PDB Short entry for 1R73 HEADER RIBOSOME 17-OCT-03 1R73 TITLE SOLUTION STRUCTURE OF TM1492, THE L29 RIBOSOMAL PROTEIN FROM TITLE 2 THERMOTOGA MARITIMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L29; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TM1492 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336 KEYWDS RIBOSOME, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.PETI,T.ETEZADY-ESFARJANI,T.HERRMANN,H.E.KLOCK,S.A.LESLEY, AUTHOR 2 K.WUETHRICH,JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 02-MAR-22 1R73 1 REMARK REVDAT 3 24-FEB-09 1R73 1 VERSN REVDAT 2 18-JAN-05 1R73 1 AUTHOR KEYWDS REMARK REVDAT 1 10-AUG-04 1R73 0 JRNL AUTH W.PETI,T.ETEZADY-ESFARJANI,T.HERRMANN,H.E.KLOCK,S.A.LESLEY, JRNL AUTH 2 K.WUETHRICH JRNL TITL NMR FOR STRUCTURAL PROTEOMICS OF THERMOTOGA MARITIMA: JRNL TITL 2 SCREENING AND STRUCTURE DETERMINATION JRNL REF J.STRUCT.FUNCT.GENOM. V. 5 205 2004 JRNL REFN ISSN 1345-711X JRNL PMID 15263836 JRNL DOI 10.1023/B:JSFG.0000029055.84242.9F REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1R73 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020517. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 3.6 MM TM1492 U-15N,13C, 20 MM REMARK 210 PHOSPHATE BUFFER, 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, XEASY REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 15 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: 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 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 20 LEU A 14 CG LEU A 14 CD1 0.280 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 1 ARG A 7 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 6 ARG A 7 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 ARG A 52 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 12 TYR A 9 CB - CA - C ANGL. DEV. = 12.8 DEGREES REMARK 500 13 TYR A 9 CB - CA - C ANGL. DEV. = 13.8 DEGREES REMARK 500 13 ARG A 52 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 13 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 14 ARG A 23 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 15 ARG A 52 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 15 ARG A 60 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 16 LYS A 47 CB - CA - C ANGL. DEV. = 12.0 DEGREES REMARK 500 19 ARG A 23 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES 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 ALA A 3 -73.90 -121.89 REMARK 500 1 SER A 4 -70.63 49.47 REMARK 500 1 MET A 34 -74.59 -82.55 REMARK 500 1 GLN A 36 -60.10 -120.73 REMARK 500 1 LYS A 38 -24.62 -141.50 REMARK 500 2 MET A 34 -75.80 -76.98 REMARK 500 3 ALA A 3 -75.33 -121.13 REMARK 500 3 SER A 4 -60.82 62.82 REMARK 500 3 ASP A 11 -38.34 -38.32 REMARK 500 3 LEU A 37 84.94 -56.93 REMARK 500 4 ALA A 3 -64.76 -121.24 REMARK 500 4 SER A 4 -71.11 32.82 REMARK 500 4 LEU A 37 109.78 -57.43 REMARK 500 4 LYS A 38 85.50 -58.44 REMARK 500 4 ASN A 39 123.77 61.54 REMARK 500 4 ARG A 65 55.19 -108.12 REMARK 500 5 ALA A 3 -70.89 -121.91 REMARK 500 5 SER A 4 -67.44 44.81 REMARK 500 5 ASP A 11 -33.03 -39.59 REMARK 500 5 LYS A 38 178.30 43.87 REMARK 500 5 ASN A 39 -53.55 65.98 REMARK 500 5 THR A 40 -11.90 65.95 REMARK 500 6 LYS A 2 -169.02 53.88 REMARK 500 6 ALA A 3 -70.74 -121.85 REMARK 500 6 SER A 4 -70.22 44.47 REMARK 500 6 LYS A 38 -77.95 -48.95 REMARK 500 6 ARG A 52 -63.66 -90.00 REMARK 500 6 ILE A 64 -84.78 -93.29 REMARK 500 7 LYS A 2 -178.08 59.35 REMARK 500 7 ALA A 3 -78.65 -121.07 REMARK 500 7 SER A 4 -60.84 66.45 REMARK 500 7 LYS A 38 57.57 -116.00 REMARK 500 7 ASN A 39 76.86 -159.97 REMARK 500 7 LEU A 62 -156.59 -131.63 REMARK 500 7 ILE A 64 -82.10 -61.60 REMARK 500 8 ASN A 39 124.09 62.52 REMARK 500 8 THR A 40 -16.97 -49.08 REMARK 500 8 ARG A 52 -60.11 -99.33 REMARK 500 9 ALA A 3 -86.10 -121.94 REMARK 500 9 SER A 4 -60.34 57.68 REMARK 500 9 ASN A 39 57.46 -24.01 REMARK 500 9 THR A 40 47.48 23.61 REMARK 500 10 LYS A 2 -31.33 -130.93 REMARK 500 10 ALA A 3 -90.62 -121.70 REMARK 500 10 SER A 4 -13.26 57.96 REMARK 500 10 LEU A 14 -73.46 -70.24 REMARK 500 10 LYS A 38 54.59 -140.55 REMARK 500 10 ASN A 39 -72.44 -136.50 REMARK 500 10 THR A 40 -20.16 70.94 REMARK 500 11 ALA A 3 -81.37 -120.81 REMARK 500 REMARK 500 THIS ENTRY HAS 85 RAMACHANDRAN OUTLIERS. 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 ALA A 3 SER A 4 1 -141.50 REMARK 500 ALA A 3 SER A 4 3 -147.48 REMARK 500 ALA A 3 SER A 4 4 -124.07 REMARK 500 ALA A 3 SER A 4 5 -127.71 REMARK 500 ALA A 3 SER A 4 6 -127.41 REMARK 500 ALA A 3 SER A 4 9 -147.16 REMARK 500 ALA A 3 SER A 4 15 -148.22 REMARK 500 ARG A 65 ARG A 66 16 -141.22 REMARK 500 MET A 1 LYS A 2 17 149.78 REMARK 500 ALA A 3 SER A 4 17 -144.40 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 52 0.11 SIDE CHAIN REMARK 500 1 ARG A 65 0.09 SIDE CHAIN REMARK 500 2 ARG A 7 0.16 SIDE CHAIN REMARK 500 2 ARG A 29 0.09 SIDE CHAIN REMARK 500 2 ARG A 48 0.08 SIDE CHAIN REMARK 500 5 ARG A 23 0.09 SIDE CHAIN REMARK 500 5 ARG A 58 0.08 SIDE CHAIN REMARK 500 6 TYR A 9 0.08 SIDE CHAIN REMARK 500 6 ARG A 48 0.12 SIDE CHAIN REMARK 500 7 ARG A 66 0.10 SIDE CHAIN REMARK 500 9 ARG A 7 0.13 SIDE CHAIN REMARK 500 9 ARG A 60 0.09 SIDE CHAIN REMARK 500 11 ARG A 29 0.11 SIDE CHAIN REMARK 500 13 ARG A 52 0.16 SIDE CHAIN REMARK 500 14 TYR A 9 0.10 SIDE CHAIN REMARK 500 14 ARG A 60 0.12 SIDE CHAIN REMARK 500 15 ARG A 65 0.10 SIDE CHAIN REMARK 500 16 ARG A 48 0.14 SIDE CHAIN REMARK 500 16 ARG A 60 0.15 SIDE CHAIN REMARK 500 16 ARG A 65 0.09 SIDE CHAIN REMARK 500 18 ARG A 29 0.09 SIDE CHAIN REMARK 500 18 ARG A 58 0.10 SIDE CHAIN REMARK 500 19 ARG A 60 0.08 SIDE CHAIN REMARK 500 19 ARG A 66 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 283349 RELATED DB: TARGETDB DBREF 1R73 A 1 66 UNP P38514 RL29_THEMA 1 66 SEQRES 1 A 66 MET LYS ALA SER GLU LEU ARG ASN TYR THR ASP GLU GLU SEQRES 2 A 66 LEU LYS ASN LEU LEU GLU GLU LYS LYS ARG GLN LEU MET SEQRES 3 A 66 GLU LEU ARG PHE GLN LEU ALA MET GLY GLN LEU LYS ASN SEQRES 4 A 66 THR SER LEU ILE LYS LEU THR LYS ARG ASP ILE ALA ARG SEQRES 5 A 66 ILE LYS THR ILE LEU ARG GLU ARG GLU LEU GLY ILE ARG SEQRES 6 A 66 ARG HELIX 1 1 SER A 4 TYR A 9 1 6 HELIX 2 2 THR A 10 GLY A 35 1 26 HELIX 3 3 ASN A 39 GLY A 63 1 25 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