HEADER RIBOSOMAL PROTEIN 15-NOV-18 6I6E TITLE CIRCULAR PERMUTANT OF RIBOSOMAL PROTEIN S6, SWAP STRAND 1 , L10A TITLE 2 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 30S RIBOSOMAL PROTEIN S6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TS9; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS (STRAIN HB8 / ATCC 27634 / SOURCE 3 DSM 579); SOURCE 4 ORGANISM_TAXID: 300852; SOURCE 5 GENE: RPSF, TTHA0245; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS CIRCULAR PERMUTANT, STRAND SWAP, GLOBLING UNFOLDING, CIS-PROLINE., KEYWDS 2 RIBOSOMAL PROTEIN, DESIGNED PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,D.T.LOGAN,M.OLIVEBERG REVDAT 4 24-JAN-24 6I6E 1 REMARK REVDAT 3 09-DEC-20 6I6E 1 JRNL REVDAT 2 22-JUL-20 6I6E 1 COMPND SOURCE REMARK ATOM REVDAT 1 27-NOV-19 6I6E 0 JRNL AUTH H.WANG,D.T.LOGAN,J.DANIELSSON,M.OLIVEBERG JRNL TITL EXPOSING THE DISTINCTIVE MODULAR BEHAVIOR OF BETA-STRANDS JRNL TITL 2 AND ALPHA-HELICES IN FOLDED PROTEINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 28775 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 33148805 JRNL DOI 10.1073/PNAS.1920455117 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 27176 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1337 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.7900 - 2.5900 1.00 2850 122 0.1678 0.1764 REMARK 3 2 2.5800 - 2.0500 1.00 2618 128 0.1284 0.1546 REMARK 3 3 2.0500 - 1.7900 1.00 2636 142 0.1153 0.1350 REMARK 3 4 1.7900 - 1.6300 1.00 2565 141 0.1150 0.1429 REMARK 3 5 1.6300 - 1.5100 1.00 2537 142 0.1093 0.1530 REMARK 3 6 1.5100 - 1.4200 1.00 2537 149 0.1147 0.1518 REMARK 3 7 1.4200 - 1.3500 1.00 2555 117 0.1498 0.1779 REMARK 3 8 1.3500 - 1.2900 1.00 2525 126 0.1598 0.1716 REMARK 3 9 1.2900 - 1.2400 1.00 2528 130 0.1847 0.2122 REMARK 3 10 1.2400 - 1.2000 1.00 2488 140 0.2201 0.2311 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6I6E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200012916. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27269 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 45.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 24.20 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 24.00 REMARK 200 R MERGE FOR SHELL (I) : 0.65400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1RIS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M MAGNESIUM CHLORIDE HEXAHYDRATE REMARK 280 0.1 M HEPES PH 7.5 22% W/V POLY (ACRYLIC ACID SODIUM SALT) 5100, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 67.57450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 17.43500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 17.43500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.78725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 17.43500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 17.43500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.36175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 17.43500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 17.43500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.78725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 17.43500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 17.43500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 101.36175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 67.57450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 -34.87000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 34.87000 REMARK 350 BIOMT3 2 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 GLY A 95 REMARK 465 ARG A 96 REMARK 465 TYR A 97 REMARK 465 GLU A 98 REMARK 465 VAL A 99 REMARK 465 ASN A 100 REMARK 465 ILE A 101 REMARK 465 VAL A 102 REMARK 465 ALA A 103 REMARK 465 ASN A 104 REMARK 465 PRO A 105 REMARK 465 ASN A 106 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 HH12 ARG A 69 OD2 ASP A 72 1.52 REMARK 500 O HOH A 206 O HOH A 218 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 204 O HOH A 204 7555 1.63 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 PRO A 49 -175.86 -66.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 6I6E A 1 94 UNP Q5SLP8 RS6_THET8 3 96 SEQADV 6I6E MET A 0 UNP Q5SLP8 INITIATING METHIONINE SEQADV 6I6E ALA A 8 UNP Q5SLP8 LEU 10 CONFLICT SEQADV 6I6E ALA A 90 UNP Q5SLP8 LYS 92 CONFLICT SEQADV 6I6E THR A 92 UNP Q5SLP8 GLN 94 CONFLICT SEQADV 6I6E THR A 93 UNP Q5SLP8 GLU 95 CONFLICT SEQADV 6I6E GLY A 95 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E ARG A 96 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E TYR A 97 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E GLU A 98 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E VAL A 99 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E ASN A 100 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E ILE A 101 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E VAL A 102 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E ALA A 103 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E ASN A 104 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E PRO A 105 UNP Q5SLP8 EXPRESSION TAG SEQADV 6I6E ASN A 106 UNP Q5SLP8 EXPRESSION TAG SEQRES 1 A 107 MET ARG TYR GLU VAL ASN ILE VAL ALA ASN PRO ASN LEU SEQRES 2 A 107 ASP GLN SER GLN LEU ALA LEU GLU LYS GLU ILE ILE GLN SEQRES 3 A 107 ARG ALA LEU GLU ASN TYR GLY ALA ARG VAL GLU LYS VAL SEQRES 4 A 107 GLU GLU LEU GLY LEU ARG ARG LEU ALA TYR PRO ILE ALA SEQRES 5 A 107 LYS ASP PRO GLN GLY TYR PHE LEU TRP TYR GLN VAL GLU SEQRES 6 A 107 MET PRO GLU ASP ARG VAL ASN ASP LEU ALA ARG GLU LEU SEQRES 7 A 107 ARG ILE ARG ASP ASN VAL ARG ARG VAL MET VAL VAL ALA SEQRES 8 A 107 SER THR THR PRO GLY ARG TYR GLU VAL ASN ILE VAL ALA SEQRES 9 A 107 ASN PRO ASN FORMUL 2 HOH *77(H2 O) HELIX 1 AA1 ASP A 13 TYR A 31 1 19 HELIX 2 AA2 PRO A 66 ASP A 68 5 3 HELIX 3 AA3 ARG A 69 ILE A 79 1 11 SHEET 1 AA1 4 ARG A 34 ARG A 45 0 SHEET 2 AA1 4 GLN A 55 GLU A 64 -1 O TRP A 60 N GLU A 39 SHEET 3 AA1 4 ARG A 1 ALA A 8 -1 N ALA A 8 O TYR A 57 SHEET 4 AA1 4 VAL A 83 ALA A 90 -1 O MET A 87 N ASN A 5 CISPEP 1 TYR A 48 PRO A 49 0 -6.43 CRYST1 34.870 34.870 135.149 90.00 90.00 90.00 P 41 21 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 0.028678 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028678 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007399 0.00000