HEADER RNA BINDING PROTEIN 27-JUL-21 7P9I TITLE STRUCTURE OF E.COLI RLMJ IN COMPLEX WITH AN RNA CONJUGATE (GAA-SAM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 23S RRNA (ADENINE(2030)-N6)-METHYLTRANSFERASE,23S RRNA COMPND 5 M6A2030 METHYLTRANSFERASE; COMPND 6 EC: 2.1.1.266; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RNA CONJUGATE (GAA-SAM); COMPND 11 CHAIN: D, E; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: RLMJ, YHIR, B3499, JW3466; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS RNA MTASES, METHYLTRANSFERASE, SAM ANALOGUE, M6A, RNA BINDING, SAM KEYWDS 2 CONJUGATE, RLMJ, CONJUGATE ANALOGUE, RNA RECOGNITION, BISUBSTRATE KEYWDS 3 ANALOGUE, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.MEYNIER,M.CATALA,S.OERUM,P.BARRAUD,C.TISNE REVDAT 3 31-JAN-24 7P9I 1 REMARK REVDAT 2 15-JUN-22 7P9I 1 JRNL REVDAT 1 01-JUN-22 7P9I 0 JRNL AUTH V.MEYNIER,L.IANNAZZO,M.CATALA,S.OERUM,E.BRAUD,C.ATDJIAN, JRNL AUTH 2 P.BARRAUD,M.FONVIELLE,C.TISNE,M.ETHEVE-QUELQUEJEU JRNL TITL SYNTHESIS OF RNA-COFACTOR CONJUGATES AND STRUCTURAL JRNL TITL 2 EXPLORATION OF RNA RECOGNITION BY AN M6A RNA JRNL TITL 3 METHYLTRANSFERASE. JRNL REF NUCLEIC ACIDS RES. V. 50 5793 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35580049 JRNL DOI 10.1093/NAR/GKAC354 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 74135 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3706 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 4.7210 - 3.7479 1.00 2775 146 0.1441 0.1788 REMARK 3 2 3.7479 - 3.2744 1.00 2739 144 0.1618 0.1971 REMARK 3 3 3.2744 - 2.9751 1.00 2736 144 0.1753 0.1925 REMARK 3 4 2.9751 - 2.7619 1.00 2741 145 0.1809 0.2180 REMARK 3 5 2.7619 - 2.5991 1.00 2741 144 0.1815 0.2113 REMARK 3 6 2.5991 - 2.4689 1.00 2738 144 0.1851 0.2370 REMARK 3 7 2.4689 - 2.3615 1.00 2726 144 0.1903 0.2073 REMARK 3 8 2.3615 - 2.2706 1.00 2725 143 0.1766 0.2071 REMARK 3 9 2.2706 - 2.1922 1.00 2713 143 0.1782 0.2177 REMARK 3 10 2.1922 - 2.1237 1.00 2715 143 0.1874 0.2260 REMARK 3 11 2.1237 - 2.0630 1.00 2728 143 0.2039 0.2376 REMARK 3 12 2.0630 - 2.0087 1.00 2712 143 0.1977 0.2608 REMARK 3 13 2.0087 - 1.9597 1.00 2710 143 0.1951 0.2205 REMARK 3 14 1.9597 - 1.9151 1.00 2723 143 0.1884 0.2361 REMARK 3 15 1.9151 - 1.8743 1.00 2718 143 0.1927 0.2146 REMARK 3 16 1.8743 - 1.8369 1.00 2693 142 0.1940 0.2249 REMARK 3 17 1.8369 - 1.8022 1.00 2712 143 0.2027 0.2224 REMARK 3 18 1.8022 - 1.7700 1.00 2690 141 0.2243 0.2893 REMARK 3 19 1.7700 - 1.7400 1.00 2731 144 0.2376 0.2857 REMARK 3 20 1.7400 - 1.7119 1.00 2768 146 0.2557 0.3176 REMARK 3 21 1.7119 - 1.6856 1.00 2675 141 0.2800 0.3505 REMARK 3 22 1.6856 - 1.6608 1.00 2697 142 0.3042 0.3414 REMARK 3 23 1.6608 - 1.6374 1.00 2711 142 0.3271 0.3583 REMARK 3 24 1.6374 - 1.6153 1.00 2725 144 0.3381 0.3649 REMARK 3 25 1.6153 - 1.5943 0.85 2282 120 0.3798 0.4220 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.72 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7P9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1292117232. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-20 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74189 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 46.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 1.41800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6QDX REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 20% W/V PEG MME REMARK 280 5000, VAPOR DIFFUSION, TEMPERATURE 293K 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 28.79500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E 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 MET A 1 REMARK 465 LEU A 2 REMARK 465 GLY A 51 REMARK 465 SER A 52 REMARK 465 GLU A 53 REMARK 465 HIS A 54 REMARK 465 ALA A 55 REMARK 465 GLU A 56 REMARK 465 ARG A 57 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 SER B 52 REMARK 465 GLU B 53 REMARK 465 HIS B 54 REMARK 465 ALA B 55 REMARK 465 GLU B 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 LYS A 32 CE NZ REMARK 470 MET A 169 CE REMARK 470 ARG A 232 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 32 CE NZ REMARK 470 ARG B 138 CG CD NE CZ NH1 NH2 REMARK 470 MET B 169 CE 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 A D 3 P A D 3 O5' 0.072 REMARK 500 A D 3 C5' A D 3 C4' -0.086 REMARK 500 A D 3 C3' A D 3 C2' -0.241 REMARK 500 A D 3 C2' A D 3 C1' 0.086 REMARK 500 A D 3 O4' A D 3 C1' -0.144 REMARK 500 A D 3 C5 A D 3 N7 -0.050 REMARK 500 A D 3 C8 A D 3 N9 -0.060 REMARK 500 A D 3 C6 A D 3 N6 0.173 REMARK 500 A D 4 P A D 4 O5' 0.086 REMARK 500 A D 4 C4' A D 4 C3' 0.077 REMARK 500 A D 4 C3' A D 4 C2' -0.248 REMARK 500 A D 4 O4' A D 4 C1' 0.111 REMARK 500 A D 4 O4' A D 4 C4' -0.194 REMARK 500 A D 4 C1' A D 4 N9 -0.096 REMARK 500 A D 4 C5 A D 4 N7 -0.051 REMARK 500 A D 4 C8 A D 4 N9 -0.062 REMARK 500 A D 4 C6 A D 4 N6 0.132 REMARK 500 A E 3 P A E 3 O5' 0.064 REMARK 500 A E 3 C5' A E 3 C4' -0.092 REMARK 500 A E 3 C3' A E 3 C2' -0.245 REMARK 500 A E 3 C2' A E 3 C1' 0.084 REMARK 500 A E 3 O4' A E 3 C1' -0.146 REMARK 500 A E 3 O4' A E 3 C4' 0.061 REMARK 500 A E 3 C5 A E 3 N7 -0.054 REMARK 500 A E 3 C8 A E 3 N9 -0.062 REMARK 500 A E 3 C6 A E 3 N6 0.171 REMARK 500 A E 4 P A E 4 O5' 0.081 REMARK 500 A E 4 C4' A E 4 C3' 0.080 REMARK 500 A E 4 C3' A E 4 C2' -0.251 REMARK 500 A E 4 O4' A E 4 C1' 0.099 REMARK 500 A E 4 O4' A E 4 C4' -0.193 REMARK 500 A E 4 C1' A E 4 N9 -0.094 REMARK 500 A E 4 C5 A E 4 N7 -0.049 REMARK 500 A E 4 C8 A E 4 N9 -0.059 REMARK 500 A E 4 C6 A E 4 N6 0.131 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 A D 3 C3' - C2' - C1' ANGL. DEV. = 6.2 DEGREES REMARK 500 A D 3 N1 - C2 - N3 ANGL. DEV. = -6.9 DEGREES REMARK 500 A D 3 C2 - N3 - C4 ANGL. DEV. = 9.7 DEGREES REMARK 500 A D 3 N3 - C4 - C5 ANGL. DEV. = -7.4 DEGREES REMARK 500 A D 3 C4 - C5 - N7 ANGL. DEV. = -3.2 DEGREES REMARK 500 A D 3 C5 - N7 - C8 ANGL. DEV. = 4.3 DEGREES REMARK 500 A D 3 N7 - C8 - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 A D 3 C8 - N9 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 A D 3 N3 - C4 - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 A D 3 C5 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 A D 4 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES REMARK 500 A D 4 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 A D 4 N1 - C2 - N3 ANGL. DEV. = -6.1 DEGREES REMARK 500 A D 4 C2 - N3 - C4 ANGL. DEV. = 9.6 DEGREES REMARK 500 A D 4 N3 - C4 - C5 ANGL. DEV. = -8.1 DEGREES REMARK 500 A D 4 C4 - C5 - N7 ANGL. DEV. = -3.5 DEGREES REMARK 500 A D 4 C5 - N7 - C8 ANGL. DEV. = 4.2 DEGREES REMARK 500 A D 4 N7 - C8 - N9 ANGL. DEV. = -3.9 DEGREES REMARK 500 A D 4 C8 - N9 - C4 ANGL. DEV. = 2.6 DEGREES REMARK 500 A D 4 N3 - C4 - N9 ANGL. DEV. = 7.5 DEGREES REMARK 500 A D 4 C5 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 A E 3 C5' - C4' - C3' ANGL. DEV. = -9.6 DEGREES REMARK 500 A E 3 C3' - C2' - C1' ANGL. DEV. = 6.5 DEGREES REMARK 500 A E 3 N1 - C2 - N3 ANGL. DEV. = -7.1 DEGREES REMARK 500 A E 3 C2 - N3 - C4 ANGL. DEV. = 9.9 DEGREES REMARK 500 A E 3 N3 - C4 - C5 ANGL. DEV. = -7.7 DEGREES REMARK 500 A E 3 C5 - N7 - C8 ANGL. DEV. = 4.3 DEGREES REMARK 500 A E 3 N7 - C8 - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 A E 3 C8 - N9 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 A E 3 N3 - C4 - N9 ANGL. DEV. = 7.9 DEGREES REMARK 500 A E 3 C5 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 A E 4 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 A E 4 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 A E 4 N1 - C2 - N3 ANGL. DEV. = -6.7 DEGREES REMARK 500 A E 4 C2 - N3 - C4 ANGL. DEV. = 9.6 DEGREES REMARK 500 A E 4 N3 - C4 - C5 ANGL. DEV. = -7.5 DEGREES REMARK 500 A E 4 C4 - C5 - N7 ANGL. DEV. = -3.5 DEGREES REMARK 500 A E 4 C5 - N7 - C8 ANGL. DEV. = 4.3 DEGREES REMARK 500 A E 4 N7 - C8 - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 A E 4 C8 - N9 - C4 ANGL. DEV. = 2.7 DEGREES REMARK 500 A E 4 N3 - C4 - N9 ANGL. DEV. = 6.8 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 89 54.86 -144.03 REMARK 500 PHE A 187 76.31 -153.63 REMARK 500 VAL A 199 -62.79 -105.80 REMARK 500 LYS A 218 61.17 66.11 REMARK 500 ARG A 232 38.76 -158.60 REMARK 500 ASP B 73 31.48 -99.59 REMARK 500 ASN B 89 55.66 -144.98 REMARK 500 PHE B 187 76.64 -151.43 REMARK 500 LYS B 218 62.08 65.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6QDX RELATED DB: PDB REMARK 900 RELATED ID: 7P8Q RELATED DB: PDB REMARK 900 RELATED ID: 7P9O RELATED DB: PDB DBREF 7P9I A 1 280 UNP P37634 RLMJ_ECOLI 1 280 DBREF 7P9I B 1 280 UNP P37634 RLMJ_ECOLI 1 280 DBREF 7P9I D 2 4 PDB 7P9I 7P9I 2 4 DBREF 7P9I E 2 4 PDB 7P9I 7P9I 2 4 SEQADV 7P9I GLN A 106 UNP P37634 LEU 106 CONFLICT SEQADV 7P9I THR A 191 UNP P37634 ILE 191 CONFLICT SEQADV 7P9I GLN B 106 UNP P37634 LEU 106 CONFLICT SEQADV 7P9I THR B 191 UNP P37634 ILE 191 CONFLICT SEQRES 1 A 280 MET LEU SER TYR ARG HIS SER PHE HIS ALA GLY ASN HIS SEQRES 2 A 280 ALA ASP VAL LEU LYS HIS THR VAL GLN SER LEU ILE ILE SEQRES 3 A 280 GLU SER LEU LYS GLU LYS ASP LYS PRO PHE LEU TYR LEU SEQRES 4 A 280 ASP THR HIS ALA GLY ALA GLY ARG TYR GLN LEU GLY SER SEQRES 5 A 280 GLU HIS ALA GLU ARG THR GLY GLU TYR LEU GLU GLY ILE SEQRES 6 A 280 ALA ARG ILE TRP GLN GLN ASP ASP LEU PRO ALA GLU LEU SEQRES 7 A 280 GLU ALA TYR ILE ASN VAL VAL LYS HIS PHE ASN ARG SER SEQRES 8 A 280 GLY GLN LEU ARG TYR TYR PRO GLY SER PRO LEU ILE ALA SEQRES 9 A 280 ARG GLN LEU LEU ARG GLU GLN ASP SER LEU GLN LEU THR SEQRES 10 A 280 GLU LEU HIS PRO SER ASP TYR PRO LEU LEU ARG SER GLU SEQRES 11 A 280 PHE GLN LYS ASP SER ARG ALA ARG VAL GLU LYS ALA ASP SEQRES 12 A 280 GLY PHE GLN GLN LEU LYS ALA LYS LEU PRO PRO VAL SER SEQRES 13 A 280 ARG ARG GLY LEU ILE LEU ILE ASP PRO PRO TYR GLU MET SEQRES 14 A 280 LYS THR ASP TYR GLN ALA VAL VAL SER GLY ILE ALA GLU SEQRES 15 A 280 GLY TYR LYS ARG PHE ALA THR GLY THR TYR ALA LEU TRP SEQRES 16 A 280 TYR PRO VAL VAL LEU ARG GLN GLN ILE LYS ARG MET ILE SEQRES 17 A 280 HIS ASP LEU GLU ALA THR GLY ILE ARG LYS ILE LEU GLN SEQRES 18 A 280 ILE GLU LEU ALA VAL LEU PRO ASP SER ASP ARG ARG GLY SEQRES 19 A 280 MET THR ALA SER GLY MET ILE VAL ILE ASN PRO PRO TRP SEQRES 20 A 280 LYS LEU GLU GLN GLN MET ASN ASN VAL LEU PRO TRP LEU SEQRES 21 A 280 HIS SER LYS LEU VAL PRO ALA GLY THR GLY HIS ALA THR SEQRES 22 A 280 VAL SER TRP ILE VAL PRO GLU SEQRES 1 B 280 MET LEU SER TYR ARG HIS SER PHE HIS ALA GLY ASN HIS SEQRES 2 B 280 ALA ASP VAL LEU LYS HIS THR VAL GLN SER LEU ILE ILE SEQRES 3 B 280 GLU SER LEU LYS GLU LYS ASP LYS PRO PHE LEU TYR LEU SEQRES 4 B 280 ASP THR HIS ALA GLY ALA GLY ARG TYR GLN LEU GLY SER SEQRES 5 B 280 GLU HIS ALA GLU ARG THR GLY GLU TYR LEU GLU GLY ILE SEQRES 6 B 280 ALA ARG ILE TRP GLN GLN ASP ASP LEU PRO ALA GLU LEU SEQRES 7 B 280 GLU ALA TYR ILE ASN VAL VAL LYS HIS PHE ASN ARG SER SEQRES 8 B 280 GLY GLN LEU ARG TYR TYR PRO GLY SER PRO LEU ILE ALA SEQRES 9 B 280 ARG GLN LEU LEU ARG GLU GLN ASP SER LEU GLN LEU THR SEQRES 10 B 280 GLU LEU HIS PRO SER ASP TYR PRO LEU LEU ARG SER GLU SEQRES 11 B 280 PHE GLN LYS ASP SER ARG ALA ARG VAL GLU LYS ALA ASP SEQRES 12 B 280 GLY PHE GLN GLN LEU LYS ALA LYS LEU PRO PRO VAL SER SEQRES 13 B 280 ARG ARG GLY LEU ILE LEU ILE ASP PRO PRO TYR GLU MET SEQRES 14 B 280 LYS THR ASP TYR GLN ALA VAL VAL SER GLY ILE ALA GLU SEQRES 15 B 280 GLY TYR LYS ARG PHE ALA THR GLY THR TYR ALA LEU TRP SEQRES 16 B 280 TYR PRO VAL VAL LEU ARG GLN GLN ILE LYS ARG MET ILE SEQRES 17 B 280 HIS ASP LEU GLU ALA THR GLY ILE ARG LYS ILE LEU GLN SEQRES 18 B 280 ILE GLU LEU ALA VAL LEU PRO ASP SER ASP ARG ARG GLY SEQRES 19 B 280 MET THR ALA SER GLY MET ILE VAL ILE ASN PRO PRO TRP SEQRES 20 B 280 LYS LEU GLU GLN GLN MET ASN ASN VAL LEU PRO TRP LEU SEQRES 21 B 280 HIS SER LYS LEU VAL PRO ALA GLY THR GLY HIS ALA THR SEQRES 22 B 280 VAL SER TRP ILE VAL PRO GLU SEQRES 1 D 3 GMP A A SEQRES 1 E 3 GMP A A HET GMP D 2 32 HET GMP E 2 32 HET 6D6 D 101 54 HET 6D6 E 101 54 HETNAM GMP GUANOSINE HETNAM 6D6 5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL](3-AMINOPROPYL) HETNAM 2 6D6 AMINO}-5'-DEOXYADENOSINE FORMUL 3 GMP 2(C10 H13 N5 O5) FORMUL 5 6D6 2(C17 H28 N8 O5) FORMUL 7 HOH *567(H2 O) HELIX 1 AA1 ASN A 12 LYS A 30 1 19 HELIX 2 AA2 GLY A 59 ILE A 68 5 10 HELIX 3 AA3 PRO A 75 GLU A 77 5 3 HELIX 4 AA4 LEU A 78 PHE A 88 1 11 HELIX 5 AA5 GLY A 99 LEU A 108 1 10 HELIX 6 AA6 SER A 122 PHE A 131 1 10 HELIX 7 AA7 GLN A 146 LYS A 151 1 6 HELIX 8 AA8 MET A 169 PHE A 187 1 19 HELIX 9 AA9 LEU A 200 THR A 214 1 15 HELIX 10 AB1 LYS A 248 VAL A 265 1 18 HELIX 11 AB2 ASN B 12 LYS B 30 1 19 HELIX 12 AB3 GLY B 59 ILE B 68 5 10 HELIX 13 AB4 PRO B 75 GLU B 77 5 3 HELIX 14 AB5 LEU B 78 PHE B 88 1 11 HELIX 15 AB6 GLY B 99 LEU B 108 1 10 HELIX 16 AB7 SER B 122 PHE B 131 1 10 HELIX 17 AB8 ASP B 143 LYS B 151 1 9 HELIX 18 AB9 MET B 169 PHE B 187 1 19 HELIX 19 AC1 LEU B 200 THR B 214 1 15 HELIX 20 AC2 LYS B 248 VAL B 265 1 18 SHEET 1 AA1 8 ALA A 137 GLU A 140 0 SHEET 2 AA1 8 SER A 113 THR A 117 1 N LEU A 116 O ARG A 138 SHEET 3 AA1 8 LEU A 37 ASP A 40 1 N TYR A 38 O GLN A 115 SHEET 4 AA1 8 GLY A 159 ILE A 163 1 O LEU A 162 N LEU A 39 SHEET 5 AA1 8 THR A 191 VAL A 198 1 O ALA A 193 N ILE A 161 SHEET 6 AA1 8 ALA A 237 ILE A 243 -1 O ILE A 241 N LEU A 194 SHEET 7 AA1 8 ILE A 219 ALA A 225 -1 N LEU A 220 O VAL A 242 SHEET 8 AA1 8 HIS A 271 VAL A 278 -1 O SER A 275 N GLN A 221 SHEET 1 AA2 2 ARG A 47 GLN A 49 0 SHEET 2 AA2 2 TYR A 96 PRO A 98 -1 O TYR A 97 N TYR A 48 SHEET 1 AA3 8 ALA B 137 GLU B 140 0 SHEET 2 AA3 8 SER B 113 THR B 117 1 N LEU B 116 O ARG B 138 SHEET 3 AA3 8 LEU B 37 ASP B 40 1 N ASP B 40 O GLN B 115 SHEET 4 AA3 8 GLY B 159 ILE B 163 1 O LEU B 160 N LEU B 39 SHEET 5 AA3 8 THR B 191 VAL B 198 1 O ALA B 193 N ILE B 161 SHEET 6 AA3 8 ALA B 237 ILE B 243 -1 O ILE B 241 N LEU B 194 SHEET 7 AA3 8 ILE B 219 ALA B 225 -1 N ILE B 222 O MET B 240 SHEET 8 AA3 8 HIS B 271 VAL B 278 -1 O HIS B 271 N ALA B 225 SHEET 1 AA4 2 ARG B 47 GLN B 49 0 SHEET 2 AA4 2 TYR B 96 PRO B 98 -1 O TYR B 97 N TYR B 48 LINK O3' GMP D 2 P A D 3 1555 1555 1.66 LINK N6 A D 3 C1 6D6 D 101 1555 1555 1.48 LINK O3' GMP E 2 P A E 3 1555 1555 1.66 LINK N6 A E 3 C1 6D6 E 101 1555 1555 1.48 CISPEP 1 LEU A 152 PRO A 153 0 0.27 CISPEP 2 LEU B 152 PRO B 153 0 -3.34 CRYST1 62.480 57.590 79.440 90.00 98.14 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 0.016005 0.000000 0.002289 0.00000 SCALE2 0.000000 0.017364 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012716 0.00000