PDB Short entry for 1C05 HEADER RIBOSOME 14-JUL-99 1C05 TITLE SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41, REFINED WITH TITLE 2 DIPOLAR COUPLINGS (MINIMIZED AVERAGE STRUCTURE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN S4 DELTA 41; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: S4 DELTA 41 (S4 RESIDUES 42-200); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET13A KEYWDS TWO SUBDOMAINS, UNIQUE TOPOLOGY, POSSIBLE HELIX-TURN-HELIX MOTIF, KEYWDS 2 RIBOSOME EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR M.A.MARKUS,R.B.GERSTNER,D.E.DRAPER,D.A.TORCHIA REVDAT 3 29-NOV-17 1C05 1 REMARK HELIX REVDAT 2 24-FEB-09 1C05 1 VERSN REVDAT 1 29-SEP-99 1C05 0 JRNL AUTH M.A.MARKUS,R.B.GERSTNER,D.E.DRAPER,D.A.TORCHIA JRNL TITL REFINING THE OVERALL STRUCTURE AND SUBDOMAIN ORIENTATION OF JRNL TITL 2 RIBOSOMAL PROTEIN S4 DELTA41 WITH DIPOLAR COUPLINGS MEASURED JRNL TITL 3 BY NMR IN UNIAXIAL LIQUID CRYSTALLINE PHASES. JRNL REF J.MOL.BIOL. V. 292 375 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10493882 JRNL DOI 10.1006/JMBI.1999.3061 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.MARKUS,R.B.GERSTNER,D.E.DRAPER,D.A.TORCHIA REMARK 1 TITL THE SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41 REMARK 1 TITL 2 REVEALS TWO SUBDOMAINS AND A POSITIVELY CHARGED SURFACE THAT REMARK 1 TITL 3 MAY INTERACT WITH RNA REMARK 1 REF EMBO J. V. 17 4559 1998 REMARK 1 REFN ISSN 0261-4189 REMARK 1 DOI 10.1093/EMBOJ/17.16.4559 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.5, X-PLOR 3.8, 4.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SUMMARY OF RESTRAINTS: 2170 NOE, 86 REMARK 3 HYDROGEN BOND, 114 DIHEDRAL ANGLE, AND 101 DIPOLAR COUPLINGS REMARK 4 REMARK 4 1C05 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000009341. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 310; 310 REMARK 210 PH : 5.4; 6.0; 6.5 REMARK 210 IONIC STRENGTH : 250 MM KCL; 80 MM KCL; 300 MM REMARK 210 KCL REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.1 MM S4 DELTA 41, U-15N,13C; REMARK 210 20 MM D4-ACETATE PH 5.4, 250 MM REMARK 210 KCL, 0.1 MM SODIUM AZIDE; 0.8 MM REMARK 210 S4 DELTA 41, U-15N; 20 MM D4- REMARK 210 ACETATE PH 5.4, 250 MM KCL, 0.1 REMARK 210 MM SODIUM AZIDE; 0.45 MM S4 REMARK 210 DELTA 41, U-15N,13C; 20 MM D4- REMARK 210 ACETATE PH 5.4, 250 MM KCL; 0.62 REMARK 210 MM S4 DELTA 41, 10% 13C; 20 MM REMARK 210 D4-ACETATE PH 5.4, 250 MM KCL; REMARK 210 0.10 MM S4 DELTA 41, U-15N; 7 MM REMARK 210 D4-ACETATE PH 5.4, 7 MM KH2PO4 REMARK 210 PH 6.5, 80 MM KCL, 5% W/V DMPC: REMARK 210 DHPC (3:1); 0.21 MM S4 DELTA 41, REMARK 210 U-15N, 85% 2H; 15N,13C,1H REMARK 210 METHIONINE; EPSILON-13C, 1H REMARK 210 TYRSOINE; BETA,GAMMA,DELTA 2H REMARK 210 PROLINE; 10 MM KH2PO4 PH 6.5, REMARK 210 300 MM KCL, 0.2 MM SODIUM AZIDE, REMARK 210 2.5 MG/ML PF1 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY; HNHA; IPAP 15N REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.7, PIPP 4.2.8 REMARK 210 METHOD USED : HYBRID DGSA PROTOCOL WITHOUT THE REMARK 210 DIPOLAR COUPLING RESTRAINTS REMARK 210 FOLLOWED BY ADDITIONAL SA WITH REMARK 210 THE DIPOLAR COUPLING RESTRAINTS REMARK 210 ADD REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED WITH NOE RESTRAINTS FROM REMARK 210 MULTIDIMENSIONAL HETERONUCLEAR EXPERIMENTS, DIHEDRAL ANGLE REMARK 210 RESTRAINTS BASED ON MEASUREMENTS OF SCALAR COUPLING CONSTANTS, REMARK 210 AND DIPOLAR COUPLING RESTRAINTS MEASURED ON SAMPLES IN PARTIALLY REMARK 210 ALIGNED PHASES. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 TYR A 20 HH22 ARG A 52 1.50 REMARK 500 H LEU A 79 O ALA A 99 1.53 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 LEU A 16 -16.45 -48.42 REMARK 500 MET A 19 -90.88 -69.63 REMARK 500 PHE A 31 -76.82 -74.00 REMARK 500 GLU A 32 -13.60 -48.97 REMARK 500 LYS A 40 102.38 52.34 REMARK 500 LEU A 60 -103.55 -57.65 REMARK 500 ASP A 81 20.62 45.17 REMARK 500 TYR A 90 179.53 -55.62 REMARK 500 PRO A 94 147.65 -36.04 REMARK 500 GLU A 102 -78.44 -46.50 REMARK 500 SER A 104 48.14 -98.66 REMARK 500 ALA A 116 3.55 -63.93 REMARK 500 ASN A 118 26.21 -157.51 REMARK 500 TYR A 119 88.92 -178.65 REMARK 500 PRO A 121 172.50 -42.24 REMARK 500 SER A 142 -0.51 -55.06 REMARK 500 PRO A 145 120.02 -36.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C06 RELATED DB: PDB REMARK 900 16 CONFORMERS DBREF 1C05 A 1 159 UNP P81288 RS4_BACST 41 198 SEQRES 1 A 159 MET LYS LEU SER GLU TYR GLY LEU GLN LEU GLN GLU LYS SEQRES 2 A 159 GLN LYS LEU ARG HIS MET TYR GLY VAL ASN GLU ARG GLN SEQRES 3 A 159 PHE ARG LYS THR PHE GLU GLU ALA GLY LYS MET PRO GLY SEQRES 4 A 159 LYS HIS GLY GLU ASN PHE MET ILE LEU LEU GLU SER ARG SEQRES 5 A 159 LEU ASP ASN LEU VAL TYR ARG LEU GLY LEU ALA ARG THR SEQRES 6 A 159 ARG ARG GLN ALA ARG GLN LEU VAL THR HIS GLY HIS ILE SEQRES 7 A 159 LEU VAL ASP GLY SER ARG VAL ASN ILE PRO SER TYR ARG SEQRES 8 A 159 VAL LYS PRO GLY GLN THR ILE ALA VAL ARG GLU LYS SER SEQRES 9 A 159 ARG ASN LEU GLN VAL ILE LYS GLU ALA LEU GLU ALA ASN SEQRES 10 A 159 ASN TYR ILE PRO ASP TYR LEU SER PHE ASP PRO GLU LYS SEQRES 11 A 159 MET GLU GLY THR TYR THR ARG LEU PRO GLU ARG SER GLU SEQRES 12 A 159 LEU PRO ALA GLU ILE ASN GLU ALA LEU ILE VAL GLU PHE SEQRES 13 A 159 TYR SER ARG HELIX 1 1 SER A 4 MET A 19 1 16 HELIX 2 2 ASN A 23 GLY A 35 1 13 HELIX 3 3 LYS A 40 ARG A 52 1 13 HELIX 4 4 ARG A 52 LEU A 60 1 9 HELIX 5 5 THR A 65 HIS A 75 1 11 HELIX 6 6 LEU A 107 ALA A 116 1 10 HELIX 7 7 GLU A 150 ARG A 159 1 10 SHEET 1 A 5 SER A 83 ARG A 84 0 SHEET 2 A 5 ILE A 78 VAL A 80 -1 N VAL A 80 O SER A 83 SHEET 3 A 5 THR A 97 VAL A 100 -1 O ALA A 99 N LEU A 79 SHEET 4 A 5 GLU A 132 TYR A 135 -1 N GLY A 133 O ILE A 98 SHEET 5 A 5 LEU A 124 ASP A 127 -1 O SER A 125 N THR A 134 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