PDB Short entry for 5MHT HEADER TRANSFERASE/DNA 22-OCT-96 5MHT TITLE TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH TITLE 2 HEMIMETHYLATED DNA AND ADOHCY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*AP*TP*GP*(5CM) COMPND 3 P*GP*CP*TP*GP*AP*C)-3'); COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)- COMPND 8 3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PROTEIN (HHAI METHYLTRANSFERASE); COMPND 13 CHAIN: A; COMPND 14 SYNONYM: MODIFICATION METHYLASE HHAI, CYTOSINE-SPECIFIC COMPND 15 METHYLTRANSFERASE HHAI, M.HHAI; COMPND 16 EC: 2.1.1.7 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 HAEMOLYTICUS; SOURCE 7 ORGANISM_TAXID: 726 KEYWDS TRANSFERASE, METHYLTRANSFERASE, RESTRICTION SYSTEM, COMPLEX KEYWDS 2 (METHYLTRANSFERASE/DNA) EXPDTA X-RAY DIFFRACTION AUTHOR X.CHENG REVDAT 3 24-FEB-09 5MHT 1 VERSN REVDAT 2 01-APR-03 5MHT 1 JRNL REVDAT 1 23-JUL-97 5MHT 0 JRNL AUTH M.O'GARA,R.J.ROBERTS,X.CHENG JRNL TITL A STRUCTURAL BASIS FOR THE PREFERENTIAL BINDING OF JRNL TITL 2 HEMIMETHYLATED DNA BY HHAI DNA METHYLTRANSFERASE. JRNL REF J.MOL.BIOL. V. 263 597 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8918941 JRNL DOI 10.1006/JMBI.1996.0601 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.O'GARA,S.KLIMASAUSKAS,R.J.ROBERTS,X.CHENG REMARK 1 TITL ENZYMATIC C5-CYTOSINE METHYLATION OF DNA: REMARK 1 TITL 2 MECHANISTIC IMPLICATIONS OF NEW CRYSTAL STRUCTURES REMARK 1 TITL 3 FOR HHAI METHYLTRANSFERASE-DNA-ADOHCY COMPLEXES REMARK 1 REF J.MOL.BIOL. V. 261 634 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.KLIMASAUSKAS,S.KUMAR,R.J.ROBERTS,X.CHENG REMARK 1 TITL HHAI METHYLTRANSFERASE FLIPS ITS TARGET BASE OUT REMARK 1 TITL 2 OF THE DNA HELIX REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 76 357 1994 REMARK 1 REFN ISSN 0092-8674 REMARK 1 REFERENCE 3 REMARK 1 AUTH X.CHENG,S.KUMAR,J.POSFAI,J.W.PFLUGRATH,R.J.ROBERTS REMARK 1 TITL CRYSTAL STRUCTURE OF THE HHAI DNA REMARK 1 TITL 2 METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL- REMARK 1 TITL 3 L-METHIONINE REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 74 299 1993 REMARK 1 REFN ISSN 0092-8674 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 16743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : NULL 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1733 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 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 : 2734 REMARK 3 NUCLEIC ACID ATOMS : 493 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 112 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) : NULL 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 3.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 29.80 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: WATER MOLECULE 345 IS SURROUNDED BY REMARK 3 THREE POSITIVELY CHANGED RESIDUES: ARG 245, LYS 193, AND REMARK 3 SYMMETRY-RELATED LYS 290. HOWEVER, THE DENSITY IS NOT GOOD REMARK 3 ENOUGH TO IDENTIFY WHAT IT MIGHT BE. WATER MOLECULE 392 IS REMARK 3 SITUATED IN BETWEEN TWO DNA PHOSPHATE GROUPS OF A 430 D AND T REMARK 3 431 D. CA-ACETATE WAS USED AS BUFFER. HOWEVER, THE DENSITY IS REMARK 3 NOT GOOD ENOUGH TO DETERMINE WHETHER IT IS A CA(2+) FOR SURE. REMARK 4 REMARK 4 5MHT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293.00 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16761 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 (%): 65.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 8000, 50 MM CA-ACETATE, 50 REMARK 280 MM SODIUM CACODYLATE PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 49.93000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.82710 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 108.40000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 49.93000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 28.82710 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 108.40000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 49.93000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 28.82710 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 108.40000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 49.93000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 28.82710 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 108.40000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 49.93000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 28.82710 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 108.40000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 49.93000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 28.82710 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 108.40000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 57.65420 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 216.80000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 57.65420 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 216.80000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 57.65420 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 216.80000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 57.65420 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 216.80000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 57.65420 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 216.80000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 57.65420 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 216.80000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 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 C 402 C5' DC C 402 C4' 0.077 REMARK 500 DC C 402 O3' DC C 402 C3' 0.112 REMARK 500 DC C 402 N1 DC C 402 C2 0.063 REMARK 500 DC C 402 N3 DC C 402 C4 0.059 REMARK 500 DC C 403 C5' DC C 403 C4' 0.046 REMARK 500 DA C 404 N9 DA C 404 C4 0.047 REMARK 500 DT C 405 C5 DT C 405 C6 0.049 REMARK 500 DG C 406 C5' DG C 406 C4' 0.070 REMARK 500 DG C 406 N9 DG C 406 C4 0.077 REMARK 500 DG C 408 C4' DG C 408 C3' 0.064 REMARK 500 DG C 408 C5 DG C 408 N7 0.057 REMARK 500 DC C 409 C5' DC C 409 C4' 0.046 REMARK 500 DT C 410 C5' DT C 410 C4' 0.059 REMARK 500 DG C 411 C2 DG C 411 N3 0.060 REMARK 500 DA C 412 N3 DA C 412 C4 0.043 REMARK 500 DA C 412 N9 DA C 412 C4 0.037 REMARK 500 DG D 422 P DG D 422 O5' 0.081 REMARK 500 DG D 422 C5' DG D 422 C4' 0.102 REMARK 500 DG D 422 N9 DG D 422 C4 0.063 REMARK 500 DT D 423 C5' DT D 423 C4' 0.078 REMARK 500 DT D 423 C5 DT D 423 C7 0.066 REMARK 500 DG D 422 O3' DT D 423 P 0.082 REMARK 500 DA D 425 P DA D 425 O5' 0.073 REMARK 500 DA D 425 N9 DA D 425 C4 0.052 REMARK 500 DG D 426 N9 DG D 426 C4 0.070 REMARK 500 DA D 425 O3' DG D 426 P -0.073 REMARK 500 DC D 427 O4' DC D 427 C4' -0.070 REMARK 500 DC D 427 C1' DC D 427 N1 0.084 REMARK 500 DC D 427 C2 DC D 427 N3 0.066 REMARK 500 DG D 428 C6 DG D 428 N1 -0.045 REMARK 500 DC D 429 C5' DC D 429 C4' 0.053 REMARK 500 DA D 430 C5' DA D 430 C4' 0.085 REMARK 500 DG D 432 C2 DG D 432 N3 0.052 REMARK 500 DG D 432 N3 DG D 432 C4 0.052 REMARK 500 DG D 432 C6 DG D 432 N1 0.045 REMARK 500 DG D 432 N9 DG D 432 C4 0.048 REMARK 500 DG D 433 C2 DG D 433 N3 0.055 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 DC C 402 C4' - C3' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 DC C 402 N1 - C2 - O2 ANGL. DEV. = 6.7 DEGREES REMARK 500 DC C 402 N3 - C2 - O2 ANGL. DEV. = -6.9 DEGREES REMARK 500 DC C 403 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC C 403 N3 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC C 403 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC C 402 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 DA C 404 C1' - O4' - C4' ANGL. DEV. = 5.0 DEGREES REMARK 500 DA C 404 O4' - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 DA C 404 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA C 404 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT C 405 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 DT C 405 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT C 405 C6 - N1 - C2 ANGL. DEV. = -3.0 DEGREES REMARK 500 DT C 405 N1 - C2 - N3 ANGL. DEV. = 5.6 DEGREES REMARK 500 DT C 405 C4 - C5 - C6 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT C 405 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT C 405 C5 - C4 - O4 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT C 405 C4 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG C 406 C1' - O4' - C4' ANGL. DEV. = 4.3 DEGREES REMARK 500 DG C 406 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG C 406 O4' - C1' - C2' ANGL. DEV. = -10.9 DEGREES REMARK 500 DG C 406 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG C 406 N3 - C4 - C5 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG C 406 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG C 406 N3 - C2 - N2 ANGL. DEV. = 5.9 DEGREES REMARK 500 DG C 406 N1 - C6 - O6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG C 408 P - O5' - C5' ANGL. DEV. = 10.9 DEGREES REMARK 500 DG C 408 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC C 409 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 DC C 409 O4' - C1' - C2' ANGL. DEV. = -7.7 DEGREES REMARK 500 DC C 409 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC C 409 N3 - C4 - C5 ANGL. DEV. = -2.9 DEGREES REMARK 500 DT C 410 C5' - C4' - O4' ANGL. DEV. = 9.3 DEGREES REMARK 500 DT C 410 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT C 410 C6 - N1 - C2 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT C 410 N1 - C2 - N3 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT C 410 C4 - C5 - C6 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG C 411 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 DG C 411 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA C 412 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 DA C 412 C1' - O4' - C4' ANGL. DEV. = -7.1 DEGREES REMARK 500 DA C 412 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG C 411 C3' - O3' - P ANGL. DEV. = 12.2 DEGREES REMARK 500 DG D 422 C1' - O4' - C4' ANGL. DEV. = 7.4 DEGREES REMARK 500 DG D 422 C3' - C2' - C1' ANGL. DEV. = 10.8 DEGREES REMARK 500 DG D 422 O4' - C1' - C2' ANGL. DEV. = -7.7 DEGREES REMARK 500 DG D 422 O4' - C1' - N9 ANGL. DEV. = 10.0 DEGREES REMARK 500 DG D 422 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG D 422 C8 - N9 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 88 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 GLN A 8 -16.71 -48.95 REMARK 500 TYR A 37 144.45 -170.88 REMARK 500 GLU A 40 134.05 -176.10 REMARK 500 ASP A 60 107.35 -14.33 REMARK 500 ASP A 144 45.51 81.07 REMARK 500 VAL A 202 -98.68 -114.50 REMARK 500 GLU A 203 -63.95 67.19 REMARK 500 LEU A 212 105.17 -44.48 REMARK 500 PHE A 259 50.31 -100.53 REMARK 500 LYS A 261 -12.20 50.81 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 DG D 422 0.07 SIDE_CHAIN REMARK 500 DC D 424 0.07 SIDE_CHAIN REMARK 500 DG D 428 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 409 DISTANCE = 5.35 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 328 DBREF 5MHT A 1 327 UNP P05102 MTH1_HAEHA 1 327 DBREF 5MHT C 402 413 PDB 5MHT 5MHT 402 413 DBREF 5MHT D 422 433 PDB 5MHT 5MHT 422 433 SEQRES 1 C 12 DC DC DA DT DG 5CM DG DC DT DG DA DC SEQRES 1 D 12 DG DT DC DA DG DC DG DC DA DT DG DG SEQRES 1 A 327 MET ILE GLU ILE LYS ASP LYS GLN LEU THR GLY LEU ARG SEQRES 2 A 327 PHE ILE ASP LEU PHE ALA GLY LEU GLY GLY PHE ARG LEU SEQRES 3 A 327 ALA LEU GLU SER CYS GLY ALA GLU CYS VAL TYR SER ASN SEQRES 4 A 327 GLU TRP ASP LYS TYR ALA GLN GLU VAL TYR GLU MET ASN SEQRES 5 A 327 PHE GLY GLU LYS PRO GLU GLY ASP ILE THR GLN VAL ASN SEQRES 6 A 327 GLU LYS THR ILE PRO ASP HIS ASP ILE LEU CYS ALA GLY SEQRES 7 A 327 PHE PRO CYS GLN ALA PHE SER ILE SER GLY LYS GLN LYS SEQRES 8 A 327 GLY PHE GLU ASP SER ARG GLY THR LEU PHE PHE ASP ILE SEQRES 9 A 327 ALA ARG ILE VAL ARG GLU LYS LYS PRO LYS VAL VAL PHE SEQRES 10 A 327 MET GLU ASN VAL LYS ASN PHE ALA SER HIS ASP ASN GLY SEQRES 11 A 327 ASN THR LEU GLU VAL VAL LYS ASN THR MET ASN GLU LEU SEQRES 12 A 327 ASP TYR SER PHE HIS ALA LYS VAL LEU ASN ALA LEU ASP SEQRES 13 A 327 TYR GLY ILE PRO GLN LYS ARG GLU ARG ILE TYR MET ILE SEQRES 14 A 327 CYS PHE ARG ASN ASP LEU ASN ILE GLN ASN PHE GLN PHE SEQRES 15 A 327 PRO LYS PRO PHE GLU LEU ASN THR PHE VAL LYS ASP LEU SEQRES 16 A 327 LEU LEU PRO ASP SER GLU VAL GLU HIS LEU VAL ILE ASP SEQRES 17 A 327 ARG LYS ASP LEU VAL MET THR ASN GLN GLU ILE GLU GLN SEQRES 18 A 327 THR THR PRO LYS THR VAL ARG LEU GLY ILE VAL GLY LYS SEQRES 19 A 327 GLY GLY GLN GLY GLU ARG ILE TYR SER THR ARG GLY ILE SEQRES 20 A 327 ALA ILE THR LEU SER ALA TYR GLY GLY GLY ILE PHE ALA SEQRES 21 A 327 LYS THR GLY GLY TYR LEU VAL ASN GLY LYS THR ARG LYS SEQRES 22 A 327 LEU HIS PRO ARG GLU CYS ALA ARG VAL MET GLY TYR PRO SEQRES 23 A 327 ASP SER TYR LYS VAL HIS PRO SER THR SER GLN ALA TYR SEQRES 24 A 327 LYS GLN PHE GLY ASN SER VAL VAL ILE ASN VAL LEU GLN SEQRES 25 A 327 TYR ILE ALA TYR ASN ILE GLY SER SER LEU ASN PHE LYS SEQRES 26 A 327 PRO TYR MODRES 5MHT 5CM C 407 DC HET 5CM C 407 20 HET SAH A 328 26 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 1 5CM C10 H16 N3 O7 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 HOH *112(H2 O) HELIX 1 1 GLY A 23 CYS A 31 1 9 HELIX 2 2 LYS A 43 PHE A 53 1 11 HELIX 3 3 ILE A 61 GLN A 63 5 3 HELIX 4 4 GLY A 92 GLU A 94 5 3 HELIX 5 5 LEU A 100 LYS A 111 5 12 HELIX 6 6 LYS A 122 ALA A 125 5 4 HELIX 7 7 HIS A 127 GLU A 142 5 16 HELIX 8 8 ALA A 154 ASP A 156 5 3 HELIX 9 9 ASN A 173 LEU A 175 5 3 HELIX 10 10 VAL A 192 ASP A 194 5 3 HELIX 11 11 ASP A 199 GLU A 201 5 3 HELIX 12 12 PRO A 276 MET A 283 1 8 HELIX 13 13 THR A 295 ASN A 304 1 10 HELIX 14 14 ILE A 308 LEU A 322 1 15 SHEET 1 A 6 HIS A 148 ASN A 153 0 SHEET 2 A 6 GLU A 164 PHE A 171 -1 N ILE A 169 O HIS A 148 SHEET 3 A 6 VAL A 115 VAL A 121 -1 N ASN A 120 O ILE A 166 SHEET 4 A 6 ILE A 74 ALA A 77 1 N LEU A 75 O VAL A 115 SHEET 5 A 6 ARG A 13 LEU A 17 1 N ILE A 15 O ILE A 74 SHEET 6 A 6 GLU A 34 ASN A 39 1 N GLU A 34 O PHE A 14 SHEET 1 B 4 LYS A 270 LYS A 273 0 SHEET 2 B 4 GLY A 264 VAL A 267 -1 N VAL A 267 O LYS A 270 SHEET 3 B 4 ARG A 240 SER A 243 1 N TYR A 242 O GLY A 264 SHEET 4 B 4 ARG A 228 ILE A 231 -1 N GLY A 230 O ILE A 241 LINK O3' DG C 406 P 5CM C 407 1555 1555 1.67 LINK O3' 5CM C 407 P DG C 408 1555 1555 1.67 SITE 1 AC1 19 PHE A 18 ALA A 19 GLY A 20 LEU A 21 SITE 2 AC1 19 GLY A 23 ASN A 39 GLU A 40 TRP A 41 SITE 3 AC1 19 ASP A 60 ILE A 61 GLY A 78 ASN A 304 SITE 4 AC1 19 SER A 305 HOH A 332 HOH A 333 HOH A 338 SITE 5 AC1 19 HOH A 340 HOH A 367 HOH A 384 CRYST1 99.860 99.860 325.200 90.00 90.00 120.00 H 3 2 18 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 0.010014 0.005782 0.000000 0.00000 SCALE2 0.000000 0.011563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003075 0.00000