HEADER RIBOSOMAL PROTEIN 02-FEB-12 2LP6 TITLE REFINED SOLUTION NMR STRUCTURE OF THE 50S RIBOSOMAL PROTEIN L35AE FROM TITLE 2 PYROCOCCUS FURIOSUS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TITLE 3 (NESG) PFR48 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L35AE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 186497; SOURCE 4 STRAIN: ATCC 43587 / DSM 3638 / JCM 8422 / VC1; SOURCE 5 GENE: PF1872, RPL35AE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PMGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET21_NESG KEYWDS STRUCTURAL GENOMICS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), KEYWDS 2 PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, RIBOSOMAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.A.SNYDER,J.M.ARAMINI,B.YU,Y.J.HUANG,R.XIAO,J.R.CORT,R.SHASTRY,L.MA, AUTHOR 2 J.LIU,B.ROST,T.B.ACTON,M.A.KENNEDY,G.T.MONTELIONE,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 5 15-MAY-24 2LP6 1 REMARK REVDAT 4 14-JUN-23 2LP6 1 REMARK SEQADV REVDAT 3 20-JUN-12 2LP6 1 JRNL REVDAT 2 11-APR-12 2LP6 1 JRNL REVDAT 1 15-FEB-12 2LP6 0 JRNL AUTH D.A.SNYDER,J.M.ARAMINI,B.YU,Y.J.HUANG,R.XIAO,J.R.CORT, JRNL AUTH 2 R.SHASTRY,L.C.MA,J.LIU,B.ROST,T.B.ACTON,M.A.KENNEDY, JRNL AUTH 3 G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE RIBOSOMAL PROTEIN RP-L35AE JRNL TITL 2 FROM PYROCOCCUS FURIOSUS. JRNL REF PROTEINS V. 80 1901 2012 JRNL REFN ISSN 0887-3585 JRNL PMID 22422653 JRNL DOI 10.1002/PROT.24071 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL REFINED STRUCTURES ARE BASED REMARK 3 ON A TOTAL OF 1402 CONFORMATIONALLY-RESTRICTING NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 153 DIHEDRAL ANGLE CONSTRAINTS, AND 56 REMARK 3 HYDROGEN BOND CONSTRAINTS (18.3 CONSTRAINTS PER RESIDUE, 7.0 REMARK 3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO REMARK 3 91 BY PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED REMARK 3 ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH REMARK 3 THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED REMARK 3 MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS REMARK 3 1.3) WITH PARAM19. REMARK 4 REMARK 4 2LP6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000102659. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.07 MM [U-100% 13C; U-100% 15N] REMARK 210 PFR48.005, 0.02 % NAN3, 10 MM REMARK 210 DTT, 5 MM CACL2, 100 MM NACL, 1 REMARK 210 X PROTEINASE INHIBITORS, 20 MM REMARK 210 MES PH 6.5, 50 UM DSS, 90% H2O/ REMARK 210 10% D2O; 1.07 MM [U-100% 13C; U- REMARK 210 100% 15N] PFR48.005, 0.02 % NAN3, REMARK 210 10 MM DTT, 5 MM CACL2, 100 MM REMARK 210 NACL, 1 X PROTEINASE INHIBITORS, REMARK 210 20 MM MES PH 6.5, 50 UM DSS, 100% REMARK 210 D2O; 0.29 MM [U-5% 13C; U-100% REMARK 210 15N] PFR48.002, 0.02 % NAN3, 10 REMARK 210 MM DTT, 5 MM CACL2, 100 MM NACL, REMARK 210 1 X PROTEINASE INHIBITORS, 20 MM REMARK 210 MES PH 6.5, 50 UM DSS, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 CCC(CO)NH TOCSY; 3D HCCH-TOCSY; REMARK 210 3D HCCH-COSY; 3D HNHA; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 2D 1H- REMARK 210 13C HSQC HIGH RESOLUTION REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.3, CYANA 3.0, REMARK 210 AUTOSTRUCTURE 2.2.1, AUTOASSIGN REMARK 210 1.9, NMRPIPE 2.3, VNMR 6.1B, REMARK 210 SPARKY 3, TALOS+, PSVS 1.4, REMARK 210 PDBSTAT 5.5, MOLPROBITY 3.19 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY REMARK 210 WITH STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE REMARK 210 STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR REMARK 210 SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE REMARK 210 USING AUTOASSIGN, FOLLOWED BY MANUAL SIDE CHAIN ASSIGNMENT. REMARK 210 AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. REMARK 210 BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM REMARK 210 TALOSPLUS, AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING REMARK 210 AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING THE C- REMARK 210 TERMINAL HIS6): BACKBONE, 98.2%, SIDE CHAIN, 90.9%, AROMATICS, REMARK 210 100%, STEREOSPECIFIC METHYL, 84.2%. FINAL STRUCTURE QUALITY REMARK 210 FACTORS (FOR RESIDUES 1 TO 91, PSVS 1.4), WHERE ORDERED RESIDUES REMARK 210 [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-12,21-76,79-87: (A) RMSD REMARK 210 (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.0. (B) MOLPROBITY REMARK 210 RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 97.0% REMARK 210 , ADDITIONALLY ALLOWED, 3.0%, DISALLOWED, 0%. (C) PROCHECK REMARK 210 SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.56/-1.89, ALL, REMARK 210 -0.26/-1.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 15.13/-1.07 (E) REMARK 210 RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1 TO 91): REMARK 210 RECALL, 0.965, PRECISION, 0.878, F-MEASURE, 0.920, DP-SCORE, REMARK 210 0.784. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 5. THE FINAL REMARK 210 FOUR UNASSIGNED HISTIDINE RESIDUES IN THE C-TERMINAL AFFINITY REMARK 210 TAG WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE REMARK 210 BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING REMARK 210 RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1,13- REMARK 210 20,77-78,88-91. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 92 REMARK 465 HIS A 93 REMARK 465 HIS A 94 REMARK 465 HIS A 95 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 ALA A 79 31.61 -88.33 REMARK 500 1 LEU A 80 111.10 -35.68 REMARK 500 1 LEU A 88 86.61 -63.34 REMARK 500 1 HIS A 90 81.14 58.29 REMARK 500 2 VAL A 7 93.57 -64.69 REMARK 500 2 HIS A 18 118.02 -160.43 REMARK 500 2 ILE A 57 96.25 -67.78 REMARK 500 2 HIS A 90 18.79 -157.79 REMARK 500 3 ASN A 16 79.57 -53.62 REMARK 500 3 ASN A 19 70.51 -156.05 REMARK 500 3 LYS A 73 -72.73 -119.69 REMARK 500 3 HIS A 90 -68.27 -137.88 REMARK 500 4 GLN A 78 75.97 -65.95 REMARK 500 5 VAL A 7 106.76 -57.98 REMARK 500 5 ASN A 19 134.99 73.17 REMARK 500 5 LEU A 80 103.79 -43.90 REMARK 500 6 VAL A 7 99.87 -66.93 REMARK 500 6 GLN A 78 -40.43 76.02 REMARK 500 6 ALA A 79 30.07 -75.81 REMARK 500 6 LEU A 88 96.40 -65.64 REMARK 500 6 HIS A 90 66.46 61.75 REMARK 500 7 VAL A 7 93.39 -67.10 REMARK 500 7 GLU A 15 -62.77 -98.62 REMARK 500 7 ALA A 79 32.47 -98.12 REMARK 500 7 LEU A 80 108.02 -51.79 REMARK 500 7 LEU A 88 97.61 -62.86 REMARK 500 7 GLU A 89 98.59 -65.62 REMARK 500 8 VAL A 7 103.74 -55.12 REMARK 500 8 ASN A 16 88.33 -69.32 REMARK 500 8 GLN A 17 -77.13 -134.62 REMARK 500 8 ASN A 30 -25.57 -147.52 REMARK 500 8 ILE A 57 98.16 -69.32 REMARK 500 8 LYS A 64 52.94 -98.73 REMARK 500 8 GLU A 89 -39.20 -159.47 REMARK 500 9 LYS A 14 -72.01 -67.47 REMARK 500 9 GLU A 15 -64.23 -132.52 REMARK 500 9 GLN A 78 73.89 -113.03 REMARK 500 10 GLU A 15 -76.70 51.91 REMARK 500 10 GLN A 17 46.62 -85.57 REMARK 500 10 HIS A 18 86.86 -63.31 REMARK 500 10 LYS A 73 -77.64 -76.68 REMARK 500 11 VAL A 7 97.53 -68.80 REMARK 500 11 ILE A 57 99.89 -67.61 REMARK 500 11 LYS A 64 46.70 -91.83 REMARK 500 11 LEU A 80 108.68 -53.11 REMARK 500 11 GLU A 89 82.72 -68.01 REMARK 500 12 SER A 13 -77.27 -65.02 REMARK 500 12 GLU A 15 -58.85 -162.76 REMARK 500 12 ASN A 16 -61.64 -123.16 REMARK 500 12 GLN A 17 -167.68 -127.25 REMARK 500 REMARK 500 THIS ENTRY HAS 75 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SQR RELATED DB: PDB REMARK 900 RELATED ID: 6173 RELATED DB: BMRB REMARK 900 RELATED ID: NESG-PFR48 RELATED DB: TARGETTRACK DBREF 2LP6 A 1 87 UNP Q8TZV6 RL35A_PYRFU 1 87 SEQADV 2LP6 LEU A 88 UNP Q8TZV6 EXPRESSION TAG SEQADV 2LP6 GLU A 89 UNP Q8TZV6 EXPRESSION TAG SEQADV 2LP6 HIS A 90 UNP Q8TZV6 EXPRESSION TAG SEQADV 2LP6 HIS A 91 UNP Q8TZV6 EXPRESSION TAG SEQADV 2LP6 HIS A 92 UNP Q8TZV6 EXPRESSION TAG SEQADV 2LP6 HIS A 93 UNP Q8TZV6 EXPRESSION TAG SEQADV 2LP6 HIS A 94 UNP Q8TZV6 EXPRESSION TAG SEQADV 2LP6 HIS A 95 UNP Q8TZV6 EXPRESSION TAG SEQRES 1 A 95 MET ARG ILE LYS GLY VAL VAL LEU SER TYR ARG ARG SER SEQRES 2 A 95 LYS GLU ASN GLN HIS ASN ASN VAL MET ILE ILE LYS PRO SEQRES 3 A 95 LEU ASP VAL ASN SER ARG GLU GLU ALA SER LYS LEU ILE SEQRES 4 A 95 GLY ARG LEU VAL LEU TRP LYS SER PRO SER GLY LYS ILE SEQRES 5 A 95 LEU LYS GLY LYS ILE VAL ARG VAL HIS GLY THR LYS GLY SEQRES 6 A 95 ALA VAL ARG ALA ARG PHE GLU LYS GLY LEU PRO GLY GLN SEQRES 7 A 95 ALA LEU GLY ASP TYR VAL GLU ILE VAL LEU GLU HIS HIS SEQRES 8 A 95 HIS HIS HIS HIS HELIX 1 1 SER A 31 LYS A 37 1 7 SHEET 1 A 7 ARG A 2 ARG A 11 0 SHEET 2 A 7 ASN A 20 PRO A 26 -1 O ILE A 23 N LEU A 8 SHEET 3 A 7 ALA A 66 PHE A 71 -1 O VAL A 67 N ILE A 24 SHEET 4 A 7 ILE A 52 HIS A 61 -1 N HIS A 61 O ALA A 66 SHEET 5 A 7 LEU A 42 LYS A 46 -1 N TRP A 45 O LEU A 53 SHEET 6 A 7 TYR A 83 VAL A 87 -1 O VAL A 87 N LEU A 42 SHEET 7 A 7 ARG A 2 ARG A 11 -1 N ILE A 3 O ILE A 86 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