HEADER OXIDOREDUCTASE/DNA 09-JUL-15 5CG9 TITLE NGTET1 IN COMPLEX WITH 5MC DNA IN SPACE GROUP P3221 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TET-LIKE DIOXYGENASE; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: UNP RESIDUES 57-321; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(P*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'); COMPND 8 CHAIN: B, E; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*TP*GP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*G)-3'); COMPND 12 CHAIN: C, F; COMPND 13 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) CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B-HIS-SUMO; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS DIOXYGENASE, 5-METHYLCYTOSINE, NGTET1, OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.HASHIMOTO,J.E.PAIS,N.DAI,X.ZHANG,Y.ZHENG,X.CHENG REVDAT 6 27-SEP-23 5CG9 1 LINK REVDAT 5 25-DEC-19 5CG9 1 REMARK REVDAT 4 27-SEP-17 5CG9 1 JRNL REMARK REVDAT 3 23-DEC-15 5CG9 1 JRNL REVDAT 2 16-SEP-15 5CG9 1 JRNL REVDAT 1 09-SEP-15 5CG9 0 JRNL AUTH H.HASHIMOTO,J.E.PAIS,N.DAI,I.R.CORREA,X.ZHANG,Y.ZHENG, JRNL AUTH 2 X.CHENG JRNL TITL STRUCTURE OF NAEGLERIA TET-LIKE DIOXYGENASE (NGTET1) IN JRNL TITL 2 COMPLEXES WITH A REACTION INTERMEDIATE JRNL TITL 3 5-HYDROXYMETHYLCYTOSINE DNA. JRNL REF NUCLEIC ACIDS RES. V. 43 10713 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26323320 JRNL DOI 10.1093/NAR/GKV870 REMARK 2 REMARK 2 RESOLUTION. 2.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 29452 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 : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1492 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 29.7441 - 5.9751 0.99 2649 141 0.1514 0.1863 REMARK 3 2 5.9751 - 4.7489 1.00 2596 142 0.1586 0.1762 REMARK 3 3 4.7489 - 4.1504 1.00 2587 137 0.1558 0.1619 REMARK 3 4 4.1504 - 3.7718 1.00 2576 137 0.1876 0.2241 REMARK 3 5 3.7718 - 3.5019 1.00 2573 141 0.2165 0.2389 REMARK 3 6 3.5019 - 3.2957 1.00 2569 133 0.2352 0.2890 REMARK 3 7 3.2957 - 3.1308 1.00 2570 137 0.2447 0.2917 REMARK 3 8 3.1308 - 2.9947 1.00 2537 135 0.2609 0.2980 REMARK 3 9 2.9947 - 2.8795 1.00 2568 136 0.2731 0.3211 REMARK 3 10 2.8795 - 2.7802 0.96 2455 131 0.2822 0.3048 REMARK 3 11 2.7802 - 2.6933 0.90 2280 122 0.2944 0.3734 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.200 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 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 5420 REMARK 3 ANGLE : 0.788 7541 REMARK 3 CHIRALITY : 0.033 836 REMARK 3 PLANARITY : 0.004 809 REMARK 3 DIHEDRAL : 20.091 2004 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 5CG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211547. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29462 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.15400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 0.89400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4LT5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) POLYETHYLENE GLYCOL 8000, REMARK 280 200 MM MG OXALOACETATE, 100 MM NA CACODYLATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 34.16933 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 17.08467 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 17.08467 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 34.16933 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 HIS D 55 REMARK 465 MET D 56 REMARK 465 LYS D 321 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 HIS A 55 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 57 CG1 CG2 CD1 REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 GLN A 64 CD OE1 NE2 REMARK 470 LYS A 69 CE NZ REMARK 470 LYS A 71 CD CE NZ REMARK 470 LYS A 89 CD CE NZ REMARK 470 LYS A 92 CD CE NZ REMARK 470 LYS A 118 NZ REMARK 470 GLU A 119 CD OE1 OE2 REMARK 470 LYS A 127 NZ REMARK 470 LYS A 136 CE NZ REMARK 470 LYS A 137 NZ REMARK 470 LYS A 227 NZ REMARK 470 LYS A 311 CE NZ REMARK 470 LYS A 315 CE NZ REMARK 470 THR A 320 OG1 CG2 REMARK 470 LYS A 321 CG CD CE NZ REMARK 470 DT C 14 O5' C5' N1 C2 O2 N3 C4 REMARK 470 DT C 14 O4 C5 C7 C6 REMARK 470 DG C 26 C4' O4' C3' O3' C2' C1' N9 REMARK 470 DG C 26 C8 N7 C5 C6 O6 N1 C2 REMARK 470 DG C 26 N2 N3 C4 REMARK 470 LYS D 59 CG CD CE NZ REMARK 470 LYS D 60 CG CD CE NZ REMARK 470 GLN D 64 CG CD OE1 NE2 REMARK 470 LYS D 69 NZ REMARK 470 LYS D 71 CG CD CE NZ REMARK 470 LYS D 89 CG CD CE NZ REMARK 470 LYS D 92 CG CD CE NZ REMARK 470 LYS D 118 CG CD CE NZ REMARK 470 GLU D 119 CG CD OE1 OE2 REMARK 470 LYS D 127 CE NZ REMARK 470 LYS D 136 CG CD CE NZ REMARK 470 LYS D 227 CE NZ REMARK 470 LYS D 261 CG CD CE NZ REMARK 470 LYS D 278 CD CE NZ REMARK 470 LYS D 311 CE NZ REMARK 470 LYS D 315 CD CE NZ REMARK 470 LYS D 318 CG CD CE NZ REMARK 470 THR D 320 OG1 CG2 REMARK 470 DT F 14 O5' 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 OD2 ASP A 231 O HOH A 501 2.08 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 DG C 19 O4' - C1' - N9 ANGL. DEV. = 1.9 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 LYS A 136 -61.06 -90.69 REMARK 500 PRO A 150 44.56 -88.83 REMARK 500 ILE A 169 -60.28 -100.48 REMARK 500 CYS A 184 -65.27 -94.37 REMARK 500 GLU A 276 -61.07 -101.16 REMARK 500 THR A 302 -65.03 -92.91 REMARK 500 PRO D 150 46.62 -87.89 REMARK 500 GLU D 276 -64.00 -108.61 REMARK 500 THR D 302 -62.78 -97.27 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 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 229 NE2 REMARK 620 2 ASP A 231 OD2 108.6 REMARK 620 3 HIS A 279 NE2 96.0 94.4 REMARK 620 4 AKG A 402 O2 97.2 95.0 160.5 REMARK 620 5 AKG A 402 O5 125.3 126.2 81.5 79.2 REMARK 620 6 HOH A 501 O 160.7 57.1 74.1 96.9 70.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 405 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 229 NE2 REMARK 620 2 ASP D 231 OD2 107.1 REMARK 620 3 HIS D 279 NE2 96.0 86.6 REMARK 620 4 AKG D 404 O2 81.1 104.5 168.9 REMARK 620 5 AKG D 404 O5 111.3 141.6 89.4 81.8 REMARK 620 6 HOH D 501 O 166.7 61.4 90.1 95.1 80.5 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 SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO D 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG D 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO F 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DG F 19 and 5CM F REMARK 800 20 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM F 20 and DG F REMARK 800 21 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CG8 RELATED DB: PDB DBREF 5CG9 A 57 321 UNP D2W6T1 D2W6T1_NAEGR 57 321 DBREF 5CG9 B 3 13 PDB 5CG9 5CG9 3 13 DBREF 5CG9 C 14 26 PDB 5CG9 5CG9 14 26 DBREF 5CG9 D 57 321 UNP D2W6T1 D2W6T1_NAEGR 57 321 DBREF 5CG9 E 3 13 PDB 5CG9 5CG9 3 13 DBREF 5CG9 F 14 26 PDB 5CG9 5CG9 14 26 SEQADV 5CG9 HIS A 55 UNP D2W6T1 EXPRESSION TAG SEQADV 5CG9 MET A 56 UNP D2W6T1 EXPRESSION TAG SEQADV 5CG9 HIS D 55 UNP D2W6T1 EXPRESSION TAG SEQADV 5CG9 MET D 56 UNP D2W6T1 EXPRESSION TAG SEQRES 1 A 267 HIS MET ILE ASN LYS LYS SER LEU LEU GLN ASN LEU LEU SEQRES 2 A 267 SER LYS CYS LYS THR THR PHE GLN GLN SER PHE THR ASN SEQRES 3 A 267 ALA ASN ILE THR LEU LYS ASP GLU LYS TRP LEU LYS ASN SEQRES 4 A 267 VAL ARG THR ALA TYR PHE VAL CYS ASP HIS ASP GLY SER SEQRES 5 A 267 VAL GLU LEU ALA TYR LEU PRO ASN VAL LEU PRO LYS GLU SEQRES 6 A 267 LEU VAL GLU GLU PHE THR GLU LYS PHE GLU SER ILE GLN SEQRES 7 A 267 THR GLY ARG LYS LYS ASP THR GLY TYR SER GLY ILE LEU SEQRES 8 A 267 ASP ASN SER MET PRO PHE ASN TYR VAL THR ALA ASP LEU SEQRES 9 A 267 SER GLN GLU LEU GLY GLN TYR LEU SER GLU ILE VAL ASN SEQRES 10 A 267 PRO GLN ILE ASN TYR TYR ILE SER LYS LEU LEU THR CYS SEQRES 11 A 267 VAL SER SER ARG THR ILE ASN TYR LEU VAL SER LEU ASN SEQRES 12 A 267 ASP SER TYR TYR ALA LEU ASN ASN CYS LEU TYR PRO SER SEQRES 13 A 267 THR ALA PHE ASN SER LEU LYS PRO SER ASN ASP GLY HIS SEQRES 14 A 267 ARG ILE ARG LYS PRO HIS LYS ASP ASN LEU ASP ILE THR SEQRES 15 A 267 PRO SER SER LEU PHE TYR PHE GLY ASN PHE GLN ASN THR SEQRES 16 A 267 GLU GLY TYR LEU GLU LEU THR ASP LYS ASN CYS LYS VAL SEQRES 17 A 267 PHE VAL GLN PRO GLY ASP VAL LEU PHE PHE LYS GLY ASN SEQRES 18 A 267 GLU TYR LYS HIS VAL VAL ALA ASN ILE THR SER GLY TRP SEQRES 19 A 267 ARG ILE GLY LEU VAL TYR PHE ALA HIS LYS GLY SER LYS SEQRES 20 A 267 THR LYS PRO TYR TYR GLU ASP THR GLN LYS ASN SER LEU SEQRES 21 A 267 LYS ILE HIS LYS GLU THR LYS SEQRES 1 B 11 DC DA DT DG DC DG DC DT DG DA DC SEQRES 1 C 13 DT DG DT DC DA DG 5CM DG DC DA DT DG DG SEQRES 1 D 267 HIS MET ILE ASN LYS LYS SER LEU LEU GLN ASN LEU LEU SEQRES 2 D 267 SER LYS CYS LYS THR THR PHE GLN GLN SER PHE THR ASN SEQRES 3 D 267 ALA ASN ILE THR LEU LYS ASP GLU LYS TRP LEU LYS ASN SEQRES 4 D 267 VAL ARG THR ALA TYR PHE VAL CYS ASP HIS ASP GLY SER SEQRES 5 D 267 VAL GLU LEU ALA TYR LEU PRO ASN VAL LEU PRO LYS GLU SEQRES 6 D 267 LEU VAL GLU GLU PHE THR GLU LYS PHE GLU SER ILE GLN SEQRES 7 D 267 THR GLY ARG LYS LYS ASP THR GLY TYR SER GLY ILE LEU SEQRES 8 D 267 ASP ASN SER MET PRO PHE ASN TYR VAL THR ALA ASP LEU SEQRES 9 D 267 SER GLN GLU LEU GLY GLN TYR LEU SER GLU ILE VAL ASN SEQRES 10 D 267 PRO GLN ILE ASN TYR TYR ILE SER LYS LEU LEU THR CYS SEQRES 11 D 267 VAL SER SER ARG THR ILE ASN TYR LEU VAL SER LEU ASN SEQRES 12 D 267 ASP SER TYR TYR ALA LEU ASN ASN CYS LEU TYR PRO SER SEQRES 13 D 267 THR ALA PHE ASN SER LEU LYS PRO SER ASN ASP GLY HIS SEQRES 14 D 267 ARG ILE ARG LYS PRO HIS LYS ASP ASN LEU ASP ILE THR SEQRES 15 D 267 PRO SER SER LEU PHE TYR PHE GLY ASN PHE GLN ASN THR SEQRES 16 D 267 GLU GLY TYR LEU GLU LEU THR ASP LYS ASN CYS LYS VAL SEQRES 17 D 267 PHE VAL GLN PRO GLY ASP VAL LEU PHE PHE LYS GLY ASN SEQRES 18 D 267 GLU TYR LYS HIS VAL VAL ALA ASN ILE THR SER GLY TRP SEQRES 19 D 267 ARG ILE GLY LEU VAL TYR PHE ALA HIS LYS GLY SER LYS SEQRES 20 D 267 THR LYS PRO TYR TYR GLU ASP THR GLN LYS ASN SER LEU SEQRES 21 D 267 LYS ILE HIS LYS GLU THR LYS SEQRES 1 E 11 DC DA DT DG DC DG DC DT DG DA DC SEQRES 1 F 13 DT DG DT DC DA DG 5CM DG DC DA DT DG DG HET 5CM C 20 20 HET 5CM F 20 20 HET SO4 A 401 5 HET AKG A 402 10 HET MN A 403 1 HET SO4 D 401 5 HET SO4 D 402 5 HET EDO D 403 4 HET AKG D 404 10 HET MN D 405 1 HET EDO F 101 4 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SO4 SULFATE ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 5CM 2(C10 H16 N3 O7 P) FORMUL 7 SO4 3(O4 S 2-) FORMUL 8 AKG 2(C5 H6 O5) FORMUL 9 MN 2(MN 2+) FORMUL 12 EDO 2(C2 H6 O2) FORMUL 16 HOH *14(H2 O) HELIX 1 AA1 ASN A 58 GLN A 75 1 18 HELIX 2 AA2 PRO A 117 GLY A 134 1 18 HELIX 3 AA3 ALA A 156 SER A 159 5 4 HELIX 4 AA4 GLN A 160 ILE A 169 1 10 HELIX 5 AA5 ILE A 169 VAL A 185 1 17 HELIX 6 AA6 SER A 186 VAL A 194 1 9 HELIX 7 AA7 ASN A 197 ASN A 205 1 9 HELIX 8 AA8 HIS A 223 LYS A 227 5 5 HELIX 9 AA9 HIS A 297 LYS A 303 1 7 HELIX 10 AB1 THR A 309 LYS A 321 1 13 HELIX 11 AB2 ASN D 58 GLN D 75 1 18 HELIX 12 AB3 PRO D 117 GLY D 134 1 18 HELIX 13 AB4 GLN D 160 ILE D 169 1 10 HELIX 14 AB5 ILE D 169 SER D 186 1 18 HELIX 15 AB6 SER D 186 VAL D 194 1 9 HELIX 16 AB7 ASN D 197 ASN D 205 1 9 HELIX 17 AB8 HIS D 297 LYS D 303 1 7 HELIX 18 AB9 GLN D 310 THR D 320 1 11 SHEET 1 AA1 9 ASN A 82 LEU A 85 0 SHEET 2 AA1 9 TYR A 98 CYS A 101 1 O PHE A 99 N THR A 84 SHEET 3 AA1 9 VAL A 107 LEU A 112 -1 O TYR A 111 N TYR A 98 SHEET 4 AA1 9 VAL A 269 PHE A 272 -1 O PHE A 271 N ALA A 110 SHEET 5 AA1 9 SER A 238 ASN A 245 -1 N LEU A 240 O LEU A 270 SHEET 6 AA1 9 TRP A 288 PHE A 295 -1 O ILE A 290 N PHE A 243 SHEET 7 AA1 9 SER A 210 LEU A 216 -1 N LEU A 216 O ARG A 289 SHEET 8 AA1 9 THR A 139 LEU A 145 -1 N GLY A 140 O PHE A 213 SHEET 9 AA1 9 TYR A 153 VAL A 154 -1 O TYR A 153 N LEU A 145 SHEET 1 AA2 4 ASN A 93 VAL A 94 0 SHEET 2 AA2 4 CYS A 260 VAL A 262 1 O LYS A 261 N VAL A 94 SHEET 3 AA2 4 LEU A 253 LEU A 255 -1 N LEU A 255 O CYS A 260 SHEET 4 AA2 4 HIS A 279 VAL A 281 -1 O VAL A 280 N GLU A 254 SHEET 1 AA310 ASN D 82 LEU D 85 0 SHEET 2 AA310 TYR D 98 CYS D 101 1 O PHE D 99 N ASN D 82 SHEET 3 AA310 VAL D 107 LEU D 112 -1 O LEU D 109 N VAL D 100 SHEET 4 AA310 VAL D 269 PHE D 272 -1 O PHE D 271 N ALA D 110 SHEET 5 AA310 SER D 238 ASN D 245 -1 N LEU D 240 O LEU D 270 SHEET 6 AA310 TRP D 288 PHE D 295 -1 O ILE D 290 N PHE D 243 SHEET 7 AA310 SER D 210 LEU D 216 -1 N ALA D 212 O VAL D 293 SHEET 8 AA310 THR D 139 LEU D 145 -1 N GLY D 140 O PHE D 213 SHEET 9 AA310 ASN D 152 VAL D 154 -1 O TYR D 153 N LEU D 145 SHEET 10 AA310 TYR D 305 THR D 309 1 O ASP D 308 N VAL D 154 SHEET 1 AA4 4 ASN D 93 VAL D 94 0 SHEET 2 AA4 4 CYS D 260 VAL D 262 1 O LYS D 261 N VAL D 94 SHEET 3 AA4 4 LEU D 253 LEU D 255 -1 N LEU D 253 O VAL D 262 SHEET 4 AA4 4 HIS D 279 VAL D 281 -1 O VAL D 280 N GLU D 254 LINK O3' DG C 19 P 5CM C 20 1555 1555 1.60 LINK O3' 5CM C 20 P DG C 21 1555 1555 1.61 LINK O3' DG F 19 P 5CM F 20 1555 1555 1.60 LINK O3' 5CM F 20 P DG F 21 1555 1555 1.61 LINK NE2 HIS A 229 MN MN A 403 1555 1555 2.14 LINK OD2 ASP A 231 MN MN A 403 1555 1555 2.15 LINK NE2 HIS A 279 MN MN A 403 1555 1555 2.23 LINK O2 AKG A 402 MN MN A 403 1555 1555 2.09 LINK O5 AKG A 402 MN MN A 403 1555 1555 2.22 LINK MN MN A 403 O HOH A 501 1555 1555 2.20 LINK NE2 HIS D 229 MN MN D 405 1555 1555 2.32 LINK OD2 ASP D 231 MN MN D 405 1555 1555 2.17 LINK NE2 HIS D 279 MN MN D 405 1555 1555 2.18 LINK O2 AKG D 404 MN MN D 405 1555 1555 1.91 LINK O5 AKG D 404 MN MN D 405 1555 1555 2.24 LINK MN MN D 405 O HOH D 501 1555 1555 2.22 SITE 1 AC1 4 GLU A 168 ALA A 202 ASN A 205 EDO D 403 SITE 1 AC2 14 ASN A 214 ARG A 224 HIS A 229 ASP A 231 SITE 2 AC2 14 LEU A 240 TYR A 242 LEU A 253 HIS A 279 SITE 3 AC2 14 VAL A 281 ARG A 289 VAL A 293 MN A 403 SITE 4 AC2 14 HOH A 501 5CM C 20 SITE 1 AC3 5 HIS A 229 ASP A 231 HIS A 279 AKG A 402 SITE 2 AC3 5 HOH A 501 SITE 1 AC4 5 ASN A 175 TYR A 201 ASN A 205 ASN D 175 SITE 2 AC4 5 TYR D 201 SITE 1 AC5 4 GLU D 168 ALA D 202 ASN D 205 EDO D 403 SITE 1 AC6 2 SO4 A 401 SO4 D 402 SITE 1 AC7 14 ASN D 214 ARG D 224 HIS D 229 ASP D 231 SITE 2 AC7 14 LEU D 240 TYR D 242 LEU D 253 HIS D 279 SITE 3 AC7 14 VAL D 281 ARG D 289 VAL D 293 MN D 405 SITE 4 AC7 14 HOH D 501 5CM F 20 SITE 1 AC8 5 HIS D 229 ASP D 231 HIS D 279 AKG D 404 SITE 2 AC8 5 HOH D 501 SITE 1 AC9 3 DG E 8 DA F 18 DG F 19 SITE 1 AD1 14 TYR D 141 ASN D 147 ARG D 224 ASP D 234 SITE 2 AD1 14 VAL D 293 PHE D 295 HIS D 297 AKG D 404 SITE 3 AD1 14 DG E 8 DC E 9 DT E 10 DA F 18 SITE 4 AD1 14 DG F 21 EDO F 101 SITE 1 AD2 14 TYR D 141 ASN D 147 TYR D 153 ARG D 224 SITE 2 AD2 14 ASP D 234 VAL D 293 PHE D 295 HIS D 297 SITE 3 AD2 14 GLN D 310 AKG D 404 DG E 6 DC E 7 SITE 4 AD2 14 DG F 19 DC F 22 CRYST1 191.216 191.216 51.254 90.00 90.00 120.00 P 32 2 1 12 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 0.005230 0.003019 0.000000 0.00000 SCALE2 0.000000 0.006039 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019511 0.00000