PDB Short entry for 1YF3 HEADER TRANSFERASE/DNA 30-DEC-04 1YF3 TITLE T4DAM IN COMPLEX WITH ADOHCY AND 13-MER OLIGONUCLEOTIDE MAKING NON- TITLE 2 AND SEMI-SPECIFIC (~1/4) CONTACT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3'; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3'; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA ADENINE METHYLASE; COMPND 11 CHAIN: A, B; COMPND 12 SYNONYM: DEOXYADENOSYL-METHYLTRANSFERASE, M.ECOT4DAM; COMPND 13 EC: 2.1.1.72; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED BY NEW ENGLAND BIOLABS; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHESIZED BY NEW ENGLAND BIOLABS; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 9 ORGANISM_TAXID: 10665; SOURCE 10 GENE: DAM; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: GM 2971; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PJW2 KEYWDS T4DAM, METHYLTRANSFERASE, DNA, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,K.LIEBERT,S.HATTMAN,A.JELTSCH,X.CHENG REVDAT 6 23-AUG-23 1YF3 1 REMARK REVDAT 5 11-OCT-17 1YF3 1 REMARK REVDAT 4 13-JUL-11 1YF3 1 VERSN REVDAT 3 24-FEB-09 1YF3 1 VERSN REVDAT 2 25-JUL-06 1YF3 1 REMARK REVDAT 1 17-MAY-05 1YF3 0 JRNL AUTH J.R.HORTON,K.LIEBERT,S.HATTMAN,A.JELTSCH,X.CHENG JRNL TITL TRANSITION FROM NONSPECIFIC TO SPECIFIC DNA INTERACTIONS JRNL TITL 2 ALONG THE SUBSTRATE-RECOGNITION PATHWAY OF DAM JRNL TITL 3 METHYLTRANSFERASE. JRNL REF CELL(CAMBRIDGE,MASS.) V. 121 349 2005 JRNL REFN ISSN 0092-8674 JRNL PMID 15882618 JRNL DOI 10.1016/J.CELL.2005.02.021 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.YANG,J.R.HORTON,L.ZHOU,X.J.ZHANG,A.DONG,X.ZHANG, REMARK 1 AUTH 2 S.L.SCHLAGMAN,V.KOSSYKH,X.CHENG REMARK 1 TITL STRUCTURE OF THE BACTERIOPHAGE T4 DNA ADENINE REMARK 1 TITL 2 METHYLTRANSFERASE REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 10 849 2003 REMARK 1 REFN ISSN 1545-9993 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 28663 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2825 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) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.37 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 237 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4027 REMARK 3 NUCLEIC ACID ATOMS : 509 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.65000 REMARK 3 B22 (A**2) : 9.35000 REMARK 3 B33 (A**2) : -10.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.55000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 28.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.024 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1YF3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031443. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2826 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29474 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.18700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: GLRF REMARK 200 STARTING MODEL: PDB ENTRY 1Q0S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG MME 5000, CITRATE-PHOSPHATE, REMARK 280 AMMONIUM SULPHATE, PH 6.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 62.90000 REMARK 290 SMTRY3 2 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 APPLY THE FOLLOWING TO CHAINS: C, D, A, 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 TYR B 239 REMARK 465 VAL B 240 REMARK 465 PHE B 241 REMARK 465 ASN B 242 REMARK 465 ILE B 243 REMARK 465 TYR B 244 REMARK 465 HIS B 245 REMARK 465 SER B 246 REMARK 465 LYS B 247 REMARK 465 GLU B 248 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 DA C 400 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA C 400 C2 N3 C4 REMARK 470 DC C 401 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC C 401 C6 REMARK 470 GLU A 53 CB CG CD OE1 OE2 REMARK 470 LYS A 75 CB CG CD CE NZ REMARK 470 GLU A 92 CG CD OE1 OE2 REMARK 470 LYS A 134 CB CG CD CE NZ REMARK 470 ASN A 135 CG OD1 ND2 REMARK 470 SER A 136 OG REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 LYS A 161 CB CG CD CE NZ REMARK 470 LEU A 163 CB CG CD1 CD2 REMARK 470 ASP A 164 CB CG OD1 OD2 REMARK 470 ASP A 180 CB CG OD1 OD2 REMARK 470 LYS A 183 CG CD CE NZ REMARK 470 ASP A 188 CG OD1 OD2 REMARK 470 GLU A 189 CG CD OE1 OE2 REMARK 470 LYS A 191 CB CG CD CE NZ REMARK 470 ASN A 195 CB CG OD1 ND2 REMARK 470 ASP A 202 CB CG OD1 OD2 REMARK 470 HIS A 216 CB CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 218 CB CG CD CE NZ REMARK 470 GLU A 219 CG CD OE1 OE2 REMARK 470 GLU A 225 CG CD OE1 OE2 REMARK 470 LYS A 229 CG CD CE NZ REMARK 470 LYS A 237 CB CG CD CE NZ REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 LYS A 247 CB CG CD CE NZ REMARK 470 GLU A 248 CB CG CD OE1 OE2 REMARK 470 LYS A 249 CB CG CD CE NZ REMARK 470 GLU B 17 CG CD OE1 OE2 REMARK 470 LYS B 72 CG CD CE NZ REMARK 470 LYS B 75 CB CG CD CE NZ REMARK 470 GLU B 85 CG CD OE1 OE2 REMARK 470 ASP B 148 CG OD1 OD2 REMARK 470 LYS B 161 CB CG CD CE NZ REMARK 470 GLU B 214 CB CG CD OE1 OE2 REMARK 470 LYS B 218 CB CG CD CE NZ REMARK 470 GLU B 219 CB CG CD OE1 OE2 REMARK 470 GLU B 225 CB CG CD OE1 OE2 REMARK 470 SER B 227 OG REMARK 470 LYS B 228 CG CD CE NZ REMARK 470 LYS B 233 CG CD CE NZ REMARK 470 ASN B 236 CB CG OD1 ND2 REMARK 470 LYS B 237 CB CG CD CE NZ REMARK 470 LYS B 238 CG CD CE NZ REMARK 470 LYS B 249 CG CD CE NZ REMARK 470 ASN B 250 CB CG OD1 ND2 REMARK 470 THR B 252 OG1 CG2 REMARK 470 ASP B 253 CG OD1 OD2 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 52 94.43 -66.91 REMARK 500 LYS A 134 10.66 -61.25 REMARK 500 ALA A 179 127.69 -170.60 REMARK 500 ASN A 211 -175.48 179.50 REMARK 500 HIS A 215 129.73 -172.18 REMARK 500 HIS A 216 -18.43 56.47 REMARK 500 ASN A 220 70.95 -104.32 REMARK 500 LYS A 228 -4.29 -59.23 REMARK 500 GLU A 248 -85.54 139.47 REMARK 500 LYS A 249 74.68 -67.32 REMARK 500 ASN A 250 -144.47 -109.38 REMARK 500 LYS B 183 -5.00 -59.19 REMARK 500 SER B 186 166.81 179.24 REMARK 500 ASN B 211 -173.19 -176.19 REMARK 500 TYR B 230 -166.76 -115.40 REMARK 500 ASN B 236 96.36 -59.35 REMARK 500 LYS B 237 -134.46 -137.07 REMARK 500 ASN B 250 -124.12 -136.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 497 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 498 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q0S RELATED DB: PDB REMARK 900 BINARY STRUCTURE OF T4DAM WITH ADOHCY REMARK 900 RELATED ID: 1Q0T RELATED DB: PDB REMARK 900 TERNARY STRUCTURE OF T4DAM WITH ADOHCY AND DNA REMARK 900 RELATED ID: 1YFJ RELATED DB: PDB REMARK 900 RELATED ID: 1YFL RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 1) AUTHOR STATES THAT Q139R, Y140F AND Q209L REFLECT REMARK 999 CONFLICTS BETWEEN DEPOSITED PROTEIN SEQUENCE AND REMARK 999 TRANSLATED DEPOSITED DNA-->PROTEIN SEQUENCE. FROM THEIR REMARK 999 ELECTRON DENSITY, IT APPEARS THE TRANSLATED DNA SEQUENCE REMARK 999 IS CORRECT. REMARK 999 2) RESIDUE 119 WERE MODELED (FOR BOTH A AND B) AS TYR IN REMARK 999 THIS STRUCTURE AS THE ELECTRON DENSITY DOES NOT SUPPORT REMARK 999 AN ASP HERE. THE ELECTRON DENSTIY FOR B119 FITS A TYR REMARK 999 RESIDUE PERFECTLY. DBREF 1YF3 A 1 259 UNP P04392 DMA_BPT4 1 259 DBREF 1YF3 B 1 259 UNP P04392 DMA_BPT4 1 259 DBREF 1YF3 C 400 412 PDB 1YF3 1YF3 400 412 DBREF 1YF3 D 422 434 PDB 1YF3 1YF3 422 434 SEQADV 1YF3 TYR A 119 UNP P04392 ASP 119 SEE REMARK 999 SEQADV 1YF3 ARG A 139 UNP P04392 GLN 139 SEE REMARK 999 SEQADV 1YF3 PHE A 140 UNP P04392 TYR 140 SEE REMARK 999 SEQADV 1YF3 LEU A 209 UNP P04392 GLN 209 SEE REMARK 999 SEQADV 1YF3 TYR B 119 UNP P04392 ASP 119 SEE REMARK 999 SEQADV 1YF3 ARG B 139 UNP P04392 GLN 139 SEE REMARK 999 SEQADV 1YF3 PHE B 140 UNP P04392 TYR 140 SEE REMARK 999 SEQADV 1YF3 LEU B 209 UNP P04392 GLN 209 SEE REMARK 999 SEQRES 1 C 13 DA DC DC DA DT DG DA DT DC DT DG DA DC SEQRES 1 D 13 DT DG DT DC DA DG DA DT DC DA DT DG DG SEQRES 1 A 259 MET LEU GLY ALA ILE ALA TYR THR GLY ASN LYS GLN SER SEQRES 2 A 259 LEU LEU PRO GLU LEU LYS SER HIS PHE PRO LYS TYR ASN SEQRES 3 A 259 ARG PHE VAL ASP LEU PHE CYS GLY GLY LEU SER VAL SER SEQRES 4 A 259 LEU ASN VAL ASN GLY PRO VAL LEU ALA ASN ASP ILE GLN SEQRES 5 A 259 GLU PRO ILE ILE GLU MET TYR LYS ARG LEU ILE ASN VAL SEQRES 6 A 259 SER TRP ASP ASP VAL LEU LYS VAL ILE LYS GLN TYR LYS SEQRES 7 A 259 LEU SER LYS THR SER LYS GLU GLU PHE LEU LYS LEU ARG SEQRES 8 A 259 GLU ASP TYR ASN LYS THR ARG ASP PRO LEU LEU LEU TYR SEQRES 9 A 259 VAL LEU HIS PHE HIS GLY PHE SER ASN MET ILE ARG ILE SEQRES 10 A 259 ASN TYR LYS GLY ASN PHE THR THR PRO PHE GLY LYS ARG SEQRES 11 A 259 THR ILE ASN LYS ASN SER GLU LYS ARG PHE ASN HIS PHE SEQRES 12 A 259 LYS GLN ASN CYS ASP LYS ILE ILE PHE SER SER LEU HIS SEQRES 13 A 259 PHE LYS ASP VAL LYS ILE LEU ASP GLY ASP PHE VAL TYR SEQRES 14 A 259 VAL ASP PRO PRO TYR LEU ILE THR VAL ALA ASP TYR ASN SEQRES 15 A 259 LYS PHE TRP SER GLU ASP GLU GLU LYS ASP LEU LEU ASN SEQRES 16 A 259 LEU LEU ASP SER LEU ASN ASP ARG GLY ILE LYS PHE GLY SEQRES 17 A 259 LEU SER ASN VAL LEU GLU HIS HIS GLY LYS GLU ASN THR SEQRES 18 A 259 LEU LEU LYS GLU TRP SER LYS LYS TYR ASN VAL LYS HIS SEQRES 19 A 259 LEU ASN LYS LYS TYR VAL PHE ASN ILE TYR HIS SER LYS SEQRES 20 A 259 GLU LYS ASN GLY THR ASP GLU VAL TYR ILE PHE ASN SEQRES 1 B 259 MET LEU GLY ALA ILE ALA TYR THR GLY ASN LYS GLN SER SEQRES 2 B 259 LEU LEU PRO GLU LEU LYS SER HIS PHE PRO LYS TYR ASN SEQRES 3 B 259 ARG PHE VAL ASP LEU PHE CYS GLY GLY LEU SER VAL SER SEQRES 4 B 259 LEU ASN VAL ASN GLY PRO VAL LEU ALA ASN ASP ILE GLN SEQRES 5 B 259 GLU PRO ILE ILE GLU MET TYR LYS ARG LEU ILE ASN VAL SEQRES 6 B 259 SER TRP ASP ASP VAL LEU LYS VAL ILE LYS GLN TYR LYS SEQRES 7 B 259 LEU SER LYS THR SER LYS GLU GLU PHE LEU LYS LEU ARG SEQRES 8 B 259 GLU ASP TYR ASN LYS THR ARG ASP PRO LEU LEU LEU TYR SEQRES 9 B 259 VAL LEU HIS PHE HIS GLY PHE SER ASN MET ILE ARG ILE SEQRES 10 B 259 ASN TYR LYS GLY ASN PHE THR THR PRO PHE GLY LYS ARG SEQRES 11 B 259 THR ILE ASN LYS ASN SER GLU LYS ARG PHE ASN HIS PHE SEQRES 12 B 259 LYS GLN ASN CYS ASP LYS ILE ILE PHE SER SER LEU HIS SEQRES 13 B 259 PHE LYS ASP VAL LYS ILE LEU ASP GLY ASP PHE VAL TYR SEQRES 14 B 259 VAL ASP PRO PRO TYR LEU ILE THR VAL ALA ASP TYR ASN SEQRES 15 B 259 LYS PHE TRP SER GLU ASP GLU GLU LYS ASP LEU LEU ASN SEQRES 16 B 259 LEU LEU ASP SER LEU ASN ASP ARG GLY ILE LYS PHE GLY SEQRES 17 B 259 LEU SER ASN VAL LEU GLU HIS HIS GLY LYS GLU ASN THR SEQRES 18 B 259 LEU LEU LYS GLU TRP SER LYS LYS TYR ASN VAL LYS HIS SEQRES 19 B 259 LEU ASN LYS LYS TYR VAL PHE ASN ILE TYR HIS SER LYS SEQRES 20 B 259 GLU LYS ASN GLY THR ASP GLU VAL TYR ILE PHE ASN HET SAH A 400 26 HET GOL A 498 6 HET SAH B 401 26 HET GOL B 497 6 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SAH 2(C14 H20 N6 O5 S) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 9 HOH *204(H2 O) HELIX 1 1 LEU A 14 HIS A 21 1 8 HELIX 2 2 VAL A 38 VAL A 42 5 5 HELIX 3 3 GLN A 52 ILE A 63 1 12 HELIX 4 4 SER A 66 TYR A 77 1 12 HELIX 5 5 SER A 83 ARG A 98 1 16 HELIX 6 6 ASP A 99 PHE A 108 1 10 HELIX 7 7 GLY A 110 MET A 114 5 5 HELIX 8 8 ASN A 135 CYS A 147 1 13 HELIX 9 9 HIS A 156 VAL A 160 5 5 HELIX 10 10 ALA A 179 TRP A 185 5 7 HELIX 11 11 SER A 186 ASP A 202 1 17 HELIX 12 12 ASN A 220 LYS A 228 1 9 HELIX 13 13 ASN A 236 HIS A 245 1 10 HELIX 14 14 LEU B 14 SER B 20 1 7 HELIX 15 15 VAL B 38 VAL B 42 5 5 HELIX 16 16 GLN B 52 ILE B 63 1 12 HELIX 17 17 SER B 66 LYS B 78 1 13 HELIX 18 18 SER B 83 ARG B 98 1 16 HELIX 19 19 ASP B 99 PHE B 108 1 10 HELIX 20 20 HIS B 109 MET B 114 5 6 HELIX 21 21 ASN B 133 CYS B 147 1 15 HELIX 22 22 HIS B 156 VAL B 160 5 5 HELIX 23 23 ALA B 179 TRP B 185 5 7 HELIX 24 24 SER B 186 ARG B 203 1 18 HELIX 25 25 ASN B 220 LYS B 229 1 10 SHEET 1 A 7 ILE A 150 SER A 153 0 SHEET 2 A 7 VAL A 46 ASN A 49 1 N VAL A 46 O ILE A 151 SHEET 3 A 7 ARG A 27 ASP A 30 1 N ASP A 30 O LEU A 47 SHEET 4 A 7 ASP A 166 VAL A 170 1 O PHE A 167 N VAL A 29 SHEET 5 A 7 LYS A 206 VAL A 212 1 O GLY A 208 N VAL A 170 SHEET 6 A 7 GLU A 254 PHE A 258 -1 O VAL A 255 N ASN A 211 SHEET 7 A 7 ASN A 231 HIS A 234 -1 N ASN A 231 O PHE A 258 SHEET 1 B 2 GLU A 214 HIS A 215 0 SHEET 2 B 2 LYS A 218 GLU A 219 -1 O LYS A 218 N HIS A 215 SHEET 1 C 7 ILE B 150 SER B 153 0 SHEET 2 C 7 VAL B 46 ASN B 49 1 N ALA B 48 O SER B 153 SHEET 3 C 7 ARG B 27 ASP B 30 1 N PHE B 28 O LEU B 47 SHEET 4 C 7 ASP B 166 VAL B 170 1 O PHE B 167 N VAL B 29 SHEET 5 C 7 LYS B 206 VAL B 212 1 O GLY B 208 N VAL B 170 SHEET 6 C 7 GLU B 254 PHE B 258 -1 O ILE B 257 N LEU B 209 SHEET 7 C 7 ASN B 231 HIS B 234 -1 N ASN B 231 O PHE B 258 SHEET 1 D 2 GLU B 214 HIS B 215 0 SHEET 2 D 2 LYS B 218 GLU B 219 -1 O LYS B 218 N HIS B 215 CISPEP 1 GLY A 44 PRO A 45 0 -0.36 CISPEP 2 GLY B 44 PRO B 45 0 -0.09 SITE 1 AC1 17 TYR A 7 ASN A 10 LYS A 11 PHE A 32 SITE 2 AC1 17 CYS A 33 GLY A 34 GLY A 35 SER A 37 SITE 3 AC1 17 ASP A 50 ILE A 51 GLN A 52 HIS A 156 SITE 4 AC1 17 PHE A 157 ASP A 171 PHE A 184 HOH A 499 SITE 5 AC1 17 HOH A 510 SITE 1 AC2 20 TYR B 7 ASN B 10 LYS B 11 PHE B 32 SITE 2 AC2 20 CYS B 33 GLY B 34 GLY B 35 SER B 37 SITE 3 AC2 20 ASP B 50 ILE B 51 GLN B 52 LEU B 155 SITE 4 AC2 20 HIS B 156 PHE B 157 ASP B 171 PRO B 173 SITE 5 AC2 20 TYR B 181 PHE B 184 HOH B 502 HOH B 505 SITE 1 AC3 7 TYR B 7 THR B 8 GLN B 52 MET B 114 SITE 2 AC3 7 ILE B 115 TYR B 181 HOH B 512 SITE 1 AC4 5 TYR A 7 THR A 8 GLN A 52 MET A 114 SITE 2 AC4 5 ILE A 115 CRYST1 38.900 125.800 73.200 90.00 104.70 90.00 P 1 21 1 4 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 0.025707 0.000000 0.006744 0.00000 SCALE2 0.000000 0.007949 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014123 0.00000