEU ARG ALA SEQRES 6 A 356 ALA ALA ARG ARG CYS PRO ASP ALA THR PHE LEU PRO SER SEQRES 7 A 356 ASP PRO ALA ALA TYR ASP GLU ALA SER GLU GLN VAL MET SEQRES 8 A 356 GLY LEU LEU ARG ASP LEU GLY HIS PRO LEU GLU VAL TRP SEQRES 9 A 356 GLY TRP ASP GLU ALA TYR LEU GLY ALA ASP LEU PRO ASP SEQRES 10 A 356 GLU SER ASP PRO VAL GLU VAL ALA GLU ARG ILE ARG THR SEQRES 11 A 356 VAL VAL ALA ALA GLU THR GLY LEU SER CYS SER VAL GLY SEQRES 12 A 356 ILE SER ASP ASN LYS GLN ARG ALA LYS VAL ALA THR GLY SEQRES 13 A 356 PHE ALA LYS PRO ALA GLY ILE TYR VAL LEU THR GLU ALA SEQRES 14 A 356 ASN TRP MET THR VAL MET GLY ASP ARG PRO PRO ASP ALA SEQRES 15 A 356 LEU TRP GLY VAL GLY PRO LYS THR THR LYS LYS LEU ALA SEQRES 16 A 356 ALA MET GLY ILE THR THR VAL ALA ASP LEU ALA VAL THR SEQRES 17 A 356 ASP PRO SER VAL LEU THR THR ALA PHE GLY PRO SER THR SEQRES 18 A 356 GLY LEU TRP LEU LEU LEU LEU ALA LYS GLY GLY GLY ASP SEQRES 19 A 356 THR GLU VAL SER SER GLU PRO TRP VAL PRO ARG SER ARG SEQRES 20 A 356 SER HIS VAL VAL THR PHE PRO GLN ASP LEU THR GLU ARG SEQRES 21 A 356 ARG GLU MET ASP SER ALA VAL ARG ASP LEU ALA LEU GLN SEQRES 22 A 356 THR LEU ALA GLU ILE VAL GLU GLN GLY ARG ILE VAL THR SEQRES 23 A 356 ARG VAL ALA VAL THR VAL ARG THR SER THR PHE TYR THR SEQRES 24 A 356 ARG THR LYS ILE ARG LYS LEU PRO ALA PRO SER THR ASP SEQRES 25 A 356 ALA GLY GLN ILE VAL ASP THR ALA LEU ALA VAL LEU ASP SEQRES 26 A 356 GLN PHE GLU LEU ASP ARG PRO VAL ARG LEU LEU GLY VAL SEQRES 27 A 356 ARG LEU GLU LEU ALA MET ASP ASP VAL PRO ARG PRO ALA SEQRES 28 A 356 VAL THR ALA GLY THR SEQRES 1 C 18 DT DC DT DG DG DG DG DT DC DC DT DA DG SEQRES 2 C 18 DG DA DC DC DC SEQRES 1 B 18 DT DC DT DG DG DG DG DT DC DC DT DA DG SEQRES 2 B 18 DG DA DC DC DC HET 0KX F 401 28 HET MG F 402 1 HET MG F 403 1 HET MG A 901 1 HET 0KX A 902 28 HET MG A 903 1 HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE HETNAM MG MAGNESIUM ION FORMUL 7 0KX 2(C9 H17 N4 O12 P3) FORMUL 8 MG 4(MG 2+) FORMUL 13 HOH *57(H2 O) HELIX 1 AA1 GLN F 12 ARG F 22 1 11 HELIX 2 AA2 PRO F 23 ARG F 26 5 4 HELIX 3 AA3 GLY F 34 ASP F 37 5 4 HELIX 4 AA4 SER F 49 GLU F 54 1 6 HELIX 5 AA5 PRO F 62 CYS F 70 1 9 HELIX 6 AA6 ASP F 79 ARG F 95 1 17 HELIX 7 AA7 ASP F 96 GLY F 98 5 3 HELIX 8 AA8 ASP F 120 GLY F 137 1 18 HELIX 9 AA9 ASN F 147 LYS F 159 1 13 HELIX 10 AB1 ASN F 170 GLY F 176 1 7 HELIX 11 AB2 PRO F 179 LEU F 183 5 5 HELIX 12 AB3 GLY F 187 ALA F 196 1 10 HELIX 13 AB4 THR F 201 VAL F 207 1 7 HELIX 14 AB5 ASP F 209 GLY F 218 1 10 HELIX 15 AB6 GLY F 218 LYS F 230 1 13 HELIX 16 AB7 GLU F 259 GLN F 281 1 23 HELIX 17 AB8 ASP F 312 GLN F 326 1 15 HELIX 18 AB9 GLN A 12 ARG A 22 1 11 HELIX 19 AC1 PRO A 23 ARG A 26 5 4 HELIX 20 AC2 SER A 49 GLU A 54 1 6 HELIX 21 AC3 PRO A 62 CYS A 70 1 9 HELIX 22 AC4 ASP A 79 ARG A 95 1 17 HELIX 23 AC5 ASP A 96 GLY A 98 5 3 HELIX 24 AC6 ASP A 120 GLY A 137 1 18 HELIX 25 AC7 ASN A 147 LYS A 159 1 13 HELIX 26 AC8 ASN A 170 GLY A 176 1 7 HELIX 27 AC9 PRO A 179 LEU A 183 5 5 HELIX 28 AD1 GLY A 187 ALA A 196 1 10 HELIX 29 AD2 THR A 201 VAL A 207 1 7 HELIX 30 AD3 ASP A 209 GLY A 218 1 10 HELIX 31 AD4 SER A 220 LYS A 230 1 11 HELIX 32 AD5 GLU A 259 GLN A 281 1 23 HELIX 33 AD6 ASP A 312 ASP A 325 1 14 SHEET 1 AA1 5 LEU F 101 TRP F 104 0 SHEET 2 AA1 5 GLU F 108 LEU F 115 -1 O TYR F 110 N GLU F 102 SHEET 3 AA1 5 THR F 2 LEU F 10 -1 N LEU F 6 O LEU F 111 SHEET 4 AA1 5 CYS F 140 SER F 145 -1 O SER F 145 N VAL F 5 SHEET 5 AA1 5 ILE F 163 VAL F 165 1 O TYR F 164 N ILE F 144 SHEET 1 AA2 3 THR F 47 ALA F 48 0 SHEET 2 AA2 3 VAL F 30 VAL F 32 -1 N VAL F 32 O THR F 47 SHEET 3 AA2 3 THR F 74 LEU F 76 1 O LEU F 76 N ILE F 31 SHEET 1 AA3 4 SER F 246 LEU F 257 0 SHEET 2 AA3 4 VAL F 333 LEU F 342 -1 O LEU F 340 N ARG F 247 SHEET 3 AA3 4 VAL F 285 VAL F 292 -1 N THR F 286 O GLU F 341 SHEET 4 AA3 4 LYS F 302 SER F 310 -1 O ARG F 304 N VAL F 288 SHEET 1 AA4 5 LEU A 101 TRP A 104 0 SHEET 2 AA4 5 GLU A 108 LEU A 115 -1 O TYR A 110 N GLU A 102 SHEET 3 AA4 5 THR A 2 LEU A 10 -1 N LEU A 6 O LEU A 111 SHEET 4 AA4 5 CYS A 140 SER A 145 -1 O SER A 145 N VAL A 5 SHEET 5 AA4 5 ILE A 163 VAL A 165 1 O TYR A 164 N ILE A 144 SHEET 1 AA5 3 THR A 47 ALA A 48 0 SHEET 2 AA5 3 ILE A 31 VAL A 32 -1 N VAL A 32 O THR A 47 SHEET 3 AA5 3 PHE A 75 LEU A 76 1 O LEU A 76 N ILE A 31 SHEET 1 AA6 4 SER A 246 THR A 252 0 SHEET 2 AA6 4 LEU A 335 LEU A 342 -1 O LEU A 340 N ARG A 247 SHEET 3 AA6 4 VAL A 285 ARG A 293 -1 N THR A 286 O GLU A 341 SHEET 4 AA6 4 THR A 299 SER A 310 -1 O ARG A 304 N VAL A 288 LINK OD2 ASP F 9 MG MG F 402 1555 1555 2.14 LINK OD1 ASP F 9 MG MG F 403 1555 1555 2.06 LINK O LEU F 10 MG MG F 403 1555 1555 2.23 LINK OD2 ASP F 107 MG MG F 402 1555 1555 2.06 LINK OD1 ASP F 107 MG MG F 403 1555 1555 2.33 LINK OD2 ASP F 107 MG MG F 403 1555 1555 2.53 LINK OE2 GLU F 108 MG MG F 402 1555 1555 1.86 LINK O1A 0KX F 401 MG MG F 402 1555 1555 2.77 LINK O1G 0KX F 401 MG MG F 403 1555 1555 2.66 LINK O2B 0KX F 401 MG MG F 403 1555 1555 2.35 LINK O1A 0KX F 401 MG MG F 403 1555 1555 2.02 LINK MG MG F 402 O3' DC H 873 1555 1555 1.90 LINK OD1 ASP A 9 MG MG A 901 1555 1555 2.01 LINK OD2 ASP A 9 MG MG A 903 1555 1555 2.10 LINK O LEU A 10 MG MG A 901 1555 1555 2.42 LINK OD1 ASP A 107 MG MG A 901 1555 1555 2.84 LINK OD2 ASP A 107 MG MG A 901 1555 1555 1.87 LINK OE2 GLU A 108 MG MG A 903 1555 1555 1.79 LINK MG MG A 901 O1G 0KX A 902 1555 1555 2.41 LINK MG MG A 901 O2B 0KX A 902 1555 1555 2.34 LINK MG MG A 901 O1A 0KX A 902 1555 1555 2.00 LINK O1A 0KX A 902 MG MG A 903 1555 1555 2.80 LINK MG MG A 903 O HOH A1007 1555 1555 2.24 LINK MG MG A 903 O3' DC C 873 1555 1555 1.78 CISPEP 1 LYS F 159 PRO F 160 0 -1.59 CISPEP 2 LYS A 159 PRO A 160 0 -6.49 SITE 1 AC1 17 ASP F 9 LEU F 10 ASP F 11 GLN F 12 SITE 2 AC1 17 PHE F 13 TYR F 14 THR F 46 THR F 47 SITE 3 AC1 17 TYR F 50 ARG F 53 ASP F 107 LYS F 159 SITE 4 AC1 17 MG F 402 MG F 403 DG G 840 DG G 841 SITE 5 AC1 17 DC H 873 SITE 1 AC2 6 ASP F 9 ASP F 107 GLU F 108 0KX F 401 SITE 2 AC2 6 MG F 403 DC H 873 SITE 1 AC3 5 ASP F 9 LEU F 10 ASP F 107 0KX F 401 SITE 2 AC3 5 MG F 402 SITE 1 AC4 5 ASP A 9 LEU A 10 ASP A 107 0KX A 902 SITE 2 AC4 5 MG A 903 SITE 1 AC5 21 ASP A 9 LEU A 10 GLN A 12 PHE A 13 SITE 2 AC5 21 TYR A 14 THR A 46 THR A 47 TYR A 50 SITE 3 AC5 21 ARG A 53 ASP A 107 LYS A 159 MG A 901 SITE 4 AC5 21 MG A 903 HOH A1005 HOH A1007 HOH A1010 SITE 5 AC5 21 HOH A1023 HOH A1026 DG B 840 DG B 841 SITE 6 AC5 21 DC C 873 SITE 1 AC6 7 ASP A 9 ASP A 107 GLU A 108 MG A 901 SITE 2 AC6 7 0KX A 902 HOH A1007 DC C 873 CRYST1 53.920 81.320 210.210 90.00 90.00 90.00 P 21 21 21 16 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 0.018546 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012297 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004757 0.00000