HEADER OXIDOREDUCTASE/DNA 23-JUL-13 4LT5 TITLE STRUCTURE OF A NAEGLERIA TET-LIKE DIOXYGENASE IN COMPLEX WITH 5- TITLE 2 METHYLCYTOSINE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAEGLERIA TET-LIKE DIOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAEGLERIA GRUBERI; SOURCE 3 ORGANISM_COMMON: AMOEBA; SOURCE 4 ORGANISM_TAXID: 5762; SOURCE 5 GENE: NAEGRDRAFT_55029; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3)-GOLD CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: RIL-CODON PLUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PXC1010; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHESIS; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: SYNTHESIS KEYWDS 5-METHYLCYTOSINE, DIOXYGENASE-DNA COMPLEX, OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.HASHIMOTO,J.E.PAIS,X.ZHANG,L.SALEH,Z.Q.FU,N.DAI,I.R.CORREA, AUTHOR 2 R.J.ROBERTS,Y.ZHENG,X.CHENG REVDAT 6 28-FEB-24 4LT5 1 REMARK SEQADV LINK REVDAT 5 15-NOV-17 4LT5 1 REMARK REVDAT 4 05-MAR-14 4LT5 1 JRNL REVDAT 3 05-FEB-14 4LT5 1 JRNL REVDAT 2 25-DEC-13 4LT5 1 JRNL REVDAT 1 18-DEC-13 4LT5 0 JRNL AUTH H.HASHIMOTO,J.E.PAIS,X.ZHANG,L.SALEH,Z.Q.FU,N.DAI, JRNL AUTH 2 I.R.CORREA,Y.ZHENG,X.CHENG JRNL TITL STRUCTURE OF A NAEGLERIA TET-LIKE DIOXYGENASE IN COMPLEX JRNL TITL 2 WITH 5-METHYLCYTOSINE DNA. JRNL REF NATURE V. 506 391 2014 JRNL REFN ISSN 0028-0836 JRNL PMID 24390346 JRNL DOI 10.1038/NATURE12905 REMARK 2 REMARK 2 RESOLUTION. 2.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17321 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 869 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 29.5481 - 5.2493 1.00 2849 174 0.1760 0.1661 REMARK 3 2 5.2493 - 4.1703 1.00 2805 87 0.1540 0.1717 REMARK 3 3 4.1703 - 3.6442 1.00 2708 174 0.1896 0.2301 REMARK 3 4 3.6442 - 3.3115 1.00 2702 174 0.2278 0.2856 REMARK 3 5 3.3115 - 3.0744 1.00 2747 87 0.2521 0.2620 REMARK 3 6 3.0744 - 2.8933 0.99 2641 173 0.2938 0.3194 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.98 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 : 0.006 2894 REMARK 3 ANGLE : 0.675 4027 REMARK 3 CHIRALITY : 0.041 435 REMARK 3 PLANARITY : 0.003 412 REMARK 3 DIHEDRAL : 20.072 1097 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 4LT5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081053. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-12; 06-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.5; 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 22-BM; 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0; 0.91931 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL - LIQUOR NITROGEN REMARK 200 COOLED; NULL REMARK 200 OPTICS : ROSENBAUM-ROCK DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR: LIQUID NITROGEN REMARK 200 COOLED; SAGITALLY FOCUSING 2ND REMARK 200 CRYSTAL, ROSENBAUM-ROCK VERTICAL REMARK 200 FOCUSING MIRROR; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD; MARMOSAIC REMARK 200 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17328 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.890 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.78300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SGXPRO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULFATE, 0.1 M BISTRIS REMARK 280 -HCL, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K. REMARK 280 20% (W/V) POLYETHYLENE GLYCOL 3350, AND 0.2 M SODIUM CITRATE, PH REMARK 280 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 41.97700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.19200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.32400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 83.19200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.97700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.32400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.97700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.32400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 83.19200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.32400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.97700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 83.19200 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: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 O2 SO4 A 412 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 560 LIES ON A SPECIAL POSITION. 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 MET A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 THR A 2 REMARK 465 THR A 3 REMARK 465 PHE A 4 REMARK 465 LYS A 5 REMARK 465 GLN A 6 REMARK 465 GLN A 7 REMARK 465 THR A 8 REMARK 465 ILE A 9 REMARK 465 LYS A 10 REMARK 465 GLU A 11 REMARK 465 LYS A 12 REMARK 465 GLU A 13 REMARK 465 THR A 14 REMARK 465 LYS A 15 REMARK 465 ARG A 16 REMARK 465 LYS A 17 REMARK 465 TYR A 18 REMARK 465 CYS A 19 REMARK 465 ILE A 20 REMARK 465 LYS A 21 REMARK 465 GLY A 22 REMARK 465 THR A 23 REMARK 465 THR A 24 REMARK 465 ALA A 25 REMARK 465 ASN A 26 REMARK 465 LEU A 27 REMARK 465 THR A 28 REMARK 465 GLN A 29 REMARK 465 THR A 30 REMARK 465 HIS A 31 REMARK 465 PRO A 32 REMARK 465 ASN A 33 REMARK 465 GLY A 34 REMARK 465 PRO A 35 REMARK 465 VAL A 36 REMARK 465 CYS A 37 REMARK 465 VAL A 38 REMARK 465 ASN A 39 REMARK 465 ARG A 40 REMARK 465 GLY A 41 REMARK 465 GLU A 42 REMARK 465 GLU A 43 REMARK 465 VAL A 44 REMARK 465 ALA A 45 REMARK 465 ASN A 46 REMARK 465 THR A 47 REMARK 465 THR A 48 REMARK 465 THR A 49 REMARK 465 LEU A 50 REMARK 465 LEU A 51 REMARK 465 ASP A 52 REMARK 465 SER A 53 REMARK 465 GLY A 54 REMARK 465 GLY A 55 REMARK 465 GLY A 56 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 ILE A 57 CG1 CG2 CD1 REMARK 470 LYS A 321 CG CD CE NZ 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 22 O4' - C1' - N1 ANGL. DEV. = 2.0 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 ASN A 114 71.18 53.15 REMARK 500 SER A 186 88.99 -153.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 229 NE2 REMARK 620 2 ASP A 231 OD2 106.6 REMARK 620 3 HIS A 279 NE2 86.0 101.4 REMARK 620 4 OGA A 413 O2 99.6 101.2 154.1 REMARK 620 5 OGA A 413 O2' 100.9 152.3 77.1 77.1 REMARK 620 6 HOH A 414 O 160.4 54.5 92.6 90.3 97.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 102 DBREF 4LT5 A 2 321 UNP D2W6T1 D2W6T1_NAEGR 2 321 DBREF 4LT5 B 1 14 PDB 4LT5 4LT5 1 14 DBREF 4LT5 C 15 28 PDB 4LT5 4LT5 15 28 SEQADV 4LT5 MET A -5 UNP D2W6T1 EXPRESSION TAG SEQADV 4LT5 HIS A -4 UNP D2W6T1 EXPRESSION TAG SEQADV 4LT5 HIS A -3 UNP D2W6T1 EXPRESSION TAG SEQADV 4LT5 HIS A -2 UNP D2W6T1 EXPRESSION TAG SEQADV 4LT5 HIS A -1 UNP D2W6T1 EXPRESSION TAG SEQADV 4LT5 HIS A 0 UNP D2W6T1 EXPRESSION TAG SEQADV 4LT5 HIS A 1 UNP D2W6T1 EXPRESSION TAG SEQRES 1 A 327 MET HIS HIS HIS HIS HIS HIS THR THR PHE LYS GLN GLN SEQRES 2 A 327 THR ILE LYS GLU LYS GLU THR LYS ARG LYS TYR CYS ILE SEQRES 3 A 327 LYS GLY THR THR ALA ASN LEU THR GLN THR HIS PRO ASN SEQRES 4 A 327 GLY PRO VAL CYS VAL ASN ARG GLY GLU GLU VAL ALA ASN SEQRES 5 A 327 THR THR THR LEU LEU ASP SER GLY GLY GLY ILE ASN LYS SEQRES 6 A 327 LYS SER LEU LEU GLN ASN LEU LEU SER LYS CYS LYS THR SEQRES 7 A 327 THR PHE GLN GLN SER PHE THR ASN ALA ASN ILE THR LEU SEQRES 8 A 327 LYS ASP GLU LYS TRP LEU LYS ASN VAL ARG THR ALA TYR SEQRES 9 A 327 PHE VAL CYS ASP HIS ASP GLY SER VAL GLU LEU ALA TYR SEQRES 10 A 327 LEU PRO ASN VAL LEU PRO LYS GLU LEU VAL GLU GLU PHE SEQRES 11 A 327 THR GLU LYS PHE GLU SER ILE GLN THR GLY ARG LYS LYS SEQRES 12 A 327 ASP THR GLY TYR SER GLY ILE LEU ASP ASN SER MET PRO SEQRES 13 A 327 PHE ASN TYR VAL THR ALA ASP LEU SER GLN GLU LEU GLY SEQRES 14 A 327 GLN TYR LEU SER GLU ILE VAL ASN PRO GLN ILE ASN TYR SEQRES 15 A 327 TYR ILE SER LYS LEU LEU THR CYS VAL SER SER ARG THR SEQRES 16 A 327 ILE ASN TYR LEU VAL SER LEU ASN ASP SER TYR TYR ALA SEQRES 17 A 327 LEU ASN ASN CYS LEU TYR PRO SER THR ALA PHE ASN SER SEQRES 18 A 327 LEU LYS PRO SER ASN ASP GLY HIS ARG ILE ARG LYS PRO SEQRES 19 A 327 HIS LYS ASP ASN LEU ASP ILE THR PRO SER SER LEU PHE SEQRES 20 A 327 TYR PHE GLY ASN PHE GLN ASN THR GLU GLY TYR LEU GLU SEQRES 21 A 327 LEU THR ASP LYS ASN CYS LYS VAL PHE VAL GLN PRO GLY SEQRES 22 A 327 ASP VAL LEU PHE PHE LYS GLY ASN GLU TYR LYS HIS VAL SEQRES 23 A 327 VAL ALA ASN ILE THR SER GLY TRP ARG ILE GLY LEU VAL SEQRES 24 A 327 TYR PHE ALA HIS LYS GLY SER LYS THR LYS PRO TYR TYR SEQRES 25 A 327 GLU ASP THR GLN LYS ASN SER LEU LYS ILE HIS LYS GLU SEQRES 26 A 327 THR LYS SEQRES 1 B 14 DA DG DA DA DT DT DG 5CM DG DT DT DC DC SEQRES 2 B 14 DA SEQRES 1 C 14 DT DG DG DA DA 5CM DG DC DA DA DT DT DC SEQRES 2 C 14 DT MODRES 4LT5 5CM B 8 DC MODRES 4LT5 5CM C 20 DC HET 5CM B 8 20 HET 5CM C 20 20 HET MN A 401 1 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET SO4 A 409 5 HET SO4 A 410 5 HET SO4 A 411 5 HET SO4 A 412 5 HET OGA A 413 10 HET EDO C 101 4 HET EDO C 102 4 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM OGA N-OXALYLGLYCINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 4 MN MN 2+ FORMUL 5 EDO 9(C2 H6 O2) FORMUL 12 SO4 4(O4 S 2-) FORMUL 16 OGA C4 H5 N O5 FORMUL 19 HOH *100(H2 O) HELIX 1 1 ILE A 57 GLN A 75 1 19 HELIX 2 2 PRO A 117 GLY A 134 1 18 HELIX 3 3 ALA A 156 SER A 159 5 4 HELIX 4 4 GLN A 160 ILE A 169 1 10 HELIX 5 5 ILE A 169 SER A 186 1 18 HELIX 6 6 SER A 186 VAL A 194 1 9 HELIX 7 7 ASN A 197 ASN A 205 1 9 HELIX 8 8 HIS A 223 LYS A 227 5 5 HELIX 9 9 LYS A 298 LYS A 303 1 6 HELIX 10 10 GLN A 310 THR A 320 1 11 SHEET 1 A10 ASN A 82 LEU A 85 0 SHEET 2 A10 TYR A 98 CYS A 101 1 O PHE A 99 N THR A 84 SHEET 3 A10 VAL A 107 LEU A 112 -1 O TYR A 111 N TYR A 98 SHEET 4 A10 VAL A 269 PHE A 272 -1 O PHE A 271 N ALA A 110 SHEET 5 A10 SER A 238 ASN A 245 -1 N LEU A 240 O LEU A 270 SHEET 6 A10 TRP A 288 PHE A 295 -1 O ILE A 290 N PHE A 243 SHEET 7 A10 SER A 210 LEU A 216 -1 N LEU A 216 O ARG A 289 SHEET 8 A10 THR A 139 LEU A 145 -1 N GLY A 140 O PHE A 213 SHEET 9 A10 ASN A 152 VAL A 154 -1 O TYR A 153 N LEU A 145 SHEET 10 A10 TYR A 305 THR A 309 1 O ASP A 308 N VAL A 154 SHEET 1 B 4 ASN A 93 VAL A 94 0 SHEET 2 B 4 CYS A 260 VAL A 262 1 O LYS A 261 N VAL A 94 SHEET 3 B 4 LEU A 253 LEU A 255 -1 N LEU A 253 O VAL A 262 SHEET 4 B 4 HIS A 279 VAL A 281 -1 O VAL A 280 N GLU A 254 LINK O3' DG B 7 P 5CM B 8 1555 1555 1.61 LINK O3' 5CM B 8 P DG B 9 1555 1555 1.61 LINK O3' DA C 19 P 5CM C 20 1555 1555 1.61 LINK O3' 5CM C 20 P DG C 21 1555 1555 1.61 LINK NE2 HIS A 229 MN MN A 401 1555 1555 2.23 LINK OD2 ASP A 231 MN MN A 401 1555 1555 2.15 LINK NE2 HIS A 279 MN MN A 401 1555 1555 2.17 LINK MN MN A 401 O2 OGA A 413 1555 1555 2.13 LINK MN MN A 401 O2' OGA A 413 1555 1555 2.16 LINK MN MN A 401 O AHOH A 414 1555 1555 2.44 SITE 1 AC1 5 HIS A 229 ASP A 231 HIS A 279 OGA A 413 SITE 2 AC1 5 HOH A 414 SITE 1 AC2 2 TYR A 252 GLU A 254 SITE 1 AC3 3 ASN A 245 PHE A 246 ASN A 248 SITE 1 AC4 4 ASN A 175 SER A 179 TYR A 201 LEU A 207 SITE 1 AC5 1 ASN A 80 SITE 1 AC6 2 ILE A 235 THR A 236 SITE 1 AC7 4 GLU A 129 ASN A 245 GLY A 287 TRP A 288 SITE 1 AC8 1 ASP A 138 SITE 1 AC9 3 GLN A 76 SER A 77 HOH A 549 SITE 1 BC1 3 PRO A 117 LYS A 118 HOH A 528 SITE 1 BC2 3 SER A 186 SER A 187 ARG A 188 SITE 1 BC3 5 PRO A 172 ASN A 175 TYR A 201 ASN A 205 SITE 2 BC3 5 HOH A 560 SITE 1 BC4 14 ASN A 214 ARG A 224 ILE A 225 HIS A 229 SITE 2 BC4 14 ASP A 231 LEU A 240 TYR A 242 LEU A 253 SITE 3 BC4 14 HIS A 279 VAL A 281 ARG A 289 VAL A 293 SITE 4 BC4 14 MN A 401 HOH A 508 SITE 1 BC5 2 DC C 22 DA C 23 SITE 1 BC6 4 DG B 9 DA C 19 DG C 21 HOH C 207 CRYST1 83.954 108.648 166.384 90.00 90.00 90.00 I 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 0.011911 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006010 0.00000