HEADER RIBOSOMAL PROTEIN 02-SEP-11 3ZZP TITLE CIRCULAR PERMUTANT OF RIBOSOMAL PROTEIN S6, LACKING EDGE STRAND BETA- TITLE 2 2 OF WILD-TYPE S6. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN S6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 3-35,55-93; COMPND 5 SYNONYM: TS9; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: CIRCULAR PERMUTANT OF THE RIBOSOMAL PROTEIN S6 FROM COMPND 8 THERMUS THERMOPHILUS, WHICH HAS A LINKER BETWEEN THE WILD-TYPE N-AND COMPND 9 C-TERMINI AND AN INCISION BETWEEN K54 AND D55 WITHOUT THE EDGE STRAND COMPND 10 BETA-2 OF WILD-TYPE S6. (RESIDUES 36-54). 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: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS PROTEIN FOLDING, RNA-BINDING, RIBOSOMAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.SARABOJI,E.HAGLUND,M.O.LINDBERG,M.OLIVEBERG,D.T.LOGAN REVDAT 5 20-DEC-23 3ZZP 1 REMARK REVDAT 4 22-MAY-19 3ZZP 1 REMARK REVDAT 3 17-JAN-18 3ZZP 1 REMARK REVDAT 2 25-JUL-12 3ZZP 1 JRNL REVDAT 1 23-NOV-11 3ZZP 0 JRNL AUTH E.HAGLUND,J.DANIELSSON,S.KADHIRVEL,M.O.LINDBERG,D.T.LOGAN, JRNL AUTH 2 M.OLIVEBERG JRNL TITL TRIMMING DOWN A PROTEIN STRUCTURE TO ITS BARE FOLDONS: JRNL TITL 2 SPATIAL ORGANIZATION OF THE COOPERATIVE UNIT. JRNL REF J.BIOL.CHEM. V. 287 2731 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22117065 JRNL DOI 10.1074/JBC.M111.312447 REMARK 2 REMARK 2 RESOLUTION. 0.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.113 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.113 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.137 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1932 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 38148 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.110 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.110 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.133 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1679 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 32611 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 606 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 733.74 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 542.32 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 9 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6866 REMARK 3 NUMBER OF RESTRAINTS : 8147 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.022 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.094 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.106 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.112 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.007 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.044 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.110 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ZZP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1290049441. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.038 REMARK 200 MONOCHROMATOR : BENT SI (111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38300 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.960 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.86 REMARK 200 R MERGE FOR SHELL (I) : 0.65000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1RIS REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9M AMMONIUM SULPHATE, 0.1M MES PH REMARK 280 6.5, 8% 1,4 DIOXANE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 11.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.33000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.33000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.40000 REMARK 290 SMTRY3 4 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: PISA 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. (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 MET A 1 REMARK 465 ASP A 2 REMARK 465 PRO A 3 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 GLN A 4 CG CD OE1 NE2 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 THR A 8 CA - CB - CG2 ANGL. DEV. = 8.4 DEGREES REMARK 500 TYR A 10 CG - CD2 - CE2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 29 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 33 NE - CZ - NH1 ANGL. DEV. = -9.5 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES 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: 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: 2BVZ RELATED DB: PDB REMARK 900 MUTANT OF THE RIBOSOMAL PROTEIN S6 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. 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: 1LOU RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN S6 REMARK 900 RELATED ID: 2BXJ RELATED DB: PDB REMARK 900 DOUBLE MUTANT OF THE RIBOSOMAL PROTEIN S6 REMARK 900 RELATED ID: 1RIS RELATED DB: PDB REMARK 900 RELATED ID: 1L1U RELATED DB: PDB REMARK 900 TERNARY COMPLEX DOCKED IN THE DECODING SITE OF THE 30S RIBOSOMAL REMARK 900 SUBUNIT REMARK 999 REMARK 999 SEQUENCE REMARK 999 CIRCULAR PERMUTANT OF THE RIBOSOMAL PROTEIN S6, WHICH HAS REMARK 999 A LINKER BETWEEN THE WILD-TYPE N- AND C-TERMINI AND AN REMARK 999 INCISION BETWEEN K54 AND D55 WITHOUT THE STRAND BETA-2 OF REMARK 999 WILD-TYPE S6 (RESIDUES 36-54). DBREF 3ZZP A 2 40 UNP P23370 RS6_THETH 55 93 DBREF 3ZZP A 45 77 UNP P23370 RS6_THETH 3 35 SEQADV 3ZZP MET A 1 UNP P23370 EXPRESSION TAG SEQADV 3ZZP THR A 7 UNP Q5SLP8 PHE 60 CONFLICT SEQADV 3ZZP THR A 8 UNP Q5SLP8 LEU 61 CONFLICT SEQADV 3ZZP ALA A 39 UNP Q5SLP8 LYS 92 CONFLICT SEQADV 3ZZP THR A 41 UNP P23370 SEE REMARK 999 SEQADV 3ZZP THR A 42 UNP P23370 SEE REMARK 999 SEQADV 3ZZP PRO A 43 UNP P23370 SEE REMARK 999 SEQADV 3ZZP GLY A 44 UNP P23370 SEE REMARK 999 SEQADV 3ZZP GLN A 62 UNP P23370 ALA 20 CONFLICT SEQADV 3ZZP ASN A 63 UNP P23370 LEU 21 CONFLICT SEQRES 1 A 77 MET ASP PRO GLN GLY TYR THR THR TRP TYR GLN VAL GLU SEQRES 2 A 77 MET PRO GLU ASP ARG VAL ASN ASP LEU ALA ARG GLU LEU SEQRES 3 A 77 ARG ILE ARG ASP ASN VAL ARG ARG VAL MET VAL VAL ALA SEQRES 4 A 77 SER THR THR PRO GLY ARG TYR GLU VAL ASN ILE VAL LEU SEQRES 5 A 77 ASN PRO ASN LEU ASP GLN SER GLN LEU GLN ASN GLU LYS SEQRES 6 A 77 GLU ILE ILE GLN ARG ALA LEU GLU ASN TYR GLY ALA FORMUL 2 HOH *129(H2 O) HELIX 1 1 PRO A 15 ILE A 28 1 14 HELIX 2 2 ASP A 57 GLY A 76 1 20 SHEET 1 AA 3 THR A 7 GLU A 13 0 SHEET 2 AA 3 ARG A 45 LEU A 52 -1 O TYR A 46 N VAL A 12 SHEET 3 AA 3 VAL A 32 ALA A 39 -1 N ARG A 33 O VAL A 51 CRYST1 22.200 40.800 68.660 90.00 90.00 90.00 P 21 21 21 4 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 0.045045 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024510 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014565 0.00000