HEADER TRANSFERASE/RNA 31-JUL-15 5AXN TITLE CRYSTAL STRUCTURE OF THG1 LIKE PROTEIN (TLP) WITH TRNA(PHE) AND GDPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA(HIS)-5'-GUANYLYLTRANSFERASE (THG1) LIKE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (75-MER); COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA ACETIVORANS; SOURCE 3 ORGANISM_TAXID: 2214; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET26B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 12 ORGANISM_TAXID: 4932 KEYWDS TRANSFERASE, TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.KIMURA,T.SUZUKI,J.YU,K.KATO,M.YAO REVDAT 3 08-NOV-23 5AXN 1 LINK REVDAT 2 26-FEB-20 5AXN 1 REMARK REVDAT 1 03-AUG-16 5AXN 0 JRNL AUTH S.KIMURA,T.SUZUKI,M.CHEN,K.KATO,J.YU,A.NAKAMURA,I.TANAKA, JRNL AUTH 2 M.YAO JRNL TITL TEMPLATE-DEPENDENT NUCLEOTIDE ADDITION IN THE REVERSE JRNL TITL 2 (3'-5') DIRECTION BY THG1-LIKE PROTEIN JRNL REF SCI ADV V. 2 01397 2016 JRNL REFN ESSN 2375-2548 JRNL PMID 27051866 JRNL DOI 10.1126/SCIADV.1501397 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 22661 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1152 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 42.7672 - 5.4024 1.00 2822 150 0.2087 0.2264 REMARK 3 2 5.4024 - 4.2893 1.00 2694 156 0.1935 0.2130 REMARK 3 3 4.2893 - 3.7475 1.00 2689 149 0.2067 0.2684 REMARK 3 4 3.7475 - 3.4050 1.00 2693 138 0.2291 0.3250 REMARK 3 5 3.4050 - 3.1610 1.00 2650 135 0.2363 0.2845 REMARK 3 6 3.1610 - 2.9747 1.00 2646 169 0.2649 0.3182 REMARK 3 7 2.9747 - 2.8258 1.00 2655 121 0.2886 0.3571 REMARK 3 8 2.8258 - 2.7028 0.99 2660 134 0.3287 0.3546 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) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.980 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 : 0.007 5497 REMARK 3 ANGLE : 0.803 7727 REMARK 3 CHIRALITY : 0.031 883 REMARK 3 PLANARITY : 0.003 727 REMARK 3 DIHEDRAL : 18.191 2285 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 5AXN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1300000129. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 - 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22669 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10300 REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.81700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3WBZ, 1EHZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, TRI-POTASSIUM CITRATE, PH REMARK 280 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 41.12750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.02600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 73.69200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.12750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.02600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.69200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.12750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 67.02600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.69200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.12750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 67.02600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.69200 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -216.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLU A 150 REMARK 465 GLY A 151 REMARK 465 GLU A 196 REMARK 465 ALA A 197 REMARK 465 ARG A 198 REMARK 465 GLU A 199 REMARK 465 ILE A 200 REMARK 465 GLN A 201 REMARK 465 GLY A 202 REMARK 465 PHE A 203 REMARK 465 ASN A 204 REMARK 465 PRO A 205 REMARK 465 VAL A 206 REMARK 465 SER A 207 REMARK 465 GLY A 208 REMARK 465 LYS A 209 REMARK 465 GLU A 210 REMARK 465 GLU A 211 REMARK 465 LYS A 212 REMARK 465 SER A 213 REMARK 465 LEU A 214 REMARK 465 ARG A 215 REMARK 465 ARG A 242 REMARK 465 ASN A 243 REMARK 465 LEU A 244 REMARK 465 GLU A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 HIS A 251 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 ARG B 242 REMARK 465 ASN B 243 REMARK 465 LEU B 244 REMARK 465 GLU B 245 REMARK 465 HIS B 246 REMARK 465 HIS B 247 REMARK 465 HIS B 248 REMARK 465 HIS B 249 REMARK 465 HIS B 250 REMARK 465 HIS B 251 REMARK 465 A P 31 REMARK 465 C P 32 REMARK 465 U P 33 REMARK 465 G P 34 REMARK 465 A P 35 REMARK 465 A P 36 REMARK 465 G P 37 REMARK 465 C P 75 REMARK 465 A P 76 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 O ASN A 24 OG1 THR A 28 2.19 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 GTP P 2 C3' - O3' - P ANGL. DEV. = -18.1 DEGREES REMARK 500 G P 3 O3' - P - OP2 ANGL. DEV. = 17.7 DEGREES REMARK 500 G P 3 O3' - P - OP1 ANGL. DEV. = -24.9 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 SER A 60 74.10 53.04 REMARK 500 ASP A 69 50.37 -108.27 REMARK 500 ARG A 163 -4.55 67.07 REMARK 500 GLU A 175 1.89 -67.83 REMARK 500 SER A 229 -177.67 -173.87 REMARK 500 LYS A 231 49.26 -97.16 REMARK 500 SER B 68 -121.47 53.18 REMARK 500 GLU B 121 -7.18 -57.93 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 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD2 REMARK 620 2 ASP A 69 OD1 90.4 REMARK 620 3 GNP A 304 O3' 101.9 140.9 REMARK 620 4 GTP P 2 O1A 99.8 77.3 64.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD1 REMARK 620 2 GLY A 22 O 85.7 REMARK 620 3 ASP A 69 OD1 86.2 117.6 REMARK 620 4 ASP A 69 OD2 131.1 100.0 48.1 REMARK 620 5 GTP P 2 O2G 72.3 76.6 153.6 156.4 REMARK 620 6 GTP P 2 O1B 155.9 89.2 116.8 72.9 83.6 REMARK 620 7 GTP P 2 O1A 92.3 158.4 83.7 97.5 82.3 83.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GNP A 304 O3G REMARK 620 2 GNP A 304 O1B 81.6 REMARK 620 3 GNP A 304 O1A 79.2 63.3 REMARK 620 4 HOH A 401 O 121.5 100.6 52.8 REMARK 620 5 HOH A 406 O 92.9 154.9 91.6 61.4 REMARK 620 6 HOH P 102 O 102.8 104.3 167.3 131.7 100.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 21 OD2 REMARK 620 2 GLY B 22 O 93.6 REMARK 620 3 ASP B 69 OD2 103.3 85.3 REMARK 620 4 GNP B 301 O2G 93.5 104.3 160.1 REMARK 620 5 GNP B 301 O2B 171.6 94.7 79.0 82.9 REMARK 620 6 GNP B 301 O2A 95.6 164.2 80.0 88.0 76.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 21 OD1 REMARK 620 2 GNP B 301 O1A 127.7 REMARK 620 3 GNP B 301 O2A 81.2 52.5 REMARK 620 4 HOH B 403 O 73.6 67.7 67.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide GTP P 2 and G P 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AXK RELATED DB: PDB REMARK 900 RELATED ID: 5AXL RELATED DB: PDB REMARK 900 RELATED ID: 5AXM RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 142ND RESIDUE IN THE ORIGINAL SEQUENCE IS PYL(PYRROLYSINE). REMARK 999 THIS IS (PYL)142W MUTANT. REMARK 999 THE RESIDUES 244-251 ARE EXPRESSION TAGS. DBREF 5AXN A 1 251 PDB 5AXN 5AXN 1 251 DBREF 5AXN B 1 251 PDB 5AXN 5AXN 1 251 DBREF 5AXN P 2 76 PDB 5AXN 5AXN 2 76 SEQRES 1 A 251 MET LYS THR ARG GLU ILE TYR ALA GLU MET ARG CYS ILE SEQRES 2 A 251 PRO PRO VAL VAL LEU ARG ALA ASP GLY ARG ASN PHE LYS SEQRES 3 A 251 ASN THR LEU SER GLY LEU GLY PHE GLU LYS PRO TYR ASP SEQRES 4 A 251 LYS THR PHE ALA ARG ALA MET ALA ASP THR ALA GLU LEU SEQRES 5 A 251 PHE ILE LYS LYS SER GLY LEU SER PRO LEU PHE ALA TYR SEQRES 6 A 251 THR PHE SER ASP GLU ILE SER PHE LEU PHE THR ASP LEU SEQRES 7 A 251 PRO PHE ASP GLY ARG VAL GLU LYS ILE ASP SER VAL VAL SEQRES 8 A 251 ALA SER PHE LEU GLY SER ALA LEU THR ILE LYS LEU ARG SEQRES 9 A 251 LEU GLU GLU PRO ILE ALA PHE ASP SER ARG LEU VAL ALA SEQRES 10 A 251 LEU GLN LYS GLU GLU ILE PRO GLU TYR PHE HIS ARG ARG SEQRES 11 A 251 GLN LEU GLU ALA TRP ARG ASN PHE VAL ALA SER TRP GLY SEQRES 12 A 251 TYR TYR ALA LEU ARG ASN GLU GLY MET GLY ARG ASN GLU SEQRES 13 A 251 ALA ALA LYS TYR LEU LYS ARG LYS LYS GLU SER GLU ILE SEQRES 14 A 251 HIS GLU MET LEU PHE GLU ARG GLY ILE ASN LEU ALA THR SEQRES 15 A 251 LEU PRO SER TRP GLN ARG ARG GLY VAL ILE ILE SER LYS SEQRES 16 A 251 GLU ALA ARG GLU ILE GLN GLY PHE ASN PRO VAL SER GLY SEQRES 17 A 251 LYS GLU GLU LYS SER LEU ARG ARG LYS ILE THR GLN ASN SEQRES 18 A 251 TRP GLU ILE PRO LYS PHE LYS SER GLU LYS GLY ILE PRO SEQRES 19 A 251 PHE LEU GLU LYS LEU ILE ASN ARG ASN LEU GLU HIS HIS SEQRES 20 A 251 HIS HIS HIS HIS SEQRES 1 B 251 MET LYS THR ARG GLU ILE TYR ALA GLU MET ARG CYS ILE SEQRES 2 B 251 PRO PRO VAL VAL LEU ARG ALA ASP GLY ARG ASN PHE LYS SEQRES 3 B 251 ASN THR LEU SER GLY LEU GLY PHE GLU LYS PRO TYR ASP SEQRES 4 B 251 LYS THR PHE ALA ARG ALA MET ALA ASP THR ALA GLU LEU SEQRES 5 B 251 PHE ILE LYS LYS SER GLY LEU SER PRO LEU PHE ALA TYR SEQRES 6 B 251 THR PHE SER ASP GLU ILE SER PHE LEU PHE THR ASP LEU SEQRES 7 B 251 PRO PHE ASP GLY ARG VAL GLU LYS ILE ASP SER VAL VAL SEQRES 8 B 251 ALA SER PHE LEU GLY SER ALA LEU THR ILE LYS LEU ARG SEQRES 9 B 251 LEU GLU GLU PRO ILE ALA PHE ASP SER ARG LEU VAL ALA SEQRES 10 B 251 LEU GLN LYS GLU GLU ILE PRO GLU TYR PHE HIS ARG ARG SEQRES 11 B 251 GLN LEU GLU ALA TRP ARG ASN PHE VAL ALA SER TRP GLY SEQRES 12 B 251 TYR TYR ALA LEU ARG ASN GLU GLY MET GLY ARG ASN GLU SEQRES 13 B 251 ALA ALA LYS TYR LEU LYS ARG LYS LYS GLU SER GLU ILE SEQRES 14 B 251 HIS GLU MET LEU PHE GLU ARG GLY ILE ASN LEU ALA THR SEQRES 15 B 251 LEU PRO SER TRP GLN ARG ARG GLY VAL ILE ILE SER LYS SEQRES 16 B 251 GLU ALA ARG GLU ILE GLN GLY PHE ASN PRO VAL SER GLY SEQRES 17 B 251 LYS GLU GLU LYS SER LEU ARG ARG LYS ILE THR GLN ASN SEQRES 18 B 251 TRP GLU ILE PRO LYS PHE LYS SER GLU LYS GLY ILE PRO SEQRES 19 B 251 PHE LEU GLU LYS LEU ILE ASN ARG ASN LEU GLU HIS HIS SEQRES 20 B 251 HIS HIS HIS HIS SEQRES 1 P 75 GTP G G A U U U A G C U C A SEQRES 2 P 75 G U U G G G A G A G C G C SEQRES 3 P 75 C A G A C U G A A G A U C SEQRES 4 P 75 U G G A G G U C C U G U G SEQRES 5 P 75 U U C G A U C C A C A G A SEQRES 6 P 75 A U C C C C A C C A HET GTP P 2 32 HET MG A 301 1 HET MG A 302 1 HET MG A 303 1 HET GNP A 304 32 HET GNP B 301 32 HET MG B 302 1 HET MG B 303 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER FORMUL 3 GTP C10 H16 N5 O14 P3 FORMUL 4 MG 5(MG 2+) FORMUL 7 GNP 2(C10 H17 N6 O13 P3) FORMUL 11 HOH *16(H2 O) HELIX 1 AA1 ASN A 24 LEU A 29 1 6 HELIX 2 AA2 ASP A 39 SER A 57 1 19 HELIX 3 AA3 LEU A 78 GLY A 82 5 5 HELIX 4 AA4 ARG A 83 ARG A 104 1 22 HELIX 5 AA5 GLU A 122 LEU A 147 1 26 HELIX 6 AA6 GLY A 153 LYS A 162 1 10 HELIX 7 AA7 LYS A 165 GLU A 175 1 11 HELIX 8 AA8 ASN A 179 LEU A 183 5 5 HELIX 9 AA9 PRO A 184 ARG A 189 1 6 HELIX 10 AB1 LYS A 231 ASN A 241 1 11 HELIX 11 AB2 ASN B 24 GLY B 33 1 10 HELIX 12 AB3 ASP B 39 SER B 57 1 19 HELIX 13 AB4 PRO B 79 GLY B 82 5 4 HELIX 14 AB5 ARG B 83 ARG B 104 1 22 HELIX 15 AB6 GLN B 119 GLU B 121 5 3 HELIX 16 AB7 GLU B 122 GLU B 150 1 29 HELIX 17 AB8 GLY B 153 LYS B 164 1 12 HELIX 18 AB9 LYS B 165 ARG B 176 1 12 HELIX 19 AC1 PRO B 184 GLY B 190 1 7 HELIX 20 AC2 LYS B 231 ASN B 241 1 11 SHEET 1 AA1 6 PHE A 111 VAL A 116 0 SHEET 2 AA1 6 VAL A 16 GLY A 22 -1 N VAL A 17 O VAL A 116 SHEET 3 AA1 6 GLU A 70 PHE A 75 -1 O ILE A 71 N ALA A 20 SHEET 4 AA1 6 ALA A 64 PHE A 67 -1 N TYR A 65 O SER A 72 SHEET 5 AA1 6 VAL A 191 SER A 194 -1 O ILE A 193 N ALA A 64 SHEET 6 AA1 6 THR A 219 ASN A 221 -1 O ASN A 221 N ILE A 192 SHEET 1 AA2 6 PHE B 111 ALA B 117 0 SHEET 2 AA2 6 VAL B 16 GLY B 22 -1 N ASP B 21 O ASP B 112 SHEET 3 AA2 6 GLU B 70 PHE B 75 -1 O ILE B 71 N ALA B 20 SHEET 4 AA2 6 ALA B 64 PHE B 67 -1 N PHE B 67 O GLU B 70 SHEET 5 AA2 6 VAL B 191 ASN B 204 -1 O VAL B 191 N THR B 66 SHEET 6 AA2 6 LYS B 209 ASN B 221 -1 O ASN B 221 N ILE B 192 LINK O3' GTP P 2 P G P 3 1555 1555 1.60 LINK OD2 ASP A 21 MG MG A 301 1555 1555 2.55 LINK OD1 ASP A 21 MG MG A 302 1555 1555 2.35 LINK O GLY A 22 MG MG A 302 1555 1555 2.09 LINK OD1 ASP A 69 MG MG A 301 1555 1555 2.50 LINK OD1 ASP A 69 MG MG A 302 1555 1555 2.69 LINK OD2 ASP A 69 MG MG A 302 1555 1555 2.70 LINK MG MG A 301 O3' GNP A 304 1555 1555 2.90 LINK MG MG A 301 O1A GTP P 2 1555 1555 2.80 LINK MG MG A 302 O2G GTP P 2 1555 1555 2.39 LINK MG MG A 302 O1B GTP P 2 1555 1555 2.07 LINK MG MG A 302 O1A GTP P 2 1555 1555 2.26 LINK MG MG A 303 O3G GNP A 304 1555 1555 2.11 LINK MG MG A 303 O1B GNP A 304 1555 1555 2.12 LINK MG MG A 303 O1A GNP A 304 1555 1555 2.79 LINK MG MG A 303 O HOH A 401 1555 1555 2.02 LINK MG MG A 303 O HOH A 406 1555 1555 2.46 LINK MG MG A 303 O HOH P 102 1555 1555 2.19 LINK OD2 ASP B 21 MG MG B 302 1555 1555 2.16 LINK OD1 ASP B 21 MG MG B 303 1555 1555 2.74 LINK O GLY B 22 MG MG B 302 1555 1555 1.97 LINK OD2 ASP B 69 MG MG B 302 1555 1555 2.23 LINK O2G GNP B 301 MG MG B 302 1555 1555 2.10 LINK O2B GNP B 301 MG MG B 302 1555 1555 2.15 LINK O2A GNP B 301 MG MG B 302 1555 1555 2.07 LINK O1A GNP B 301 MG MG B 303 1555 1555 2.88 LINK O2A GNP B 301 MG MG B 303 1555 1555 2.81 LINK MG MG B 303 O HOH B 403 1555 1555 2.93 CISPEP 1 PRO A 14 PRO A 15 0 -4.46 CISPEP 2 LYS A 36 PRO A 37 0 -2.20 CISPEP 3 SER A 68 ASP A 69 0 3.33 CISPEP 4 GLU A 230 LYS A 231 0 0.46 CISPEP 5 PRO B 14 PRO B 15 0 6.06 CISPEP 6 LYS B 36 PRO B 37 0 -4.00 SITE 1 AC1 5 ASP A 21 ASP A 69 MG A 302 GNP A 304 SITE 2 AC1 5 GTP P 2 SITE 1 AC2 5 ASP A 21 GLY A 22 ASP A 69 MG A 301 SITE 2 AC2 5 GTP P 2 SITE 1 AC3 5 GNP A 304 HOH A 401 HOH A 406 LYS B 86 SITE 2 AC3 5 HOH P 102 SITE 1 AC4 11 ARG A 19 ARG A 114 GLU A 133 MG A 301 SITE 2 AC4 11 MG A 303 HOH A 401 HOH A 404 ARG B 83 SITE 3 AC4 11 LYS B 86 GTP P 2 C P 72 SITE 1 AC5 15 ASP B 21 GLY B 22 ARG B 23 ASN B 24 SITE 2 AC5 15 PHE B 25 LYS B 26 GLU B 35 PRO B 37 SITE 3 AC5 15 ASP B 39 PHE B 42 SER B 68 ASP B 69 SITE 4 AC5 15 MG B 302 MG B 303 HOH B 403 SITE 1 AC6 4 ASP B 21 GLY B 22 ASP B 69 GNP B 301 SITE 1 AC7 3 ASP B 21 GNP B 301 HOH B 403 SITE 1 AC8 17 ASP A 21 GLY A 22 ASN A 24 PHE A 25 SITE 2 AC8 17 LYS A 26 ASP A 69 TYR A 144 ALA A 158 SITE 3 AC8 17 MG A 301 MG A 302 GNP A 304 HOH A 405 SITE 4 AC8 17 G P 4 C P 70 C P 71 HOH P 101 SITE 5 AC8 17 HOH P 102 CRYST1 82.255 134.052 147.384 90.00 90.00 90.00 I 2 2 2 16 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 0.012157 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007460 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006785 0.00000