HEADER RIBOSOMAL PROTEIN 05-JUL-05 2BVZ TITLE MUTANT OF THE RIBOSOMAL PROTEIN S6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 30S RIBOSOMAL PROTEIN S6; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBONUCLEOPROTEIN, RIBOSOMAL PROTEIN, RNA-BINDING, RRNA-BINDING, S6 KEYWDS 2 MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR D.E.OTZEN REVDAT 3 13-DEC-23 2BVZ 1 REMARK REVDAT 2 24-FEB-09 2BVZ 1 VERSN REVDAT 1 26-OCT-05 2BVZ 0 JRNL AUTH D.E.OTZEN JRNL TITL ANTAGONISM, NON-NATIVE INTERACTIONS AND NON-TWO-STATE JRNL TITL 2 FOLDING IN S6 REVEALED BY DOUBLE-MUTANT CYCLE ANALYSIS. JRNL REF PROTEIN ENG.DES.SEL. V. 18 547 2005 JRNL REFN ISSN 1741-0126 JRNL PMID 16230299 JRNL DOI 10.1093/PROTEIN/GZI063 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 335031.560 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 5911 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 643 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 819 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 95 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 814 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 52 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.87000 REMARK 3 B22 (A**2) : 2.38000 REMARK 3 B33 (A**2) : -1.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.140 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.720 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.290 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 37.66 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BVZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1290024729. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6127 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 23.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1LOU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NA-CITRATE, 0.1M TRIS-CL PH 8.5, REMARK 280 17.5% (V/V) PEG400 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.30250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.00200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.30250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.00200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.30250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 53.00200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.30250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 53.00200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2039 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2047 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LEU 75 TO ALA REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 99 REMARK 465 ASN A 100 REMARK 465 ALA A 101 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 98 CA C O CB CG CD1 CD2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CQM RELATED DB: PDB REMARK 900 PROTEIN AGGREGATION AND ALZHEIMER'S DISEASE: CRYSTALLOGRAPHIC REMARK 900 ANALYSIS OF THE PHENOMENON. ENGINEEREDVERSION OF THE RIBOSOMAL REMARK 900 PROTEIN S6 USED AS A STABLESCAFFOLD TO STUDY OLIGOMERIZATION. REMARK 900 RELATED ID: 1CQN RELATED DB: PDB REMARK 900 PROTEIN AGGREGATION AND ALZHEIMER'S DISEASE: CRYSTALLOGRAPHIC REMARK 900 ANALYSIS OF THE PHENOMENON. ENGINEEREDVERSION OF THE RIBOSOMAL REMARK 900 PROTEIN S6 USED AS A STABLESCAFFOLD TO STUDY OLIGOMERIZATION. REMARK 900 RELATED ID: 1EG0 RELATED DB: PDB REMARK 900 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM REMARK 900 MAP OF THE E .COLI 70S RIBOSOME REMARK 900 RELATED ID: 1LOU RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN S6 REMARK 900 RELATED ID: 1QJH RELATED DB: PDB REMARK 900 PROTEIN AGGREGATION AND ALZHEIMER'S DISEASE: CRYSTALLOGRAPHIC REMARK 900 ANALYSIS OF THE PHENOMENON. ENGINEERED VERSION OF THE RIBOSOMAL REMARK 900 PROTEIN S6 USED AS A STABLE SCAFFOLD TO STUDY OLIGOMERIZATION. REMARK 900 RELATED ID: 1RIS RELATED DB: PDB REMARK 900 RELATED ID: 1TWT RELATED DB: PDB REMARK 900 MODEL STRUCTURE OF THE T. THERMOPHILUS 70S RIBOSOME, 30SSUBUNIT OF REMARK 900 70S ROBOSOME. THIS FILE, 1TWT, CONTAINS ONLYMOLECULES OF THE 30S REMARK 900 RIBOSOMAL SUBUNIT. THE 50S SUBUNIT ISIN THE PDB FILE 1TWV. DBREF 2BVZ A 1 101 UNP P23370 RS6_THETH 1 101 SEQADV 2BVZ ALA A 75 UNP P23370 LEU 75 ENGINEERED MUTATION SEQRES 1 A 101 MET ARG ARG TYR GLU VAL ASN ILE VAL LEU ASN PRO ASN SEQRES 2 A 101 LEU ASP GLN SER GLN LEU ALA LEU GLU LYS GLU ILE ILE SEQRES 3 A 101 GLN ARG ALA LEU GLU ASN TYR GLY ALA ARG VAL GLU LYS SEQRES 4 A 101 VAL GLU GLU LEU GLY LEU ARG ARG LEU ALA TYR PRO ILE SEQRES 5 A 101 ALA LYS ASP PRO GLN GLY TYR PHE LEU TRP TYR GLN VAL SEQRES 6 A 101 GLU MET PRO GLU ASP ARG VAL ASN ASP ALA ALA ARG GLU SEQRES 7 A 101 LEU ARG ILE ARG ASP ASN VAL ARG ARG VAL MET VAL VAL SEQRES 8 A 101 LYS SER GLN GLU PRO PHE LEU ALA ASN ALA FORMUL 2 HOH *52(H2 O) HELIX 1 1 ASP A 15 TYR A 33 1 19 HELIX 2 2 PRO A 68 ASP A 70 5 3 HELIX 3 3 ARG A 71 ARG A 82 1 12 SHEET 1 AA 4 ARG A 36 ILE A 52 0 SHEET 2 AA 4 ASP A 55 MET A 67 -1 O ASP A 55 N ILE A 52 SHEET 3 AA 4 ARG A 2 LEU A 10 -1 O ARG A 2 N MET A 67 SHEET 4 AA 4 VAL A 85 LYS A 92 -1 N ARG A 86 O VAL A 9 CRYST1 52.605 106.004 41.138 90.00 90.00 90.00 C 2 2 2 8 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 0.019010 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024308 0.00000