HEADER TRANSFERASE/RNA 18-JAN-10 3ADC TITLE CRYSTAL STRUCTURE OF O-PHOSPHOSERYL-TRNA KINASE COMPLEXED WITH TITLE 2 SELENOCYSTEINE TRNA AND AMPPNP (CRYSTAL TYPE 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-SERYL-TRNA(SEC) KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: O-PHOSPHOSERYL-TRNA(SEC) KINASE, PSTK; COMPND 5 EC: 2.7.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SELENOCYSTEINE TRNA; COMPND 9 CHAIN: C, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_COMMON: METHANOCOCCUS JANNASCHII; SOURCE 4 ORGANISM_TAXID: 243232; SOURCE 5 STRAIN: DSM 2661; SOURCE 6 GENE: MJ1538; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCOLD II; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: METHANOPYRUS KANDLERI; SOURCE 15 ORGANISM_TAXID: 2320; SOURCE 16 OTHER_DETAILS: TRNASEC WAS PREPARED BY IN VITRO TRANSCRIPTION WITH SOURCE 17 T7 RNA POLYMERASE. KEYWDS PROTEIN-RNA COMPLEX, TRNA, ATP-BINDING, KINASE, NUCLEOTIDE-BINDING, KEYWDS 2 TRANSFERASE, TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.ITOH,S.CHIBA,S.SEKINE,S.YOKOYAMA REVDAT 4 15-NOV-23 3ADC 1 REMARK REVDAT 3 01-NOV-23 3ADC 1 REMARK DBREF SEQADV LINK REVDAT 2 01-SEP-10 3ADC 1 JRNL REVDAT 1 28-JUL-10 3ADC 0 JRNL AUTH S.CHIBA,Y.ITOH,S.SEKINE,S.YOKOYAMA JRNL TITL STRUCTURAL BASIS FOR THE MAJOR ROLE OF O-PHOSPHOSERYL-TRNA JRNL TITL 2 KINASE IN THE UGA-SPECIFIC ENCODING OF SELENOCYSTEINE JRNL REF MOL.CELL V. 39 410 2010 JRNL REFN ISSN 1097-2765 JRNL PMID 20705242 JRNL DOI 10.1016/J.MOLCEL.2010.07.018 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1829374.780 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 25842 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1326 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3810 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE : 0.3990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 213 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4069 REMARK 3 NUCLEIC ACID ATOMS : 3854 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 129.4 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 112.8 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 17.78000 REMARK 3 B22 (A**2) : -3.80000 REMARK 3 B33 (A**2) : -13.98000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.51 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.50 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.57 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.140 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.760 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.560 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.560 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.350 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 63.85 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : ANP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : ANP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3ADC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000029112. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A 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 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25889 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 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 (%) : 95.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : 0.12400 REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.66600 REMARK 200 R SYM FOR SHELL (I) : 0.66600 REMARK 200 FOR SHELL : 2.320 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: PDB ENTRY 3ADB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14.5% PEG 3350, 40MM SODIUM CITRATE REMARK 280 -HCL (PH 5.2), 260MM AMMONIUM TARTRATE, 5.0MM MAGNESIUM CHLORIDE, REMARK 280 1.0MM AMPPNP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 48.41200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 131.77900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.41200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 131.77900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 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 MSE A -10 REMARK 465 ASN A -9 REMARK 465 HIS A -8 REMARK 465 LYS A -7 REMARK 465 VAL A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 LYS A 180 REMARK 465 ASN A 181 REMARK 465 LYS A 182 REMARK 465 ASN A 183 REMARK 465 MSE B -10 REMARK 465 ASN B -9 REMARK 465 HIS B -8 REMARK 465 LYS B -7 REMARK 465 VAL B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 TYR B 174 REMARK 465 VAL B 175 REMARK 465 LEU B 176 REMARK 465 GLU B 177 REMARK 465 GLU B 178 REMARK 465 ASN B 179 REMARK 465 LYS B 180 REMARK 465 ASN B 181 REMARK 465 LYS B 182 REMARK 465 ASN B 183 REMARK 465 ASN B 184 REMARK 465 U C 33 REMARK 465 U C 34 REMARK 465 C C 35 REMARK 465 A C 36 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 G C 1 P G C 1 OP3 -0.086 REMARK 500 G D 1 P G D 1 OP3 -0.085 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 GLU A 169 170.30 -59.99 REMARK 500 TYR A 174 -74.84 -116.78 REMARK 500 GLU A 230 -72.14 -67.98 REMARK 500 SER A 247 45.41 -102.37 REMARK 500 ALA B 104 142.15 -172.98 REMARK 500 GLU B 169 172.44 -59.56 REMARK 500 LYS B 172 -73.25 -82.91 REMARK 500 LYS B 206 58.00 37.86 REMARK 500 GLU B 230 -74.46 -60.15 REMARK 500 SER B 247 37.91 -97.69 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 A2003 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 14 OG REMARK 620 2 HOH A1001 O 102.1 REMARK 620 3 HOH A1002 O 98.7 90.6 REMARK 620 4 HOH A1003 O 79.4 178.4 89.1 REMARK 620 5 ANP A2001 O3G 167.7 87.1 72.7 91.4 REMARK 620 6 ANP A2001 O2B 91.3 98.1 165.1 81.9 95.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B2004 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 14 OG REMARK 620 2 HOH B1004 O 101.0 REMARK 620 3 HOH B1005 O 96.0 91.0 REMARK 620 4 HOH B1006 O 82.0 175.9 85.9 REMARK 620 5 ANP B2002 O3G 166.6 87.1 73.1 89.5 REMARK 620 6 ANP B2002 O2B 93.9 97.6 165.4 84.9 95.5 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 ANP A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP B 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 2004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ADB RELATED DB: PDB REMARK 900 THE SAME PROTEIN-RNA COMPLEX WITH DIFFERENT CELL PARAMETERS REMARK 900 RELATED ID: 3ADD RELATED DB: PDB REMARK 900 THE SAME PROTEIN-RNA COMPLEX WITH DIFFERENT CELL PARAMETERS REMARK 999 REMARK 999 SEQUENCE REMARK 999 RNA USES NON-SEQUENTIAL NUMBERING. NUMBER 17 IS SIMPLY SKIPPED IN REMARK 999 BOTH RNA. DBREF 3ADC A 1 248 UNP Q58933 PSTK_METJA 1 248 DBREF 3ADC B 1 248 UNP Q58933 PSTK_METJA 1 248 DBREF 3ADC C 1 76 PDB 3ADC 3ADC 1 76 DBREF 3ADC D 1 76 PDB 3ADC 3ADC 1 76 SEQADV 3ADC MSE A -10 UNP Q58933 EXPRESSION TAG SEQADV 3ADC ASN A -9 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS A -8 UNP Q58933 EXPRESSION TAG SEQADV 3ADC LYS A -7 UNP Q58933 EXPRESSION TAG SEQADV 3ADC VAL A -6 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS A -5 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS A -4 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS A -3 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS A -2 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS A -1 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS A 0 UNP Q58933 EXPRESSION TAG SEQADV 3ADC MSE B -10 UNP Q58933 EXPRESSION TAG SEQADV 3ADC ASN B -9 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS B -8 UNP Q58933 EXPRESSION TAG SEQADV 3ADC LYS B -7 UNP Q58933 EXPRESSION TAG SEQADV 3ADC VAL B -6 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS B -5 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS B -4 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS B -3 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS B -2 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS B -1 UNP Q58933 EXPRESSION TAG SEQADV 3ADC HIS B 0 UNP Q58933 EXPRESSION TAG SEQRES 1 A 259 MSE ASN HIS LYS VAL HIS HIS HIS HIS HIS HIS MSE LEU SEQRES 2 A 259 ILE ILE LEU THR GLY LEU PRO GLY VAL GLY LYS SER THR SEQRES 3 A 259 PHE SER LYS ASN LEU ALA LYS ILE LEU SER LYS ASN ASN SEQRES 4 A 259 ILE ASP VAL ILE VAL LEU GLY SER ASP LEU ILE ARG GLU SEQRES 5 A 259 SER PHE PRO VAL TRP LYS GLU LYS TYR GLU GLU PHE ILE SEQRES 6 A 259 LYS LYS SER THR TYR ARG LEU ILE ASP SER ALA LEU LYS SEQRES 7 A 259 ASN TYR TRP VAL ILE VAL ASP ASP THR ASN TYR TYR ASN SEQRES 8 A 259 SER MSE ARG ARG ASP LEU ILE ASN ILE ALA LYS LYS TYR SEQRES 9 A 259 ASN LYS ASN TYR ALA ILE ILE TYR LEU LYS ALA SER LEU SEQRES 10 A 259 ASP VAL LEU ILE ARG ARG ASN ILE GLU ARG GLY GLU LYS SEQRES 11 A 259 ILE PRO ASN GLU VAL ILE LYS LYS MSE TYR GLU LYS PHE SEQRES 12 A 259 ASP GLU PRO GLY LYS LYS TYR LYS TRP ASP GLU PRO PHE SEQRES 13 A 259 LEU ILE ILE ASP THR THR LYS ASP ILE ASP PHE ASN GLU SEQRES 14 A 259 ILE ALA LYS LYS LEU ILE GLU LYS SER LYS GLU ILE PRO SEQRES 15 A 259 LYS PHE TYR VAL LEU GLU GLU ASN LYS ASN LYS ASN ASN SEQRES 16 A 259 ASN ILE SER ASP LYS ILE ASP LYS GLU THR ARG LYS ILE SEQRES 17 A 259 VAL SER GLU TYR ILE LYS SER LYS LYS LEU ASP LYS ASP SEQRES 18 A 259 LYS ILE LYS GLU VAL VAL GLU LEU ARG LYS GLU PHE LEU SEQRES 19 A 259 LYS LYS ILE LYS LYS MSE GLU GLU VAL ASP ALA ASP ARG SEQRES 20 A 259 VAL LEU LYS GLU PHE LYS ASP LEU LEU ASN SER TYR SEQRES 1 B 259 MSE ASN HIS LYS VAL HIS HIS HIS HIS HIS HIS MSE LEU SEQRES 2 B 259 ILE ILE LEU THR GLY LEU PRO GLY VAL GLY LYS SER THR SEQRES 3 B 259 PHE SER LYS ASN LEU ALA LYS ILE LEU SER LYS ASN ASN SEQRES 4 B 259 ILE ASP VAL ILE VAL LEU GLY SER ASP LEU ILE ARG GLU SEQRES 5 B 259 SER PHE PRO VAL TRP LYS GLU LYS TYR GLU GLU PHE ILE SEQRES 6 B 259 LYS LYS SER THR TYR ARG LEU ILE ASP SER ALA LEU LYS SEQRES 7 B 259 ASN TYR TRP VAL ILE VAL ASP ASP THR ASN TYR TYR ASN SEQRES 8 B 259 SER MSE ARG ARG ASP LEU ILE ASN ILE ALA LYS LYS TYR SEQRES 9 B 259 ASN LYS ASN TYR ALA ILE ILE TYR LEU LYS ALA SER LEU SEQRES 10 B 259 ASP VAL LEU ILE ARG ARG ASN ILE GLU ARG GLY GLU LYS SEQRES 11 B 259 ILE PRO ASN GLU VAL ILE LYS LYS MSE TYR GLU LYS PHE SEQRES 12 B 259 ASP GLU PRO GLY LYS LYS TYR LYS TRP ASP GLU PRO PHE SEQRES 13 B 259 LEU ILE ILE ASP THR THR LYS ASP ILE ASP PHE ASN GLU SEQRES 14 B 259 ILE ALA LYS LYS LEU ILE GLU LYS SER LYS GLU ILE PRO SEQRES 15 B 259 LYS PHE TYR VAL LEU GLU GLU ASN LYS ASN LYS ASN ASN SEQRES 16 B 259 ASN ILE SER ASP LYS ILE ASP LYS GLU THR ARG LYS ILE SEQRES 17 B 259 VAL SER GLU TYR ILE LYS SER LYS LYS LEU ASP LYS ASP SEQRES 18 B 259 LYS ILE LYS GLU VAL VAL GLU LEU ARG LYS GLU PHE LEU SEQRES 19 B 259 LYS LYS ILE LYS LYS MSE GLU GLU VAL ASP ALA ASP ARG SEQRES 20 B 259 VAL LEU LYS GLU PHE LYS ASP LEU LEU ASN SER TYR SEQRES 1 C 92 G G C C G C C G C C A C C SEQRES 2 C 92 G G G G U G G U C C C C G SEQRES 3 C 92 G G C C G G A C U U C A G SEQRES 4 C 92 A U C C G G C G C G C C C SEQRES 5 C 92 C G A G U G G G G C G C G SEQRES 6 C 92 G G G U U C A A U U C C C SEQRES 7 C 92 C G C G G C G G C C G C C SEQRES 8 C 92 A SEQRES 1 D 92 G G C C G C C G C C A C C SEQRES 2 D 92 G G G G U G G U C C C C G SEQRES 3 D 92 G G C C G G A C U U C A G SEQRES 4 D 92 A U C C G G C G C G C C C SEQRES 5 D 92 C G A G U G G G G C G C G SEQRES 6 D 92 G G G U U C A A U U C C C SEQRES 7 D 92 C G C G G C G G C C G C C SEQRES 8 D 92 A MODRES 3ADC MSE A 1 MET SELENOMETHIONINE MODRES 3ADC MSE A 82 MET SELENOMETHIONINE MODRES 3ADC MSE A 128 MET SELENOMETHIONINE MODRES 3ADC MSE A 229 MET SELENOMETHIONINE MODRES 3ADC MSE B 1 MET SELENOMETHIONINE MODRES 3ADC MSE B 82 MET SELENOMETHIONINE MODRES 3ADC MSE B 128 MET SELENOMETHIONINE MODRES 3ADC MSE B 229 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 82 8 HET MSE A 128 8 HET MSE A 229 8 HET MSE B 1 8 HET MSE B 82 8 HET MSE B 128 8 HET MSE B 229 8 HET ANP A2001 31 HET MG A2003 1 HET ANP B2002 31 HET MG B2004 1 HETNAM MSE SELENOMETHIONINE HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 5 ANP 2(C10 H17 N6 O12 P3) FORMUL 6 MG 2(MG 2+) FORMUL 9 HOH *36(H2 O) HELIX 1 1 GLY A 12 ASN A 27 1 16 HELIX 2 2 SER A 36 GLU A 41 1 6 HELIX 3 3 LYS A 49 LEU A 66 1 18 HELIX 4 4 TYR A 79 TYR A 93 1 15 HELIX 5 5 SER A 105 GLU A 115 1 11 HELIX 6 6 PRO A 121 PHE A 132 1 12 HELIX 7 7 ASP A 155 GLU A 169 1 15 HELIX 8 8 ASN A 184 LYS A 205 1 22 HELIX 9 9 ASP A 208 LYS A 227 1 20 HELIX 10 10 ASP A 233 SER A 247 1 15 HELIX 11 11 GLY B 12 ASN B 27 1 16 HELIX 12 12 SER B 36 GLU B 41 1 6 HELIX 13 13 LYS B 49 LEU B 66 1 18 HELIX 14 14 TYR B 79 TYR B 93 1 15 HELIX 15 15 SER B 105 GLU B 115 1 11 HELIX 16 16 PRO B 121 LYS B 131 1 11 HELIX 17 17 TYR B 139 GLU B 143 5 5 HELIX 18 18 ASP B 155 GLU B 169 1 15 HELIX 19 19 ASN B 185 LYS B 206 1 22 HELIX 20 20 ASP B 208 LYS B 227 1 20 HELIX 21 21 ASP B 233 SER B 247 1 15 SHEET 1 A 5 VAL A 31 LEU A 34 0 SHEET 2 A 5 TRP A 70 VAL A 73 1 O ILE A 72 N ILE A 32 SHEET 3 A 5 MSE A 1 THR A 6 1 N ILE A 3 O VAL A 73 SHEET 4 A 5 ASN A 96 LYS A 103 1 O ILE A 100 N ILE A 4 SHEET 5 A 5 LEU A 146 ASP A 149 1 O ILE A 148 N LYS A 103 SHEET 1 B 5 VAL B 31 LEU B 34 0 SHEET 2 B 5 TRP B 70 VAL B 73 1 O ILE B 72 N ILE B 32 SHEET 3 B 5 LEU B 2 THR B 6 1 N ILE B 3 O VAL B 73 SHEET 4 B 5 TYR B 97 LYS B 103 1 O ILE B 100 N ILE B 4 SHEET 5 B 5 LEU B 146 ASP B 149 1 O ILE B 148 N LYS B 103 LINK C HIS A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N LEU A 2 1555 1555 1.33 LINK C SER A 81 N MSE A 82 1555 1555 1.34 LINK C MSE A 82 N ARG A 83 1555 1555 1.33 LINK C LYS A 127 N MSE A 128 1555 1555 1.33 LINK C MSE A 128 N TYR A 129 1555 1555 1.33 LINK C LYS A 228 N MSE A 229 1555 1555 1.33 LINK C MSE A 229 N GLU A 230 1555 1555 1.32 LINK C HIS B 0 N MSE B 1 1555 1555 1.32 LINK C MSE B 1 N LEU B 2 1555 1555 1.33 LINK C SER B 81 N MSE B 82 1555 1555 1.33 LINK C MSE B 82 N ARG B 83 1555 1555 1.33 LINK C LYS B 127 N MSE B 128 1555 1555 1.33 LINK C MSE B 128 N TYR B 129 1555 1555 1.33 LINK C LYS B 228 N MSE B 229 1555 1555 1.33 LINK C MSE B 229 N GLU B 230 1555 1555 1.34 LINK OG SER A 14 MG MG A2003 1555 1555 1.87 LINK O HOH A1001 MG MG A2003 1555 1555 2.09 LINK O HOH A1002 MG MG A2003 1555 1555 2.10 LINK O HOH A1003 MG MG A2003 1555 1555 2.10 LINK O3G ANP A2001 MG MG A2003 1555 1555 2.01 LINK O2B ANP A2001 MG MG A2003 1555 1555 2.07 LINK OG SER B 14 MG MG B2004 1555 1555 1.87 LINK O HOH B1004 MG MG B2004 1555 1555 2.11 LINK O HOH B1005 MG MG B2004 1555 1555 2.09 LINK O HOH B1006 MG MG B2004 1555 1555 2.09 LINK O3G ANP B2002 MG MG B2004 1555 1555 2.01 LINK O2B ANP B2002 MG MG B2004 1555 1555 2.07 SITE 1 AC1 16 PRO A 9 GLY A 10 VAL A 11 GLY A 12 SITE 2 AC1 16 LYS A 13 SER A 14 THR A 15 ASP A 37 SITE 3 AC1 16 ARG A 112 ARG A 116 THR A 150 HOH A1001 SITE 4 AC1 16 HOH A1002 HOH A1003 MG A2003 G C 37 SITE 1 AC2 6 SER A 14 ASP A 74 HOH A1001 HOH A1002 SITE 2 AC2 6 HOH A1003 ANP A2001 SITE 1 AC3 15 PRO B 9 GLY B 10 VAL B 11 GLY B 12 SITE 2 AC3 15 LYS B 13 SER B 14 THR B 15 ASP B 37 SITE 3 AC3 15 ARG B 112 ARG B 116 THR B 150 HOH B1004 SITE 4 AC3 15 HOH B1005 HOH B1006 MG B2004 SITE 1 AC4 6 SER B 14 ASP B 74 HOH B1004 HOH B1005 SITE 2 AC4 6 HOH B1006 ANP B2002 CRYST1 96.824 263.558 46.122 90.00 90.00 90.00 P 21 21 2 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 0.010328 0.000000 0.000000 0.00000 SCALE2 0.000000 0.003794 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021682 0.00000