PDB Short entry for 6GCD HEADER DNA BINDING PROTEIN 17-APR-18 6GCD TITLE DNA BINDING DOMAIN OF RESTRICTION ENDONUCLEASE MCRBC IN COMPLEX WITH TITLE 2 5-HYDROXYMETHYLCYTOSINE 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*AP*GP*AP*(5HC)P*CP*GP*GP*TP*AP*GP*C)-3'); COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*CP*TP*AP*(5HC)P*CP*GP*GP*TP*CP*TP*C)-3'); COMPND 13 CHAIN: D; 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-HYDROXYMETHYLCYTOSINE, RESTRICTION ENDONUCLEASE, MCRBC, BASE KEYWDS 2 FLIPPING, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.SASNAUSKAS,E.MANAKOVA REVDAT 3 17-JAN-24 6GCD 1 REMARK REVDAT 2 24-OCT-18 6GCD 1 JRNL REVDAT 1 19-SEP-18 6GCD 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.270 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 64054 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) : 0.166 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.090 REMARK 3 FREE R VALUE TEST SET COUNT : 6465 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 23.8810 - 5.5701 0.99 1892 239 0.1833 0.1834 REMARK 3 2 5.5701 - 4.4303 1.00 1913 223 0.1385 0.1708 REMARK 3 3 4.4303 - 3.8730 1.00 1955 193 0.1364 0.1513 REMARK 3 4 3.8730 - 3.5201 1.00 1937 207 0.1496 0.1892 REMARK 3 5 3.5201 - 3.2685 1.00 1863 223 0.1498 0.2039 REMARK 3 6 3.2685 - 3.0762 1.00 1959 209 0.1670 0.2101 REMARK 3 7 3.0762 - 2.9224 1.00 1940 193 0.1653 0.2442 REMARK 3 8 2.9224 - 2.7954 1.00 1890 216 0.1693 0.2039 REMARK 3 9 2.7954 - 2.6879 0.99 1941 214 0.1752 0.2163 REMARK 3 10 2.6879 - 2.5953 0.99 1898 192 0.1763 0.2662 REMARK 3 11 2.5953 - 2.5142 0.99 1949 204 0.1762 0.2280 REMARK 3 12 2.5142 - 2.4425 1.00 1902 222 0.1796 0.2850 REMARK 3 13 2.4425 - 2.3782 1.00 1922 195 0.1641 0.2259 REMARK 3 14 2.3782 - 2.3202 1.00 1975 201 0.1566 0.2155 REMARK 3 15 2.3202 - 2.2675 1.00 1906 211 0.1574 0.2517 REMARK 3 16 2.2675 - 2.2193 1.00 1903 211 0.1547 0.2096 REMARK 3 17 2.2193 - 2.1749 1.00 1928 243 0.1640 0.2317 REMARK 3 18 2.1749 - 2.1339 1.00 1905 241 0.1668 0.2012 REMARK 3 19 2.1339 - 2.0958 1.00 1875 236 0.1639 0.2505 REMARK 3 20 2.0958 - 2.0603 1.00 1962 212 0.1825 0.2410 REMARK 3 21 2.0603 - 2.0271 1.00 1908 217 0.1864 0.2478 REMARK 3 22 2.0271 - 1.9959 1.00 1901 201 0.1743 0.2473 REMARK 3 23 1.9959 - 1.9666 1.00 1923 249 0.1754 0.2186 REMARK 3 24 1.9666 - 1.9389 1.00 1943 215 0.1823 0.2548 REMARK 3 25 1.9389 - 1.9127 1.00 1851 239 0.1917 0.2509 REMARK 3 26 1.9127 - 1.8879 1.00 1934 221 0.1963 0.2576 REMARK 3 27 1.8879 - 1.8643 1.00 1926 223 0.2030 0.2545 REMARK 3 28 1.8643 - 1.8419 1.00 1929 187 0.2224 0.2960 REMARK 3 29 1.8419 - 1.8204 1.00 1920 218 0.2494 0.3157 REMARK 3 30 1.8204 - 1.8000 1.00 1939 210 0.2674 0.3120 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.80 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 : 0.018 3781 REMARK 3 ANGLE : 1.525 5326 REMARK 3 CHIRALITY : 0.100 552 REMARK 3 PLANARITY : 0.010 518 REMARK 3 DIHEDRAL : 13.862 2630 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 6GCD 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_1200009727. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU R-AXIS IV REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64054 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 23.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 18.30 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 48.7300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.00 REMARK 200 R MERGE FOR SHELL (I) : 0.45100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.055 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 (%): 35.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM BIS-TRIS, PH 5.5, 0.2 M AMMONIUM REMARK 280 -ACETATE AND 14% PEG4000, VAPOR DIFFUSION, 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 18.03550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.85400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.46700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.85400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.03550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.46700 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: 4900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 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 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 SER B 154 REMARK 465 GLY B 155 REMARK 465 LYS B 156 REMARK 465 SER B 157 REMARK 465 VAL B 158 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 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 OG SER B 22 OP1 DG C 12 2.04 REMARK 500 OG SER A 22 OP1 DG C 12 2.09 REMARK 500 NH2 ARG A 136 O HOH A 201 2.16 REMARK 500 O HOH A 293 O HOH A 307 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 GLU B 2 CD GLU B 2 OE2 0.071 REMARK 500 PHE B 39 CE2 PHE B 39 CD2 0.143 REMARK 500 DC C 7 O3' DC C 7 C3' -0.038 REMARK 500 DG C 9 O3' DG C 9 C3' -0.039 REMARK 500 DA D 5 O3' DA D 5 C3' -0.038 REMARK 500 DG D 8 N7 DG D 8 C8 0.036 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 LEU A 37 CA - CB - CG ANGL. DEV. = 14.7 DEGREES REMARK 500 LEU A 37 CB - CG - CD1 ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG A 136 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG C 2 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG C 2 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA C 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA C 5 O3' - P - OP2 ANGL. DEV. = 6.7 DEGREES REMARK 500 DG C 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 9 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 DG D 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG D 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT D 4 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT D 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT D 10 O5' - P - OP2 ANGL. DEV. = -8.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 25 44.91 -87.32 REMARK 500 ASN A 61 87.74 -160.83 REMARK 500 TYR A 64 149.60 -175.02 REMARK 500 SER A 96 -124.98 -121.82 REMARK 500 ALA A 123 -67.33 -102.64 REMARK 500 ASN A 153 43.29 -107.17 REMARK 500 SER A 154 -75.82 -150.14 REMARK 500 ASP B 25 47.33 -83.80 REMARK 500 ASN B 61 91.82 -163.79 REMARK 500 TYR B 64 144.61 -175.20 REMARK 500 SER B 95 -107.39 -91.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 6GCD A 1 161 UNP P15005 MCRB_ECOLI 1 161 DBREF 6GCD B 1 161 UNP P15005 MCRB_ECOLI 1 161 DBREF 6GCD C 2 13 PDB 6GCD 6GCD 2 13 DBREF 6GCD D 2 13 PDB 6GCD 6GCD 2 13 SEQADV 6GCD LEU A 162 UNP P15005 EXPRESSION TAG SEQADV 6GCD GLU A 163 UNP P15005 EXPRESSION TAG SEQADV 6GCD GLY A 164 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS A 165 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS A 166 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS A 167 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS A 168 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS A 169 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS A 170 UNP P15005 EXPRESSION TAG SEQADV 6GCD LEU B 162 UNP P15005 EXPRESSION TAG SEQADV 6GCD GLU B 163 UNP P15005 EXPRESSION TAG SEQADV 6GCD GLY B 164 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS B 165 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS B 166 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS B 167 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS B 168 UNP P15005 EXPRESSION TAG SEQADV 6GCD HIS B 169 UNP P15005 EXPRESSION TAG SEQADV 6GCD 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 CME 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 CME 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 C 12 DG DA DG DA 5HC DC DG DG DT DA DG DC SEQRES 1 D 12 DG DC DT DA 5HC DC DG DG DT DC DT DC MODRES 6GCD CME A 124 CYS MODIFIED RESIDUE MODRES 6GCD CME B 124 CYS MODIFIED RESIDUE HET CME A 124 10 HET CME B 124 10 HET 5HC C 6 42 HET 5HC D 6 42 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM 5HC 2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 5HC PHOSPHATE) FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 3 5HC 2(C10 H16 N3 O8 P) FORMUL 5 HOH *218(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 SER A 129 GLY A 131 5 3 HELIX 5 AA5 ASP A 133 ASN A 153 1 21 HELIX 6 AA6 ILE B 4 GLN B 18 1 15 HELIX 7 AA7 LYS B 71 PHE B 73 5 3 HELIX 8 AA8 THR B 101 GLY B 111 1 11 HELIX 9 AA9 SER B 129 GLY B 131 5 3 HELIX 10 AB1 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 CME 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 C ALA A 123 N CME A 124 1555 1555 1.33 LINK C CME A 124 N SER A 125 1555 1555 1.33 LINK C ALA B 123 N CME B 124 1555 1555 1.32 LINK C CME B 124 N SER B 125 1555 1555 1.31 LINK O3'A DA C 5 P A5HC C 6 1555 1555 1.60 LINK O3'B DA C 5 P B5HC C 6 1555 1555 1.59 LINK O3'A5HC C 6 P A DC C 7 1555 1555 1.61 LINK O3'B5HC C 6 P B DC C 7 1555 1555 1.61 LINK O3'A DA D 5 P A5HC D 6 1555 1555 1.60 LINK O3'B DA D 5 P B5HC D 6 1555 1555 1.59 LINK O3'A5HC D 6 P A DC D 7 1555 1555 1.60 LINK O3'B5HC D 6 P B DC D 7 1555 1555 1.61 CRYST1 36.071 68.934 143.708 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 0.027723 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006959 0.00000