HEADER RIBOSOMAL PROTEIN 31-MAR-17 5NKO TITLE SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF S. AUREUS HIBERNATING TITLE 2 PROMOTING FACTOR (CTD-SAHPF) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME HIBERNATION PROMOTION FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, UNP RESIDUES 131-190; COMPND 5 SYNONYM: HPF,HIBERNATION PROMOTING FACTOR SAHPF; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS (STRAIN NCTC 8325); SOURCE 3 ORGANISM_TAXID: 93061; SOURCE 4 STRAIN: NCTC 8325; SOURCE 5 VARIANT: SAHPF; SOURCE 6 GENE: HPF, SAOUHSC_00767; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGS21A KEYWDS STAPHYLOCOCCUS AUREUS, HIBERNATION, PATHOGEN, RIBOSOME, HIBERNATING KEYWDS 2 PROMOTING FACTOR, HPF, RIBOSOMAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.S.USACHEV,I.S.KHUSAINOV,R.K.AYUPOV,S.Z.VALIDOV,B.KIEFFER, AUTHOR 2 M.M.YUSUPOV REVDAT 4 14-JUN-23 5NKO 1 REMARK REVDAT 3 08-MAY-19 5NKO 1 REMARK REVDAT 2 26-JUL-17 5NKO 1 REVDAT 1 05-JUL-17 5NKO 0 JRNL AUTH I.KHUSAINOV,Q.VICENS,R.AYUPOV,K.USACHEV,A.MYASNIKOV, JRNL AUTH 2 A.SIMONETTI,S.VALIDOV,B.KIEFFER,G.YUSUPOVA,M.YUSUPOV, JRNL AUTH 3 Y.HASHEM JRNL TITL STRUCTURES AND DYNAMICS OF HIBERNATING RIBOSOMES FROM JRNL TITL 2 STAPHYLOCOCCUS AUREUS MEDIATED BY INTERMOLECULAR JRNL TITL 3 INTERACTIONS OF HPF. JRNL REF EMBO J. V. 36 2073 2017 JRNL REFN ESSN 1460-2075 JRNL PMID 28645916 JRNL DOI 10.15252/EMBJ.201696105 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA, CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5NKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200003945. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.6 REMARK 210 IONIC STRENGTH : 250 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 2.0 MM [U-99% 13C; U-99% 15N] C REMARK 210 -TERMINAL DOMAIN OF SAHPF, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 250 MM REMARK 210 NH4CL, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY ALIPHATIC; 3D 1H REMARK 210 -13C NOESY AROMATIC; 3D 1H-15N REMARK 210 NOESY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA, TOPSPIN, CNS, PROCHECK / REMARK 210 PROCHECK-NMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 1 LYS A 178 5.57 -65.64 REMARK 500 1 LYS A 181 -168.93 -110.97 REMARK 500 1 GLU A 189 179.86 66.72 REMARK 500 1 LYS B 178 5.44 -65.88 REMARK 500 1 LYS B 181 -168.78 -111.07 REMARK 500 1 GLU B 189 179.74 66.41 REMARK 500 2 ASP A 169 64.70 63.94 REMARK 500 2 GLU A 189 -61.55 72.31 REMARK 500 2 ASP B 169 65.19 63.39 REMARK 500 2 GLU B 189 -61.65 72.06 REMARK 500 3 SER A 172 119.93 -160.15 REMARK 500 3 LYS A 178 4.14 -63.90 REMARK 500 3 LYS A 181 -167.60 -112.44 REMARK 500 3 LYS B 178 3.95 -64.05 REMARK 500 3 LYS B 181 -167.40 -112.74 REMARK 500 4 LYS A 142 109.71 -49.76 REMARK 500 4 ASP A 169 64.52 68.24 REMARK 500 4 LYS A 178 4.06 -61.55 REMARK 500 4 LYS B 142 109.78 -49.77 REMARK 500 4 ASP B 169 63.90 68.58 REMARK 500 4 LYS B 178 4.28 -61.59 REMARK 500 6 ASP A 169 64.55 75.42 REMARK 500 6 LYS A 178 4.41 -64.21 REMARK 500 6 ASP B 169 64.67 75.45 REMARK 500 6 LYS B 178 4.55 -64.27 REMARK 500 7 ASP A 169 64.69 66.65 REMARK 500 7 LYS A 181 -168.93 -110.85 REMARK 500 7 SER A 188 -54.44 -131.27 REMARK 500 7 ASP B 169 64.62 66.50 REMARK 500 7 LYS B 181 -168.86 -110.62 REMARK 500 7 SER B 188 -54.63 -131.25 REMARK 500 8 LYS A 142 109.42 -50.39 REMARK 500 8 LYS A 178 4.29 -62.01 REMARK 500 8 LYS A 181 -169.55 -101.11 REMARK 500 8 LYS B 142 109.43 -50.47 REMARK 500 8 LYS B 178 4.57 -61.99 REMARK 500 8 LYS B 181 -169.53 -101.09 REMARK 500 9 GLU A 167 -60.57 -97.67 REMARK 500 9 LYS A 178 4.20 -69.75 REMARK 500 9 LYS A 181 -169.09 -110.89 REMARK 500 9 GLU B 167 -60.46 -97.58 REMARK 500 9 LYS B 178 4.90 -69.64 REMARK 500 9 LYS B 181 -169.12 -110.67 REMARK 500 10 LYS A 178 4.24 -61.30 REMARK 500 10 LYS B 178 4.58 -61.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 139 SER A 140 2 -120.96 REMARK 500 LEU A 141 LYS A 142 2 -148.33 REMARK 500 LYS A 142 PRO A 143 2 -137.01 REMARK 500 PHE B 139 SER B 140 2 -120.98 REMARK 500 LEU B 141 LYS B 142 2 -148.44 REMARK 500 LYS B 142 PRO B 143 2 -136.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 166 0.09 SIDE CHAIN REMARK 500 1 ARG B 166 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34120 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF S. AUREUS REMARK 900 HIBERNATING PROMOTING FACTOR (CTD-SAHPF) DBREF 5NKO A 131 190 UNP Q2G055 HPF_STAA8 131 190 DBREF 5NKO B 131 190 UNP Q2G055 HPF_STAA8 131 190 SEQADV 5NKO MET A 130 UNP Q2G055 INITIATING METHIONINE SEQADV 5NKO MET B 130 UNP Q2G055 INITIATING METHIONINE SEQRES 1 A 61 MET ILE GLU ILE ILE ARG SER LYS GLU PHE SER LEU LYS SEQRES 2 A 61 PRO MET ASP SER GLU GLU ALA VAL LEU GLN MET ASN LEU SEQRES 3 A 61 LEU GLY HIS ASP PHE PHE VAL PHE THR ASP ARG GLU THR SEQRES 4 A 61 ASP GLY THR SER ILE VAL TYR ARG ARG LYS ASP GLY LYS SEQRES 5 A 61 TYR GLY LEU ILE GLN THR SER GLU GLN SEQRES 1 B 61 MET ILE GLU ILE ILE ARG SER LYS GLU PHE SER LEU LYS SEQRES 2 B 61 PRO MET ASP SER GLU GLU ALA VAL LEU GLN MET ASN LEU SEQRES 3 B 61 LEU GLY HIS ASP PHE PHE VAL PHE THR ASP ARG GLU THR SEQRES 4 B 61 ASP GLY THR SER ILE VAL TYR ARG ARG LYS ASP GLY LYS SEQRES 5 B 61 TYR GLY LEU ILE GLN THR SER GLU GLN HELIX 1 AA1 ASP A 145 GLY A 157 1 13 HELIX 2 AA2 ASP B 145 GLY B 157 1 13 SHEET 1 AA1 4 ILE A 133 SER A 136 0 SHEET 2 AA1 4 LYS B 181 THR B 187 1 O TYR B 182 N ILE A 134 SHEET 3 AA1 4 THR B 171 ARG B 177 -1 N THR B 171 O THR B 187 SHEET 4 AA1 4 PHE B 160 THR B 164 -1 N PHE B 161 O VAL B 174 SHEET 1 AA2 4 PHE A 160 THR A 164 0 SHEET 2 AA2 4 THR A 171 ARG A 177 -1 O VAL A 174 N PHE A 161 SHEET 3 AA2 4 LYS A 181 THR A 187 -1 O THR A 187 N THR A 171 SHEET 4 AA2 4 ILE B 133 SER B 136 1 O ILE B 134 N TYR A 182 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 MODEL 1