HEADER TRANSFERASE/DNA 17-MAY-95 1DCT TITLE DNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA CAVEAT 1DCT C49 F 10 HAS WRONG CHIRALITY AT ATOM C1' C49 G 10 HAS WRONG CAVEAT 2 1DCT CHIRALITY AT ATOM C1' COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*CP*CP*AP*GP*CP*AP*GP*GP*(C49) COMPND 3 P*CP*AP*CP*CP*AP*GP*TP*G)-3'); COMPND 4 CHAIN: F, G; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*TP*GP*GP*(C5M) COMPND 8 P*CP*TP*GP*CP*TP*GP*G)-3'); COMPND 9 CHAIN: M, N; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PROTEIN (MODIFICATION METHYLASE HAEIII); COMPND 13 CHAIN: A, B; COMPND 14 SYNONYM: CYTOSINE-SPECIFIC METHYLTRANSFERASE, HAEIII, M.HAEIII; COMPND 15 EC: 2.1.1.73 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE BIOTYPE AEGYPTIUS; SOURCE 7 ORGANISM_TAXID: 725; SOURCE 8 STRAIN: BIOTYPE AEGYPTIUS KEYWDS ENZYME, CYTOSINE METHYLASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.M.REINISCH,L.CHEN,G.L.VERDINE,W.N.LIPSCOMB REVDAT 4 20-NOV-19 1DCT 1 CAVEAT LINK REVDAT 3 24-FEB-09 1DCT 1 VERSN REVDAT 2 01-APR-03 1DCT 1 JRNL REVDAT 1 15-SEP-95 1DCT 0 JRNL AUTH K.M.REINISCH,L.CHEN,G.L.VERDINE,W.N.LIPSCOMB JRNL TITL THE CRYSTAL STRUCTURE OF HAEIII METHYLTRANSFERASE JRNL TITL 2 CONVALENTLY COMPLEXED TO DNA: AN EXTRAHELICAL CYTOSINE AND JRNL TITL 3 REARRANGED BASE PAIRING. JRNL REF CELL(CAMBRIDGE,MASS.) V. 82 143 1995 JRNL REFN ISSN 0092-8674 JRNL PMID 7606780 JRNL DOI 10.1016/0092-8674(95)90060-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.M.REINISCH,L.CHEN,G.L.VERDINE,W.N.LIPSCOMB REMARK 1 TITL CRYSTALLIZATION AND PRELIMANARY CRYSTALLOGRAPHIC ANALYSIS OF REMARK 1 TITL 2 A DNA (CYTOSINE-5) -METHYLTRANSFERASE FROM HAEMOPHILUS REMARK 1 TITL 3 AEGYPTIUS BOUND COVALENTLY TO DNA REMARK 1 REF J.MOL.BIOL. V. 238 626 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 22801 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.326 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5230 REMARK 3 NUCLEIC ACID ATOMS : 1408 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 0 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 2.330 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DCT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000172739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 113.00 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26866 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.50, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277.00K 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 28.78500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.89500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.02000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.89500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.78500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.02000 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 300 REMARK: THIS FILE CONTAINS 2 PROTEIN-DNA COMPLEXES IN THE REMARK 300 ASYMMETRIC UNIT. PROTEIN MONOMER A IS COVALENTLY BOUND TO REMARK 300 A DNA DUPLEX CONSISTING OF CHAINS F AND M, AND PROTEIN REMARK 300 MONOMER B IS COVALENTLY LINKED TO A DUPLEX CONSISTING OF REMARK 300 CHAINS G AND N. THERE ARE TWO SPECIAL NUCLEOTIDE BASES REMARK 300 INCORPORATED INTO EACH DNA DUPLEX - ONE IRREGULAR BASE IN REMARK 300 EACH CHAIN. ONE OF THESE BASES IS A CYTOSINE METHYLATED AT REMARK 300 THE 5-POSITION, AND THE OTHER (DESCRIBED IN MORE DETAIL REMARK 300 BELOW) IS USED TO COVALENTLY LINK THE DNA TO THE PROTEIN. REMARK 300 REMARK 300 THE DNA AT THE RECOGNITION SITE IS VERY DISTORTED: THERE IS REMARK 300 AN EXTRAHELICAL CYTOSINE (THE MODIFIED ONE COVALENTLY REMARK 300 LINKED TO THE PROTEIN VIA CYS 71: +C F 10 AND +C G 10) AND REMARK 300 BASE PAIRING IN THE DNA RECOGNITION SEQUENCE IS REMARK 300 REORGANIZED. THERE ARE ALSO TWO CA+2 IONS IN THE REMARK 300 ASYMMETRIC UNIT. 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 APPLY THE FOLLOWING TO CHAINS: F, M, A 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 APPLY THE FOLLOWING TO CHAINS: G, N, 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 DA G 1 REMARK 465 DC G 2 REMARK 465 DG N 18 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 DC G 3 P OP1 OP2 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 HD22 ASN B 210 HH21 ARG B 278 1.12 REMARK 500 HD22 ASN A 210 HH21 ARG A 278 1.30 REMARK 500 O2P C49 G 10 HH12 ARG B 155 1.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG F 8 O3' DG F 8 C3' -0.045 REMARK 500 DG F 9 O3' DG F 9 C3' -0.066 REMARK 500 DC F 11 O3' DC F 11 C3' -0.045 REMARK 500 DC F 13 O3' DC F 13 C3' -0.037 REMARK 500 DT M 1 O3' DT M 1 C3' -0.046 REMARK 500 DG M 6 O3' DG M 6 C3' -0.040 REMARK 500 DT M 8 O3' DT M 8 C3' -0.091 REMARK 500 DG M 9 O3' DG M 9 C3' -0.049 REMARK 500 DG M 10 O3' DG M 10 C3' -0.063 REMARK 500 DC M 15 O3' DC M 15 C3' -0.042 REMARK 500 DG G 5 O3' DG G 5 C3' -0.046 REMARK 500 DG G 8 O3' DG G 8 C3' -0.037 REMARK 500 DC G 11 O3' DC G 11 C3' -0.040 REMARK 500 DC G 13 O3' DC G 13 C3' -0.055 REMARK 500 DC G 14 O4' DC G 14 C4' -0.065 REMARK 500 DT N 1 O3' DT N 1 C3' -0.052 REMARK 500 DG N 6 O3' DG N 6 C3' -0.042 REMARK 500 DT N 8 O3' DT N 8 C3' -0.096 REMARK 500 DG N 9 O3' DG N 9 C3' -0.050 REMARK 500 DG N 10 O4' DG N 10 C4' -0.063 REMARK 500 DG N 10 O3' DG N 10 C3' -0.059 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DA F 1 C6 - N1 - C2 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA F 1 N1 - C2 - N3 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA F 1 C5 - C6 - N1 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC F 2 O4' - C4' - C3' ANGL. DEV. = 6.1 DEGREES REMARK 500 DC F 2 C1' - O4' - C4' ANGL. DEV. = -7.4 DEGREES REMARK 500 DC F 3 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 DA F 4 C6 - N1 - C2 ANGL. DEV. = 5.2 DEGREES REMARK 500 DA F 4 N1 - C2 - N3 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA F 4 C5 - C6 - N1 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG F 5 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES REMARK 500 DG F 5 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DG F 5 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA F 7 C6 - N1 - C2 ANGL. DEV. = 4.7 DEGREES REMARK 500 DA F 7 N1 - C2 - N3 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG F 8 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DG F 8 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC F 11 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 DA F 12 C6 - N1 - C2 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA F 12 N1 - C2 - N3 ANGL. DEV. = -4.1 DEGREES REMARK 500 DC F 13 O4' - C4' - C3' ANGL. DEV. = 5.5 DEGREES REMARK 500 DC F 13 C1' - O4' - C4' ANGL. DEV. = -9.2 DEGREES REMARK 500 DC F 13 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DA F 15 P - O5' - C5' ANGL. DEV. = -12.6 DEGREES REMARK 500 DA F 15 C6 - N1 - C2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA F 15 N1 - C2 - N3 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG F 16 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT F 17 C2 - N3 - C4 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG F 18 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT M 1 N1 - C2 - N3 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT M 1 C2 - N3 - C4 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA M 3 C6 - N1 - C2 ANGL. DEV. = 4.7 DEGREES REMARK 500 DA M 3 N1 - C2 - N3 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC M 4 N3 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 DT M 5 N1 - C2 - N3 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT M 5 C2 - N3 - C4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG M 6 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG M 7 P - O5' - C5' ANGL. DEV. = -11.1 DEGREES REMARK 500 DG M 7 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 DG M 7 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT M 8 C2 - N3 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG M 9 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG M 10 P - O5' - C5' ANGL. DEV. = -11.1 DEGREES REMARK 500 DT M 13 C2 - N3 - C4 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG M 14 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC M 15 P - O5' - C5' ANGL. DEV. = -10.2 DEGREES REMARK 500 DT M 16 C2 - N3 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG M 18 C1' - O4' - C4' ANGL. DEV. = -8.2 DEGREES REMARK 500 DA G 4 C6 - N1 - C2 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA G 4 N1 - C2 - N3 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG G 5 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 87 ANGLE DEVIATIONS. 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 SER A 33 1.17 -62.87 REMARK 500 TRP A 35 -50.32 -27.45 REMARK 500 PRO A 69 148.16 -38.25 REMARK 500 PRO A 70 125.72 -35.19 REMARK 500 GLN A 72 -36.39 -38.87 REMARK 500 SER A 79 58.53 17.82 REMARK 500 LEU A 80 20.33 -54.41 REMARK 500 ASP A 85 139.45 -171.68 REMARK 500 LYS A 102 61.21 34.62 REMARK 500 ASN A 110 -177.88 179.09 REMARK 500 ALA A 150 24.58 -70.23 REMARK 500 ASN A 166 51.33 36.61 REMARK 500 PRO A 174 173.87 -48.61 REMARK 500 VAL A 184 -19.32 -142.97 REMARK 500 ASN A 191 54.56 -161.06 REMARK 500 LYS A 205 -32.59 -30.92 REMARK 500 PRO A 209 118.68 -38.26 REMARK 500 ASN A 210 19.51 54.06 REMARK 500 HIS A 211 43.58 -80.16 REMARK 500 MET A 223 0.88 -69.06 REMARK 500 SER A 241 97.16 170.54 REMARK 500 LEU A 261 131.92 -178.84 REMARK 500 GLU A 269 -48.99 -29.22 REMARK 500 HIS A 270 -1.05 -52.99 REMARK 500 LYS A 302 -70.50 -60.27 REMARK 500 PHE B 7 48.44 33.04 REMARK 500 SER B 33 -4.04 -59.83 REMARK 500 TRP B 35 -59.02 -25.92 REMARK 500 SER B 79 66.30 32.83 REMARK 500 LYS B 102 73.63 37.15 REMARK 500 ASN B 110 -178.88 -173.49 REMARK 500 ARG B 118 -27.94 -39.36 REMARK 500 ALA B 150 46.18 -69.08 REMARK 500 PRO B 174 171.65 -59.30 REMARK 500 PRO B 179 152.31 -40.93 REMARK 500 TRP B 186 -60.03 -3.58 REMARK 500 ASN B 191 20.59 -159.10 REMARK 500 ASP B 197 126.68 -23.50 REMARK 500 LYS B 198 30.26 72.42 REMARK 500 PRO B 209 112.42 -33.43 REMARK 500 LYS B 259 -74.59 -12.49 REMARK 500 ASN B 260 52.03 -116.98 REMARK 500 GLU B 269 -47.82 -21.11 REMARK 500 HIS B 270 1.43 -55.50 REMARK 500 LEU B 297 -36.80 -36.87 REMARK 500 VAL B 310 -71.70 -45.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA F 1 0.09 SIDE CHAIN REMARK 500 DT F 17 0.06 SIDE CHAIN REMARK 500 DG M 17 0.06 SIDE CHAIN REMARK 500 TYR A 147 0.08 SIDE CHAIN REMARK 500 TYR B 38 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: DAA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: DAB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1002 DBREF 1DCT A 1 324 UNP P20589 MTH3_HAEAE 1 324 DBREF 1DCT B 1 324 UNP P20589 MTH3_HAEAE 1 324 DBREF 1DCT F 1 18 PDB 1DCT 1DCT 1 18 DBREF 1DCT M 1 18 PDB 1DCT 1DCT 1 18 DBREF 1DCT G 1 18 PDB 1DCT 1DCT 1 18 DBREF 1DCT N 1 18 PDB 1DCT 1DCT 1 18 SEQRES 1 F 18 DA DC DC DA DG DC DA DG DG C49 DC DA DC SEQRES 2 F 18 DC DA DG DT DG SEQRES 1 M 18 DT DC DA DC DT DG DG DT DG DG 5CM DC DT SEQRES 2 M 18 DG DC DT DG DG SEQRES 1 G 18 DA DC DC DA DG DC DA DG DG C49 DC DA DC SEQRES 2 G 18 DC DA DG DT DG SEQRES 1 N 18 DT DC DA DC DT DG DG DT DG DG 5CM DC DT SEQRES 2 N 18 DG DC DT DG DG SEQRES 1 A 324 MET ASN LEU ILE SER LEU PHE SER GLY ALA GLY GLY LEU SEQRES 2 A 324 ASP LEU GLY PHE GLN LYS ALA GLY PHE ARG ILE ILE CYS SEQRES 3 A 324 ALA ASN GLU TYR ASP LYS SER ILE TRP LYS THR TYR GLU SEQRES 4 A 324 SER ASN HIS SER ALA LYS LEU ILE LYS GLY ASP ILE SER SEQRES 5 A 324 LYS ILE SER SER ASP GLU PHE PRO LYS CYS ASP GLY ILE SEQRES 6 A 324 ILE GLY GLY PRO PRO CYS GLN SER TRP SER GLU GLY GLY SEQRES 7 A 324 SER LEU ARG GLY ILE ASP ASP PRO ARG GLY LYS LEU PHE SEQRES 8 A 324 TYR GLU TYR ILE ARG ILE LEU LYS GLN LYS LYS PRO ILE SEQRES 9 A 324 PHE PHE LEU ALA GLU ASN VAL LYS GLY MET MET ALA GLN SEQRES 10 A 324 ARG HIS ASN LYS ALA VAL GLN GLU PHE ILE GLN GLU PHE SEQRES 11 A 324 ASP ASN ALA GLY TYR ASP VAL HIS ILE ILE LEU LEU ASN SEQRES 12 A 324 ALA ASN ASP TYR GLY VAL ALA GLN ASP ARG LYS ARG VAL SEQRES 13 A 324 PHE TYR ILE GLY PHE ARG LYS GLU LEU ASN ILE ASN TYR SEQRES 14 A 324 LEU PRO PRO ILE PRO HIS LEU ILE LYS PRO THR PHE LYS SEQRES 15 A 324 ASP VAL ILE TRP ASP LEU LYS ASP ASN PRO ILE PRO ALA SEQRES 16 A 324 LEU ASP LYS ASN LYS THR ASN GLY ASN LYS CYS ILE TYR SEQRES 17 A 324 PRO ASN HIS GLU TYR PHE ILE GLY SER TYR SER THR ILE SEQRES 18 A 324 PHE MET SER ARG ASN ARG VAL ARG GLN TRP ASN GLU PRO SEQRES 19 A 324 ALA PHE THR VAL GLN ALA SER GLY ARG GLN CYS GLN LEU SEQRES 20 A 324 HIS PRO GLN ALA PRO VAL MET LEU LYS VAL SER LYS ASN SEQRES 21 A 324 LEU ASN LYS PHE VAL GLU GLY LYS GLU HIS LEU TYR ARG SEQRES 22 A 324 ARG LEU THR VAL ARG GLU CYS ALA ARG VAL GLN GLY PHE SEQRES 23 A 324 PRO ASP ASP PHE ILE PHE HIS TYR GLU SER LEU ASN ASP SEQRES 24 A 324 GLY TYR LYS MET ILE GLY ASN ALA VAL PRO VAL ASN LEU SEQRES 25 A 324 ALA TYR GLU ILE ALA LYS THR ILE LYS SER ALA LEU SEQRES 1 B 324 MET ASN LEU ILE SER LEU PHE SER GLY ALA GLY GLY LEU SEQRES 2 B 324 ASP LEU GLY PHE GLN LYS ALA GLY PHE ARG ILE ILE CYS SEQRES 3 B 324 ALA ASN GLU TYR ASP LYS SER ILE TRP LYS THR TYR GLU SEQRES 4 B 324 SER ASN HIS SER ALA LYS LEU ILE LYS GLY ASP ILE SER SEQRES 5 B 324 LYS ILE SER SER ASP GLU PHE PRO LYS CYS ASP GLY ILE SEQRES 6 B 324 ILE GLY GLY PRO PRO CYS GLN SER TRP SER GLU GLY GLY SEQRES 7 B 324 SER LEU ARG GLY ILE ASP ASP PRO ARG GLY LYS LEU PHE SEQRES 8 B 324 TYR GLU TYR ILE ARG ILE LEU LYS GLN LYS LYS PRO ILE SEQRES 9 B 324 PHE PHE LEU ALA GLU ASN VAL LYS GLY MET MET ALA GLN SEQRES 10 B 324 ARG HIS ASN LYS ALA VAL GLN GLU PHE ILE GLN GLU PHE SEQRES 11 B 324 ASP ASN ALA GLY TYR ASP VAL HIS ILE ILE LEU LEU ASN SEQRES 12 B 324 ALA ASN ASP TYR GLY VAL ALA GLN ASP ARG LYS ARG VAL SEQRES 13 B 324 PHE TYR ILE GLY PHE ARG LYS GLU LEU ASN ILE ASN TYR SEQRES 14 B 324 LEU PRO PRO ILE PRO HIS LEU ILE LYS PRO THR PHE LYS SEQRES 15 B 324 ASP VAL ILE TRP ASP LEU LYS ASP ASN PRO ILE PRO ALA SEQRES 16 B 324 LEU ASP LYS ASN LYS THR ASN GLY ASN LYS CYS ILE TYR SEQRES 17 B 324 PRO ASN HIS GLU TYR PHE ILE GLY SER TYR SER THR ILE SEQRES 18 B 324 PHE MET SER ARG ASN ARG VAL ARG GLN TRP ASN GLU PRO SEQRES 19 B 324 ALA PHE THR VAL GLN ALA SER GLY ARG GLN CYS GLN LEU SEQRES 20 B 324 HIS PRO GLN ALA PRO VAL MET LEU LYS VAL SER LYS ASN SEQRES 21 B 324 LEU ASN LYS PHE VAL GLU GLY LYS GLU HIS LEU TYR ARG SEQRES 22 B 324 ARG LEU THR VAL ARG GLU CYS ALA ARG VAL GLN GLY PHE SEQRES 23 B 324 PRO ASP ASP PHE ILE PHE HIS TYR GLU SER LEU ASN ASP SEQRES 24 B 324 GLY TYR LYS MET ILE GLY ASN ALA VAL PRO VAL ASN LEU SEQRES 25 B 324 ALA TYR GLU ILE ALA LYS THR ILE LYS SER ALA LEU MODRES 1DCT C49 F 10 DC MODRES 1DCT 5CM M 11 DC MODRES 1DCT C49 G 10 DC MODRES 1DCT 5CM N 11 DC HET C49 F 10 21 HET 5CM M 11 20 HET C49 G 10 21 HET 5CM N 11 20 HET CA A1001 1 HET CA B1002 1 HETNAM C49 4-THIO,5-FLUORO,5-METHYL-2'-DEOXY-CYTIDINE-5'- HETNAM 2 C49 MONOPHOSPHATE HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION FORMUL 1 C49 2(C10 H15 F N3 O7 P S) FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 7 CA 2(CA 2+) HELIX 1 1 GLY A 12 ALA A 20 1 9 HELIX 2 2 LYS A 32 ASN A 41 1 10 HELIX 3 3 SER A 56 GLU A 58 5 3 HELIX 4 4 PRO A 86 LYS A 101 1 16 HELIX 5 5 LYS A 112 MET A 115 5 4 HELIX 6 6 GLN A 117 GLY A 134 5 18 HELIX 7 7 ALA A 144 TYR A 147 5 4 HELIX 8 8 LYS A 163 LEU A 165 5 3 HELIX 9 9 PHE A 181 ASP A 183 5 3 HELIX 10 10 TRP A 186 ASN A 191 5 6 HELIX 11 11 GLY A 203 LYS A 205 5 3 HELIX 12 12 THR A 220 MET A 223 1 4 HELIX 13 13 GLY A 242 GLN A 244 5 3 HELIX 14 14 GLU A 269 LEU A 271 5 3 HELIX 15 15 VAL A 277 GLN A 284 1 8 HELIX 16 16 LEU A 297 GLY A 305 1 9 HELIX 17 17 VAL A 310 SER A 322 1 13 HELIX 18 18 GLY B 12 LYS B 19 1 8 HELIX 19 19 LYS B 32 ASN B 41 1 10 HELIX 20 20 ILE B 51 LYS B 53 5 3 HELIX 21 21 SER B 56 GLU B 58 5 3 HELIX 22 22 PRO B 86 LYS B 101 1 16 HELIX 23 23 LYS B 112 MET B 115 5 4 HELIX 24 24 GLN B 117 ASN B 132 5 16 HELIX 25 25 ALA B 144 ASP B 146 5 3 HELIX 26 26 LYS B 163 LEU B 165 5 3 HELIX 27 27 PHE B 181 ASP B 183 5 3 HELIX 28 28 TRP B 186 LEU B 188 5 3 HELIX 29 29 GLY B 203 LYS B 205 5 3 HELIX 30 30 THR B 220 MET B 223 1 4 HELIX 31 31 GLY B 242 GLN B 244 5 3 HELIX 32 32 GLU B 269 LEU B 271 5 3 HELIX 33 33 VAL B 277 ARG B 282 1 6 HELIX 34 34 LEU B 297 GLY B 305 1 9 HELIX 35 35 VAL B 310 SER B 322 1 13 SHEET 1 A 5 PHE A 105 ALA A 108 0 SHEET 2 A 5 GLY A 64 GLY A 67 1 N ILE A 65 O PHE A 105 SHEET 3 A 5 ASN A 2 LEU A 6 1 N ILE A 4 O GLY A 64 SHEET 4 A 5 ARG A 23 GLU A 29 1 N ARG A 23 O LEU A 3 SHEET 5 A 5 LYS A 45 LYS A 48 1 N LYS A 45 O ALA A 27 SHEET 1 B 3 GLU A 109 VAL A 111 0 SHEET 2 B 3 LYS A 154 ARG A 162 -1 N VAL A 156 O ASN A 110 SHEET 3 B 3 TYR A 135 ASN A 143 -1 N LEU A 142 O ARG A 155 SHEET 1 C 7 TYR B 135 ASN B 143 0 SHEET 2 C 7 LYS B 154 ARG B 162 -1 N PHE B 161 O ASP B 136 SHEET 3 C 7 PHE B 105 VAL B 111 -1 N ASN B 110 O VAL B 156 SHEET 4 C 7 GLY B 64 GLY B 67 1 N ILE B 65 O PHE B 105 SHEET 5 C 7 ASN B 2 SER B 5 1 N ILE B 4 O GLY B 64 SHEET 6 C 7 ARG B 23 GLU B 29 1 N ARG B 23 O LEU B 3 SHEET 7 C 7 LYS B 45 LYS B 48 1 N LYS B 45 O ALA B 27 SHEET 1 D 2 LEU B 255 SER B 258 0 SHEET 2 D 2 LEU B 261 LYS B 263 -1 N LYS B 263 O LEU B 255 SSBOND 1 CYS B 245 CYS B 280 1555 1555 2.97 LINK O3' DG F 9 P C49 F 10 1555 1555 1.58 LINK O3' C49 F 10 P DC F 11 1555 1555 1.61 LINK C6 C49 F 10 SG CYS A 71 1555 1555 1.78 LINK O3' DG M 10 P 5CM M 11 1555 1555 1.59 LINK O3' 5CM M 11 P DC M 12 1555 1555 1.60 LINK O3' DG G 9 P C49 G 10 1555 1555 1.60 LINK O3' C49 G 10 P DC G 11 1555 1555 1.60 LINK C6 C49 G 10 SG CYS B 71 1555 1555 1.78 LINK O3' DG N 10 P 5CM N 11 1555 1555 1.59 LINK O3' 5CM N 11 P DC N 12 1555 1555 1.62 LINK OD1 ASN A 166 CA CA A1001 1555 1555 2.11 LINK OD1 ASN B 166 CA CA B1002 1555 1555 2.37 SITE 1 DAA 8 DG F 8 DG F 9 C49 F 10 DC F 11 SITE 2 DAA 8 DC M 12 5CM M 11 DG M 10 DG M 9 SITE 1 DAB 8 DG G 8 DG G 9 C49 G 10 DC G 11 SITE 2 DAB 8 DC N 12 5CM N 11 DG N 10 DG N 9 SITE 1 AC1 2 ASN A 166 GLU B 233 SITE 1 AC2 2 ASN B 166 DG M 17 CRYST1 57.570 108.040 155.790 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 0.017370 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006419 0.00000