PDB Short entry for 6GCE HEADER DNA BINDING PROTEIN 17-APR-18 6GCE TITLE DNA BINDING DOMAIN OF RESTRICTION ENDONUCLEASE MCRBC IN COMPLEX WITH TITLE 2 5-FORMYLCYTOSINE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5-METHYLCYTOSINE-SPECIFIC RESTRICTION ENZYME B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ECOKMCRBC; COMPND 5 EC: 3.1.21.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*CP*TP*AP*(5FC)P*CP*GP*GP*TP*CP*TP*C)-3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: MCRB, RGLB, B4346, JW5871; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI STR. K-12 SUBSTR. DH10B; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 316385; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS 5-FORMYLCYTOSINE, RESTRICTION ENDONUCLEASE, MCRBC, BASE FLIPPING, DNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.SASNAUSKAS REVDAT 2 24-OCT-18 6GCE 1 JRNL REVDAT 1 19-SEP-18 6GCE 0 JRNL AUTH E.ZAGORSKAITE,E.MANAKOVA,G.SASNAUSKAS JRNL TITL RECOGNITION OF MODIFIED CYTOSINE VARIANTS BY THE DNA-BINDING JRNL TITL 2 DOMAIN OF METHYL-DIRECTED ENDONUCLEASE MCRBC. JRNL REF FEBS LETT. V. 592 3335 2018 JRNL REFN ISSN 1873-3468 JRNL PMID 30194838 JRNL DOI 10.1002/1873-3468.13244 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.3_1479 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.860 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 92903 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.150 REMARK 3 FREE R VALUE TEST SET COUNT : 9430 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 35.0970 - 4.9671 0.96 2647 320 0.1721 0.1728 REMARK 3 2 4.9671 - 3.9443 0.98 2719 321 0.1279 0.1529 REMARK 3 3 3.9443 - 3.4462 0.98 2727 341 0.1429 0.1664 REMARK 3 4 3.4462 - 3.1313 0.98 2743 313 0.1543 0.1752 REMARK 3 5 3.1313 - 2.9070 0.99 2789 299 0.1646 0.2196 REMARK 3 6 2.9070 - 2.7357 0.99 2761 308 0.1655 0.1992 REMARK 3 7 2.7357 - 2.5987 1.00 2751 349 0.1703 0.2044 REMARK 3 8 2.5987 - 2.4856 1.00 2793 306 0.1538 0.1875 REMARK 3 9 2.4856 - 2.3899 1.00 2762 335 0.1562 0.2104 REMARK 3 10 2.3899 - 2.3075 1.00 2838 312 0.1517 0.1951 REMARK 3 11 2.3075 - 2.2354 1.00 2803 310 0.1523 0.1930 REMARK 3 12 2.2354 - 2.1715 1.00 2791 315 0.1561 0.2108 REMARK 3 13 2.1715 - 2.1143 1.00 2782 308 0.1644 0.2253 REMARK 3 14 2.1143 - 2.0627 1.00 2815 312 0.1680 0.2384 REMARK 3 15 2.0627 - 2.0158 1.00 2773 307 0.1663 0.2301 REMARK 3 16 2.0158 - 1.9729 1.00 2849 314 0.1601 0.2347 REMARK 3 17 1.9729 - 1.9335 1.00 2802 270 0.1686 0.2204 REMARK 3 18 1.9335 - 1.8970 1.00 2801 299 0.1838 0.2309 REMARK 3 19 1.8970 - 1.8631 1.00 2817 341 0.1774 0.2462 REMARK 3 20 1.8631 - 1.8315 1.00 2729 352 0.1973 0.2630 REMARK 3 21 1.8315 - 1.8020 1.00 2823 276 0.2075 0.2484 REMARK 3 22 1.8020 - 1.7743 1.00 2844 325 0.2139 0.2821 REMARK 3 23 1.7743 - 1.7482 1.00 2742 327 0.2188 0.2530 REMARK 3 24 1.7482 - 1.7236 1.00 2775 321 0.2195 0.2811 REMARK 3 25 1.7236 - 1.7003 1.00 2848 270 0.2277 0.2946 REMARK 3 26 1.7003 - 1.6782 1.00 2801 292 0.2494 0.2976 REMARK 3 27 1.6782 - 1.6572 1.00 2770 339 0.2712 0.3267 REMARK 3 28 1.6572 - 1.6372 1.00 2777 350 0.2684 0.3209 REMARK 3 29 1.6372 - 1.6182 1.00 2841 279 0.2781 0.3223 REMARK 3 30 1.6182 - 1.6000 0.99 2760 319 0.2998 0.3371 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.46 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 : 0.010 3674 REMARK 3 ANGLE : 1.046 5187 REMARK 3 CHIRALITY : 0.064 550 REMARK 3 PLANARITY : 0.005 498 REMARK 3 DIHEDRAL : 19.914 1373 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 6GCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.001 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92903 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 35.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.44800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.390 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3SSC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LICL, 22% PEG4000, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 18.08750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.13250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.99400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.13250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.08750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.99400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, C 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 ILE A 159 REMARK 465 PRO A 160 REMARK 465 PRO A 161 REMARK 465 LEU A 162 REMARK 465 GLU A 163 REMARK 465 GLY A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 ILE B 159 REMARK 465 PRO B 160 REMARK 465 PRO B 161 REMARK 465 LEU B 162 REMARK 465 GLU B 163 REMARK 465 GLY B 164 REMARK 465 HIS B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 REMARK 465 HIS B 169 REMARK 465 HIS B 170 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 MET A 1 CG SD CE REMARK 470 GLN A 17 OE1 NE2 REMARK 470 ARG A 19 CD NE CZ NH1 NH2 REMARK 470 LYS A 36 NZ REMARK 470 GLU A 55 CG CD OE1 OE2 REMARK 470 GLU A 87 CG CD OE1 OE2 REMARK 470 GLN A 93 CG CD OE1 NE2 REMARK 470 SER A 95 OG REMARK 470 SER A 96 OG REMARK 470 LYS A 115 CE NZ REMARK 470 LYS A 127 NZ REMARK 470 GLN A 130 CG CD OE1 NE2 REMARK 470 LYS B 13 CE NZ REMARK 470 ARG B 19 CD NE CZ NH1 NH2 REMARK 470 LYS B 24 CE NZ REMARK 470 GLU B 55 CG CD OE1 OE2 REMARK 470 HIS B 89 CG ND1 CD2 CE1 NE2 REMARK 470 GLN B 91 CD OE1 NE2 REMARK 470 SER B 95 OG REMARK 470 LYS B 100 NZ REMARK 470 LYS B 115 CE NZ REMARK 470 GLN B 130 CG CD OE1 NE2 REMARK 470 ARG B 136 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 156 CG CD CE NZ 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 B 351 O HOH B 356 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 328 O HOH B 316 2555 2.13 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 DC D 3 O3' DT D 4 P -0.099 REMARK 500 DT C 10 P DT C 10 OP1 -0.133 REMARK 500 DT C 10 P DT C 10 OP2 -0.106 REMARK 500 DA C 11 P DA C 11 OP1 -0.117 REMARK 500 DA C 11 P DA C 11 O5' -0.064 REMARK 500 DA C 11 O3' DG C 12 P -0.083 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 ARG B 34 CD - NE - CZ ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG B 34 NE - CZ - NH1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG B 34 NE - CZ - NH2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DT D 4 O3' - P - OP2 ANGL. DEV. = 8.2 DEGREES REMARK 500 DT C 10 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 25 38.43 -89.06 REMARK 500 ASN A 61 90.16 -161.29 REMARK 500 TYR A 64 144.02 -176.30 REMARK 500 SER A 96 -78.59 -103.34 REMARK 500 ALA A 123 -60.85 -107.71 REMARK 500 ASP B 25 46.58 -88.50 REMARK 500 ASN B 61 89.72 -160.38 REMARK 500 TYR B 64 144.70 -174.54 REMARK 500 SER B 95 -80.45 -96.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GCD RELATED DB: PDB REMARK 900 5HMC DNA DBREF 6GCE A 1 161 UNP P15005 MCRB_ECOLI 1 161 DBREF 6GCE B 1 161 UNP P15005 MCRB_ECOLI 1 161 DBREF 6GCE D 2 13 PDB 6GCE 6GCE 2 13 DBREF 6GCE C 2 13 PDB 6GCE 6GCE 2 13 SEQADV 6GCE LEU A 162 UNP P15005 EXPRESSION TAG SEQADV 6GCE GLU A 163 UNP P15005 EXPRESSION TAG SEQADV 6GCE GLY A 164 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS A 165 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS A 166 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS A 167 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS A 168 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS A 169 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS A 170 UNP P15005 EXPRESSION TAG SEQADV 6GCE LEU B 162 UNP P15005 EXPRESSION TAG SEQADV 6GCE GLU B 163 UNP P15005 EXPRESSION TAG SEQADV 6GCE GLY B 164 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS B 165 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS B 166 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS B 167 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS B 168 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS B 169 UNP P15005 EXPRESSION TAG SEQADV 6GCE HIS B 170 UNP P15005 EXPRESSION TAG SEQRES 1 A 170 MET GLU SER ILE GLN PRO TRP ILE GLU LYS PHE ILE LYS SEQRES 2 A 170 GLN ALA GLN GLN GLN ARG SER GLN SER THR LYS ASP TYR SEQRES 3 A 170 PRO THR SER TYR ARG ASN LEU ARG VAL LYS LEU SER PHE SEQRES 4 A 170 GLY TYR GLY ASN PHE THR SER ILE PRO TRP PHE ALA PHE SEQRES 5 A 170 LEU GLY GLU GLY GLN GLU ALA SER ASN GLY ILE TYR PRO SEQRES 6 A 170 VAL ILE LEU TYR TYR LYS ASP PHE ASP GLU LEU VAL LEU SEQRES 7 A 170 ALA TYR GLY ILE SER ASP THR ASN GLU PRO HIS ALA GLN SEQRES 8 A 170 TRP GLN PHE SER SER ASP ILE PRO LYS THR ILE ALA GLU SEQRES 9 A 170 TYR PHE GLN ALA THR SER GLY VAL TYR PRO LYS LYS TYR SEQRES 10 A 170 GLY GLN SER TYR TYR ALA CYS SER GLN LYS VAL SER GLN SEQRES 11 A 170 GLY ILE ASP TYR THR ARG PHE ALA SER MET LEU ASP ASN SEQRES 12 A 170 ILE ILE ASN ASP TYR LYS LEU ILE PHE ASN SER GLY LYS SEQRES 13 A 170 SER VAL ILE PRO PRO LEU GLU GLY HIS HIS HIS HIS HIS SEQRES 14 A 170 HIS SEQRES 1 B 170 MET GLU SER ILE GLN PRO TRP ILE GLU LYS PHE ILE LYS SEQRES 2 B 170 GLN ALA GLN GLN GLN ARG SER GLN SER THR LYS ASP TYR SEQRES 3 B 170 PRO THR SER TYR ARG ASN LEU ARG VAL LYS LEU SER PHE SEQRES 4 B 170 GLY TYR GLY ASN PHE THR SER ILE PRO TRP PHE ALA PHE SEQRES 5 B 170 LEU GLY GLU GLY GLN GLU ALA SER ASN GLY ILE TYR PRO SEQRES 6 B 170 VAL ILE LEU TYR TYR LYS ASP PHE ASP GLU LEU VAL LEU SEQRES 7 B 170 ALA TYR GLY ILE SER ASP THR ASN GLU PRO HIS ALA GLN SEQRES 8 B 170 TRP GLN PHE SER SER ASP ILE PRO LYS THR ILE ALA GLU SEQRES 9 B 170 TYR PHE GLN ALA THR SER GLY VAL TYR PRO LYS LYS TYR SEQRES 10 B 170 GLY GLN SER TYR TYR ALA CYS SER GLN LYS VAL SER GLN SEQRES 11 B 170 GLY ILE ASP TYR THR ARG PHE ALA SER MET LEU ASP ASN SEQRES 12 B 170 ILE ILE ASN ASP TYR LYS LEU ILE PHE ASN SER GLY LYS SEQRES 13 B 170 SER VAL ILE PRO PRO LEU GLU GLY HIS HIS HIS HIS HIS SEQRES 14 B 170 HIS SEQRES 1 D 12 DG DC DT DA 5FC DC DG DG DT DC DT DC SEQRES 1 C 12 DG DA DG DA DC DC DG DG DT DA DG DC HET 5FC D 6 42 HETNAM 5FC 5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETSYN 5FC 2'-DEOXY-5-FORMYLCYTIDINE-5'-MONOPHOSPHATE FORMUL 3 5FC C10 H14 N3 O8 P FORMUL 5 HOH *370(H2 O) HELIX 1 AA1 ILE A 4 GLN A 18 1 15 HELIX 2 AA2 LYS A 71 PHE A 73 5 3 HELIX 3 AA3 THR A 101 GLY A 111 1 11 HELIX 4 AA4 ASP A 133 PHE A 152 1 20 HELIX 5 AA5 ILE B 4 GLN B 18 1 15 HELIX 6 AA6 LYS B 71 PHE B 73 5 3 HELIX 7 AA7 THR B 101 GLY B 111 1 11 HELIX 8 AA8 SER B 129 GLY B 131 5 3 HELIX 9 AA9 ASP B 133 LYS B 149 1 17 SHEET 1 AA1 6 SER A 29 TYR A 30 0 SHEET 2 AA1 6 LEU A 33 SER A 38 -1 O LEU A 33 N TYR A 30 SHEET 3 AA1 6 TRP A 49 LEU A 53 -1 O ALA A 51 N LYS A 36 SHEET 4 AA1 6 ILE A 63 TYR A 70 -1 O ILE A 67 N PHE A 50 SHEET 5 AA1 6 GLU A 75 ILE A 82 -1 O VAL A 77 N LEU A 68 SHEET 6 AA1 6 TYR A 121 LYS A 127 -1 O CYS A 124 N LEU A 78 SHEET 1 AA2 6 SER B 29 TYR B 30 0 SHEET 2 AA2 6 LEU B 33 SER B 38 -1 O LEU B 33 N TYR B 30 SHEET 3 AA2 6 TRP B 49 LEU B 53 -1 O ALA B 51 N LYS B 36 SHEET 4 AA2 6 ILE B 63 TYR B 70 -1 O ILE B 67 N PHE B 50 SHEET 5 AA2 6 GLU B 75 ILE B 82 -1 O VAL B 77 N LEU B 68 SHEET 6 AA2 6 TYR B 121 LYS B 127 -1 O GLN B 126 N LEU B 76 LINK O3'A DA D 5 P A5FC D 6 1555 1555 1.61 LINK O3'B DA D 5 P B5FC D 6 1555 1555 1.61 LINK O3'A5FC D 6 P A DC D 7 1555 1555 1.61 LINK O3'B5FC D 6 P B DC D 7 1555 1555 1.61 CRYST1 36.175 69.988 144.265 90.00 90.00 90.00 P 21 21 21 8 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 0.027643 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006932 0.00000