PDB Short entry for 3FMT HEADER REPLICATION INHIBITOR/DNA 22-DEC-08 3FMT TITLE CRYSTAL STRUCTURE OF SEQA BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN SEQA; COMPND 3 CHAIN: A, B, E, F; COMPND 4 FRAGMENT: SEQADELTA(41-59); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*AP*GP*TP*CP*GP*(6MA) COMPND 9 P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3'; COMPND 10 CHAIN: C, G; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP COMPND 14 *CP*GP*AP*C)-3'; COMPND 15 CHAIN: D, H; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: B0687, JW0674, SEQA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: METHYLATED OLIGONUCLEOTIDE; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: UNMETHYLATED OLIGONUCLEOTIDE KEYWDS PROTEIN-DNA COMPLEX, HEMIMETHYLATED GATC, DNA REPLICATION, KEYWDS 2 SEQUESTRATION, DNA REPLICATION INHIBITOR, DNA-BINDING, REPLICATION KEYWDS 3 INHIBITOR-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.S.CHUNG,T.BRENDLER,S.AUSTIN,A.GUARNE REVDAT 5 06-SEP-23 3FMT 1 REMARK REVDAT 4 20-OCT-21 3FMT 1 REMARK SEQADV LINK REVDAT 3 26-JUL-17 3FMT 1 SOURCE REMARK REVDAT 2 23-JUN-09 3FMT 1 JRNL REVDAT 1 28-APR-09 3FMT 0 JRNL AUTH Y.S.CHUNG,T.BRENDLER,S.AUSTIN,A.GUARNE JRNL TITL STRUCTURAL INSIGHTS INTO THE COOPERATIVE BINDING OF SEQA TO JRNL TITL 2 A TANDEM GATC REPEAT JRNL REF NUCLEIC ACIDS RES. V. 37 3143 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19304745 JRNL DOI 10.1093/NAR/GKP151 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.S.CHUNG,A.GUARNE REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF SEQA BOUND TO A PAIR OF HEMIMETHYLATED GATC SITES REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 64 567 2008 REMARK 1 REFN ESSN 1744-3091 REMARK 2 REMARK 2 RESOLUTION. 2.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 30285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1533 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 35.1743 - 6.6212 0.99 2712 142 0.1674 0.1795 REMARK 3 2 6.6212 - 5.2611 1.00 2677 158 0.2097 0.2356 REMARK 3 3 5.2611 - 4.5977 1.00 2761 136 0.1871 0.2318 REMARK 3 4 4.5977 - 4.1781 1.00 2706 128 0.1857 0.1874 REMARK 3 5 4.1781 - 3.8790 1.00 2714 160 0.2021 0.2296 REMARK 3 6 3.8790 - 3.6506 1.00 2670 153 0.2268 0.2373 REMARK 3 7 3.6506 - 3.4679 1.00 2750 121 0.2328 0.2839 REMARK 3 8 3.4679 - 3.3171 1.00 2708 137 0.2508 0.3171 REMARK 3 9 3.3171 - 3.1895 0.99 2725 156 0.2572 0.3081 REMARK 3 10 3.1895 - 3.0795 0.92 2482 138 0.3088 0.2639 REMARK 3 11 3.0795 - 2.9832 0.69 1847 104 0.3162 0.3745 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 : 0.30 REMARK 3 B_SOL : 27.56 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.830 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 76.39 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 7226 REMARK 3 ANGLE : 0.877 10104 REMARK 3 CHIRALITY : 0.049 1140 REMARK 3 PLANARITY : 0.003 976 REMARK 3 DIHEDRAL : 14.761 3088 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 : 4 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B RESID 1:162 REMARK 3 SELECTION : CHAIN F RESID 1:162 REMARK 3 ATOM PAIRS NUMBER : 1274 REMARK 3 RMSD : 0.035 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A RESID 1:162 REMARK 3 SELECTION : CHAIN E RESID 1:162 REMARK 3 ATOM PAIRS NUMBER : 1297 REMARK 3 RMSD : 0.003 REMARK 3 NCS GROUP : 3 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN D RESID 1:22 REMARK 3 SELECTION : CHAIN H RESID 1:22 REMARK 3 ATOM PAIRS NUMBER : 425 REMARK 3 RMSD : 0.003 REMARK 3 NCS GROUP : 4 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN C RESID 1:22 REMARK 3 SELECTION : CHAIN G RESID 1:22 REMARK 3 ATOM PAIRS NUMBER : 454 REMARK 3 RMSD : 0.003 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3FMT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30745 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.980 REMARK 200 RESOLUTION RANGE LOW (A) : 35.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.06700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.52700 REMARK 200 R SYM FOR SHELL (I) : 0.45700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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 1LRR AND 1XRX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% MPD, 0.4 M AMMONIUM ACETATE, 0.1 M REMARK 280 SODIUM CITRATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 60.91950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.17189 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 93.04433 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 60.91950 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 35.17189 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 93.04433 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 60.91950 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 35.17189 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 93.04433 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 70.34378 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 186.08867 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 70.34378 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 186.08867 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 70.34378 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 186.08867 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 350 REMARK 350 BIOMOLECULE: 2 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: 10610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H 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 SER B 36 REMARK 465 ALA B 37 REMARK 465 ALA B 38 REMARK 465 SER B 39 REMARK 465 GLN B 40 REMARK 465 DC D 2 REMARK 465 SER F 36 REMARK 465 ALA F 37 REMARK 465 ALA F 38 REMARK 465 SER F 39 REMARK 465 GLN F 40 REMARK 465 DC H 2 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 ARG B 116 CD - NE - CZ ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG B 116 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 116 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG C 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 9 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG C 13 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 DA D 8 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC D 15 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG D 16 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG F 116 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG F 116 NE - CZ - NH1 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG F 116 NE - CZ - NH2 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG G 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC G 9 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG G 13 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA H 8 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC H 15 O4' - C1' - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG H 16 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 62 12.95 -145.32 REMARK 500 ASP A 102 99.02 -169.30 REMARK 500 ASN A 150 72.94 -66.27 REMARK 500 LYS B 19 -66.90 -92.80 REMARK 500 ASN B 150 80.02 -68.45 REMARK 500 VAL E 62 13.01 -145.29 REMARK 500 ASP E 102 99.13 -169.23 REMARK 500 ASN E 150 72.99 -66.26 REMARK 500 LYS F 19 -66.84 -92.91 REMARK 500 ASN F 150 79.84 -68.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD E 182 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 182 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 183 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD E 183 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LRR RELATED DB: PDB REMARK 900 STRUCTURE OF C-TERMINAL DOMAIN OF SEQA BOUND TO A SINGLE REMARK 900 HEMIMETHYLATED GATC REMARK 900 RELATED ID: 1XRX RELATED DB: PDB REMARK 900 STRUCTURE OF OLIGOMERIZATION DOMAIN OF SEQA REMARK 900 RELATED ID: 1J3E RELATED DB: PDB REMARK 900 STRUCTURE OF C-TERMINAL DOMAIN OF SEQA BOUND TO A 6MA-G MISMATCH REMARK 900 RELATED ID: 1IU3 RELATED DB: PDB REMARK 900 STRUCTURE OF C-TERMINAL DOMAIN OF SEQA BOUND TO A SINGLE REMARK 900 HEMIMETHYLATED GATC DBREF 3FMT A 1 40 UNP P0AFY8 SEQA_ECOLI 1 40 DBREF 3FMT A 60 181 UNP P0AFY8 SEQA_ECOLI 60 181 DBREF 3FMT B 1 40 UNP P0AFY8 SEQA_ECOLI 1 40 DBREF 3FMT B 60 181 UNP P0AFY8 SEQA_ECOLI 60 181 DBREF 3FMT E 1 40 UNP P0AFY8 SEQA_ECOLI 1 40 DBREF 3FMT E 60 181 UNP P0AFY8 SEQA_ECOLI 60 181 DBREF 3FMT F 1 40 UNP P0AFY8 SEQA_ECOLI 1 40 DBREF 3FMT F 60 181 UNP P0AFY8 SEQA_ECOLI 60 181 DBREF 3FMT C 1 22 PDB 3FMT 3FMT 1 22 DBREF 3FMT G 1 22 PDB 3FMT 3FMT 1 22 DBREF 3FMT D 1 22 PDB 3FMT 3FMT 1 22 DBREF 3FMT H 1 22 PDB 3FMT 3FMT 1 22 SEQADV 3FMT ARG A 25 UNP P0AFY8 ALA 25 ENGINEERED MUTATION SEQADV 3FMT ARG B 25 UNP P0AFY8 ALA 25 ENGINEERED MUTATION SEQADV 3FMT ARG E 25 UNP P0AFY8 ALA 25 ENGINEERED MUTATION SEQADV 3FMT ARG F 25 UNP P0AFY8 ALA 25 ENGINEERED MUTATION SEQRES 1 A 162 MET LYS THR ILE GLU VAL ASP ASP GLU LEU TYR SER TYR SEQRES 2 A 162 ILE ALA SER HIS THR LYS HIS ILE GLY GLU SER ARG SER SEQRES 3 A 162 ASP ILE LEU ARG ARG MET LEU LYS PHE SER ALA ALA SER SEQRES 4 A 162 GLN LYS PRO VAL LYS THR ILE LYS ASP LYS VAL ARG ALA SEQRES 5 A 162 MET ARG GLU LEU LEU LEU SER ASP GLU TYR ALA GLU GLN SEQRES 6 A 162 LYS ARG ALA VAL ASN ARG PHE MET LEU LEU LEU SER THR SEQRES 7 A 162 LEU TYR SER LEU ASP ALA GLN ALA PHE ALA GLU ALA THR SEQRES 8 A 162 GLU SER LEU HIS GLY ARG THR ARG VAL TYR PHE ALA ALA SEQRES 9 A 162 ASP GLU GLN THR LEU LEU LYS ASN GLY ASN GLN THR LYS SEQRES 10 A 162 PRO LYS HIS VAL PRO GLY THR PRO TYR TRP VAL ILE THR SEQRES 11 A 162 ASN THR ASN THR GLY ARG LYS CYS SER MET ILE GLU HIS SEQRES 12 A 162 ILE MET GLN SER MET GLN PHE PRO ALA GLU LEU ILE GLU SEQRES 13 A 162 LYS VAL CYS GLY THR ILE SEQRES 1 B 162 MET LYS THR ILE GLU VAL ASP ASP GLU LEU TYR SER TYR SEQRES 2 B 162 ILE ALA SER HIS THR LYS HIS ILE GLY GLU SER ARG SER SEQRES 3 B 162 ASP ILE LEU ARG ARG MET LEU LYS PHE SER ALA ALA SER SEQRES 4 B 162 GLN LYS PRO VAL LYS THR ILE LYS ASP LYS VAL ARG ALA SEQRES 5 B 162 MET ARG GLU LEU LEU LEU SER ASP GLU TYR ALA GLU GLN SEQRES 6 B 162 LYS ARG ALA VAL ASN ARG PHE MET LEU LEU LEU SER THR SEQRES 7 B 162 LEU TYR SER LEU ASP ALA GLN ALA PHE ALA GLU ALA THR SEQRES 8 B 162 GLU SER LEU HIS GLY ARG THR ARG VAL TYR PHE ALA ALA SEQRES 9 B 162 ASP GLU GLN THR LEU LEU LYS ASN GLY ASN GLN THR LYS SEQRES 10 B 162 PRO LYS HIS VAL PRO GLY THR PRO TYR TRP VAL ILE THR SEQRES 11 B 162 ASN THR ASN THR GLY ARG LYS CYS SER MET ILE GLU HIS SEQRES 12 B 162 ILE MET GLN SER MET GLN PHE PRO ALA GLU LEU ILE GLU SEQRES 13 B 162 LYS VAL CYS GLY THR ILE SEQRES 1 C 22 DG DA DG DT DC DG 6MA DT DC DG DG DC DG SEQRES 2 C 22 DG DG 6MA DT DC DC DT DT DA SEQRES 1 D 22 DT DC DT DA DA DG DG DA DT DC DC DC DG SEQRES 2 D 22 DC DC DG DA DT DC DG DA DC SEQRES 1 E 162 MET LYS THR ILE GLU VAL ASP ASP GLU LEU TYR SER TYR SEQRES 2 E 162 ILE ALA SER HIS THR LYS HIS ILE GLY GLU SER ARG SER SEQRES 3 E 162 ASP ILE LEU ARG ARG MET LEU LYS PHE SER ALA ALA SER SEQRES 4 E 162 GLN LYS PRO VAL LYS THR ILE LYS ASP LYS VAL ARG ALA SEQRES 5 E 162 MET ARG GLU LEU LEU LEU SER ASP GLU TYR ALA GLU GLN SEQRES 6 E 162 LYS ARG ALA VAL ASN ARG PHE MET LEU LEU LEU SER THR SEQRES 7 E 162 LEU TYR SER LEU ASP ALA GLN ALA PHE ALA GLU ALA THR SEQRES 8 E 162 GLU SER LEU HIS GLY ARG THR ARG VAL TYR PHE ALA ALA SEQRES 9 E 162 ASP GLU GLN THR LEU LEU LYS ASN GLY ASN GLN THR LYS SEQRES 10 E 162 PRO LYS HIS VAL PRO GLY THR PRO TYR TRP VAL ILE THR SEQRES 11 E 162 ASN THR ASN THR GLY ARG LYS CYS SER MET ILE GLU HIS SEQRES 12 E 162 ILE MET GLN SER MET GLN PHE PRO ALA GLU LEU ILE GLU SEQRES 13 E 162 LYS VAL CYS GLY THR ILE SEQRES 1 F 162 MET LYS THR ILE GLU VAL ASP ASP GLU LEU TYR SER TYR SEQRES 2 F 162 ILE ALA SER HIS THR LYS HIS ILE GLY GLU SER ARG SER SEQRES 3 F 162 ASP ILE LEU ARG ARG MET LEU LYS PHE SER ALA ALA SER SEQRES 4 F 162 GLN LYS PRO VAL LYS THR ILE LYS ASP LYS VAL ARG ALA SEQRES 5 F 162 MET ARG GLU LEU LEU LEU SER ASP GLU TYR ALA GLU GLN SEQRES 6 F 162 LYS ARG ALA VAL ASN ARG PHE MET LEU LEU LEU SER THR SEQRES 7 F 162 LEU TYR SER LEU ASP ALA GLN ALA PHE ALA GLU ALA THR SEQRES 8 F 162 GLU SER LEU HIS GLY ARG THR ARG VAL TYR PHE ALA ALA SEQRES 9 F 162 ASP GLU GLN THR LEU LEU LYS ASN GLY ASN GLN THR LYS SEQRES 10 F 162 PRO LYS HIS VAL PRO GLY THR PRO TYR TRP VAL ILE THR SEQRES 11 F 162 ASN THR ASN THR GLY ARG LYS CYS SER MET ILE GLU HIS SEQRES 12 F 162 ILE MET GLN SER MET GLN PHE PRO ALA GLU LEU ILE GLU SEQRES 13 F 162 LYS VAL CYS GLY THR ILE SEQRES 1 G 22 DG DA DG DT DC DG 6MA DT DC DG DG DC DG SEQRES 2 G 22 DG DG 6MA DT DC DC DT DT DA SEQRES 1 H 22 DT DC DT DA DA DG DG DA DT DC DC DC DG SEQRES 2 H 22 DC DC DG DA DT DC DG DA DC MODRES 3FMT 6MA C 7 A MODRES 3FMT 6MA C 16 A MODRES 3FMT 6MA G 7 A MODRES 3FMT 6MA G 16 A HET 6MA C 7 22 HET 6MA C 16 22 HET 6MA G 7 22 HET 6MA G 16 22 HET MPD A 182 8 HET MPD A 183 8 HET MPD E 182 8 HET MPD E 183 8 HETNAM 6MA N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 6MA 4(C11 H16 N5 O6 P) FORMUL 9 MPD 4(C6 H14 O2) FORMUL 13 HOH *31(H2 O) HELIX 1 1 ASP A 7 SER A 16 1 10 HELIX 2 2 SER A 24 SER A 36 1 13 HELIX 3 3 ALA A 37 SER A 39 5 3 HELIX 4 4 THR A 64 SER A 78 1 15 HELIX 5 5 SER A 78 GLN A 84 1 7 HELIX 6 6 ARG A 86 ASP A 102 1 17 HELIX 7 7 ASP A 102 SER A 112 1 11 HELIX 8 8 ASP A 124 GLY A 132 1 9 HELIX 9 9 ASN A 152 MET A 167 1 16 HELIX 10 10 PRO A 170 ILE A 181 1 12 HELIX 11 11 ASP B 7 HIS B 17 1 11 HELIX 12 12 SER B 24 LYS B 34 1 11 HELIX 13 13 THR B 64 SER B 78 1 15 HELIX 14 14 SER B 78 GLN B 84 1 7 HELIX 15 15 ARG B 86 ASP B 102 1 17 HELIX 16 16 ASP B 102 SER B 112 1 11 HELIX 17 17 ASP B 124 GLY B 132 1 9 HELIX 18 18 ASN B 152 MET B 167 1 16 HELIX 19 19 PRO B 170 GLY B 179 1 10 HELIX 20 20 ASP E 7 SER E 16 1 10 HELIX 21 21 SER E 24 SER E 36 1 13 HELIX 22 22 ALA E 37 SER E 39 5 3 HELIX 23 23 THR E 64 SER E 78 1 15 HELIX 24 24 SER E 78 GLN E 84 1 7 HELIX 25 25 ARG E 86 ASP E 102 1 17 HELIX 26 26 ASP E 102 SER E 112 1 11 HELIX 27 27 ASP E 124 GLY E 132 1 9 HELIX 28 28 ASN E 152 MET E 167 1 16 HELIX 29 29 PRO E 170 ILE E 181 1 12 HELIX 30 30 ASP F 7 HIS F 17 1 11 HELIX 31 31 SER F 24 LYS F 34 1 11 HELIX 32 32 THR F 64 SER F 78 1 15 HELIX 33 33 SER F 78 GLN F 84 1 7 HELIX 34 34 ARG F 86 ASP F 102 1 17 HELIX 35 35 ASP F 102 SER F 112 1 11 HELIX 36 36 ASP F 124 GLY F 132 1 9 HELIX 37 37 ASN F 152 MET F 167 1 16 HELIX 38 38 PRO F 170 GLY F 179 1 10 SHEET 1 A 2 LYS A 2 VAL A 6 0 SHEET 2 A 2 LYS B 2 VAL B 6 -1 O LYS B 2 N VAL A 6 SHEET 1 B 3 PHE A 121 ALA A 122 0 SHEET 2 B 3 TRP A 146 ILE A 148 -1 O TRP A 146 N ALA A 122 SHEET 3 B 3 PRO A 137 HIS A 139 -1 N LYS A 138 O VAL A 147 SHEET 1 C 3 PHE B 121 ALA B 122 0 SHEET 2 C 3 TRP B 146 ILE B 148 -1 O TRP B 146 N ALA B 122 SHEET 3 C 3 PRO B 137 HIS B 139 -1 N LYS B 138 O VAL B 147 SHEET 1 D 2 LYS E 2 VAL E 6 0 SHEET 2 D 2 LYS F 2 VAL F 6 -1 O LYS F 2 N VAL E 6 SHEET 1 E 3 PHE E 121 ALA E 122 0 SHEET 2 E 3 TRP E 146 ILE E 148 -1 O TRP E 146 N ALA E 122 SHEET 3 E 3 PRO E 137 HIS E 139 -1 N LYS E 138 O VAL E 147 SHEET 1 F 3 PHE F 121 ALA F 122 0 SHEET 2 F 3 TRP F 146 ILE F 148 -1 O TRP F 146 N ALA F 122 SHEET 3 F 3 PRO F 137 HIS F 139 -1 N LYS F 138 O VAL F 147 LINK O3' DG C 6 P 6MA C 7 1555 1555 1.59 LINK O3' 6MA C 7 P DT C 8 1555 1555 1.60 LINK O3' DG C 15 P 6MA C 16 1555 1555 1.60 LINK O3' 6MA C 16 P DT C 17 1555 1555 1.60 LINK O3' DG G 6 P 6MA G 7 1555 1555 1.60 LINK O3' 6MA G 7 P DT G 8 1555 1555 1.60 LINK O3' DG G 15 P 6MA G 16 1555 1555 1.60 LINK O3' 6MA G 16 P DT G 17 1555 1555 1.60 SITE 1 AC1 2 LEU B 76 THR E 180 SITE 1 AC2 2 THR A 180 LEU F 76 SITE 1 AC3 4 ARG A 30 LYS A 34 GLU B 9 TYR B 13 SITE 1 AC4 4 ARG E 30 LYS E 34 GLU F 9 TYR F 13 CRYST1 121.839 121.839 279.133 90.00 90.00 120.00 H 3 36 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 0.008208 0.004739 0.000000 0.00000 SCALE2 0.000000 0.009477 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003583 0.00000