HEADER RNA BINDING PROTEIN/RNA 28-FEB-18 5ZEY TITLE M. SMEGMATIS TRANS-TRANSLATION STATE 70S RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: TMRNA; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: A-TRNAFMET; COMPND 6 CHAIN: B; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: SSRA-BINDING PROTEIN; COMPND 9 CHAIN: C; COMPND 10 SYNONYM: SMALL PROTEIN B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / SOURCE 3 MC(2)155); SOURCE 4 ORGANISM_TAXID: 246196; SOURCE 5 STRAIN: ATCC 700084 / MC(2)155; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 8 ORGANISM_TAXID: 562; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / SOURCE 11 MC(2)155); SOURCE 12 ORGANISM_TAXID: 246196; SOURCE 13 STRAIN: ATCC 700084 / MC(2)155 KEYWDS TRANS-TRANSLATING STATE, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR S.MISHRA,T.AHMED,A.TYAGI,J.SHI,S.BHUSHAN REVDAT 3 27-MAR-24 5ZEY 1 REMARK REVDAT 2 03-JUN-20 5ZEY 1 HEADER KEYWDS REVDAT 1 26-SEP-18 5ZEY 0 JRNL AUTH S.MISHRA,T.AHMED,A.TYAGI,J.SHI,S.BHUSHAN JRNL TITL STRUCTURES OF MYCOBACTERIUM SMEGMATIS 70S RIBOSOMES IN JRNL TITL 2 COMPLEX WITH HPF, TMRNA, AND P-TRNA. JRNL REF SCI REP V. 8 13587 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 30206241 JRNL DOI 10.1038/S41598-018-31850-3 REMARK 2 REMARK 2 RESOLUTION. 12.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 12.50 REMARK 3 NUMBER OF PARTICLES : 391837 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 5ZEY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-18. REMARK 100 THE DEPOSITION ID IS D_1300006937. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : TMRNA AND SMPB IN TRANS REMARK 245 -TRANSLATING STATE OF M. REMARK 245 SMEGMATIS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON II (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 150.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 OP2 G A 152 O2' C A 165 1.29 REMARK 500 OP1 A A 238 N2 G A 243 1.58 REMARK 500 O2' C A 26 OP2 A A 27 1.61 REMARK 500 O2' G A 339 N7 A A 340 1.78 REMARK 500 O2' A A 91 NE2 GLN C 132 1.86 REMARK 500 O GLY C 32 CD2 LEU C 89 1.87 REMARK 500 O2' U A 13 NZ LYS C 120 1.98 REMARK 500 N2 G A 152 C5' A A 196 1.99 REMARK 500 N1 A A 200 O6 G A 228 2.01 REMARK 500 N1 A A 200 C6 G A 228 2.04 REMARK 500 N7 G A 60 O4 U A 79 2.11 REMARK 500 O2 U A 127 N2 G A 140 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 C B 1 P C B 1 OP3 -0.127 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 C 3 86.98 -155.83 REMARK 500 LYS C 4 90.04 57.41 REMARK 500 SER C 5 -91.21 54.66 REMARK 500 SER C 7 -36.18 -137.31 REMARK 500 LYS C 11 -17.39 -154.71 REMARK 500 VAL C 13 113.33 66.87 REMARK 500 LEU C 26 -71.15 -145.82 REMARK 500 GLN C 47 79.06 -116.16 REMARK 500 LEU C 50 58.24 -117.39 REMARK 500 ASP C 59 -86.61 63.57 REMARK 500 ASN C 66 80.53 56.45 REMARK 500 ALA C 70 -77.69 -61.95 REMARK 500 HIS C 73 -96.22 -111.53 REMARK 500 ASN C 79 -169.93 59.44 REMARK 500 HIS C 80 68.15 -164.12 REMARK 500 ALA C 81 87.23 56.48 REMARK 500 ARG C 83 61.23 -109.31 REMARK 500 LEU C 90 -151.89 -162.74 REMARK 500 ARG C 103 43.45 -107.04 REMARK 500 ASP C 104 -80.49 -125.37 REMARK 500 ASN C 106 73.89 55.84 REMARK 500 LEU C 112 -103.45 -110.53 REMARK 500 THR C 117 -153.96 -84.45 REMARK 500 ASP C 118 81.43 -66.62 REMARK 500 HIS C 134 -136.76 59.91 REMARK 500 ARG C 137 -75.19 58.32 REMARK 500 ALA C 141 -28.85 -154.43 REMARK 500 GLN C 146 -58.74 -126.84 REMARK 500 LYS C 160 -100.25 56.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-6925 RELATED DB: EMDB REMARK 900 STRUCTURE OF THE TRANS-TRANSLATING STATE MODEL OF M. SMEGMATIS DBREF1 5ZEY A 1 369 GB CP000480.1 DBREF2 5ZEY A 118168627 2169257 2169625 DBREF1 5ZEY B 1 77 GB CP016018.1 DBREF2 5ZEY B 1036415628 565475 565551 DBREF 5ZEY C 1 161 UNP A0QU63 SSRP_MYCS2 1 161 SEQRES 1 A 369 G G G G C U G A A C G G U SEQRES 2 A 369 U U C G A C U U C G A G C SEQRES 3 A 369 A U C G A A U C C A G G G SEQRES 4 A 369 A A G C G U G C C G G U G SEQRES 5 A 369 C A G G C A A G A G A C C SEQRES 6 A 369 A C C G U A A G C G U C G SEQRES 7 A 369 U U G C A A C C A A U U A SEQRES 8 A 369 A G C G C C G A U U C C A SEQRES 9 A 369 A U C A G C G C G A C U A SEQRES 10 A 369 C G C C C U C G C U G C C SEQRES 11 A 369 U A A G C G A C G G C U G SEQRES 12 A 369 G U C U G U C A G A C C G SEQRES 13 A 369 G G A G U G C C C U C G G SEQRES 14 A 369 C C C G G A U C C U G G C SEQRES 15 A 369 A U C A G C U A G A G G G SEQRES 16 A 369 A C C C A C C C A C G G G SEQRES 17 A 369 U U C G G U C G C G G G A SEQRES 18 A 369 C C U G U G G G G A C A U SEQRES 19 A 369 C A A A C A G C G A C U G SEQRES 20 A 369 G G A U C G U C A U C U C SEQRES 21 A 369 G G C U U G U U C G U G U SEQRES 22 A 369 G A C C G G G A G A U C C SEQRES 23 A 369 G A G U A G A G A C A U A SEQRES 24 A 369 G C G A A C U G C G C A C SEQRES 25 A 369 G G A G A A G C C U C G A SEQRES 26 A 369 G G A C A U G C C G U A G SEQRES 27 A 369 G A C C C G G G U U C A A SEQRES 28 A 369 U U C C C G G C A G C U C SEQRES 29 A 369 C A C C A SEQRES 1 B 77 C G C G G G G U G G A G C SEQRES 2 B 77 A G C C U G G U A G C U C SEQRES 3 B 77 G U C G G G C U C A U A A SEQRES 4 B 77 C C C G A A G A U C G U C SEQRES 5 B 77 G G U U C A A A U C C G G SEQRES 6 B 77 C C C C C G C A A C C A SEQRES 1 C 161 MET THR LYS LYS SER ALA SER SER ASN ASN LYS VAL VAL SEQRES 2 C 161 ALA THR ASN ARG LYS ALA ARG HIS ASN TYR THR ILE LEU SEQRES 3 C 161 ASP THR TYR GLU ALA GLY ILE VAL LEU MET GLY THR GLU SEQRES 4 C 161 VAL LYS SER LEU ARG GLU GLY GLN ALA SER LEU ALA ASP SEQRES 5 C 161 ALA PHE ALA THR VAL ASP ASP GLY GLU ILE TRP LEU ARG SEQRES 6 C 161 ASN VAL HIS ILE ALA GLU TYR HIS HIS GLY THR TRP THR SEQRES 7 C 161 ASN HIS ALA PRO ARG ARG ASN ARG LYS LEU LEU LEU HIS SEQRES 8 C 161 ARG LYS GLN ILE ASP ASN LEU ILE GLY LYS ILE ARG ASP SEQRES 9 C 161 GLY ASN LEU THR LEU VAL PRO LEU SER ILE TYR PHE THR SEQRES 10 C 161 ASP GLY LYS VAL LYS VAL GLU LEU ALA LEU ALA ARG GLY SEQRES 11 C 161 LYS GLN ALA HIS ASP LYS ARG GLN ASP LEU ALA ARG ARG SEQRES 12 C 161 ASP ALA GLN ARG GLU VAL ILE ARG GLU LEU GLY ARG ARG SEQRES 13 C 161 ALA LYS GLY LYS ILE HELIX 1 AA1 LYS C 18 TYR C 23 1 6 HELIX 2 AA2 HIS C 91 ARG C 103 1 13 HELIX 3 AA3 GLN C 146 GLY C 159 1 14 SHEET 1 AA1 2 GLY C 32 ILE C 33 0 SHEET 2 AA1 2 LEU C 88 LEU C 89 -1 O LEU C 89 N GLY C 32 SHEET 1 AA2 2 VAL C 57 ASP C 58 0 SHEET 2 AA2 2 GLU C 61 ILE C 62 -1 O GLU C 61 N ASP C 58 SHEET 1 AA3 2 VAL C 110 PHE C 116 0 SHEET 2 AA3 2 VAL C 121 ALA C 126 -1 O GLU C 124 N LEU C 112 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000