HEADER RIBOSOMAL PROTEIN 08-AUG-99 1CQM TITLE PROTEIN AGGREGATION AND ALZHEIMER'S DISEASE: CRYSTALLOGRAPHIC ANALYSIS TITLE 2 OF THE PHENOMENON. ENGINEERED VERSION OF THE RIBOSOMAL PROTEIN S6 TITLE 3 USED AS A STABLE SCAFFOLD TO STUDY OLIGOMERIZATION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN S6; COMPND 3 CHAIN: A, B; 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 ALZHEIMER DISEASE, RIBOSOMAL PROTEIN S6, OLIGOMERIZATION, RIBOSOMAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR O.KRISTENSEN,D.E.OTZEN,M.OLIVEBERG REVDAT 6 07-FEB-24 1CQM 1 SEQADV REVDAT 5 31-JAN-18 1CQM 1 REMARK REVDAT 4 01-FEB-17 1CQM 1 AUTHOR VERSN REVDAT 3 24-FEB-09 1CQM 1 VERSN REVDAT 2 01-APR-03 1CQM 1 JRNL REVDAT 1 08-SEP-00 1CQM 0 JRNL AUTH D.E.OTZEN,O.KRISTENSEN,M.OLIVEBERG JRNL TITL DESIGNED PROTEIN TETRAMER ZIPPED TOGETHER WITH A HYDROPHOBIC JRNL TITL 2 ALZHEIMER HOMOLOGY: A STRUCTURAL CLUE TO AMYLOID ASSEMBLY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 97 9907 2000 JRNL REFN ISSN 0027-8424 JRNL PMID 10944185 JRNL DOI 10.1073/PNAS.160086297 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.LINDAHL,L.A.SVENSSON,A.LILJAS,S.E.SEDELNIKOVA, REMARK 1 AUTH 2 I.A.ELISEIKINA,N.P.FOMENKOVA,N.NEVSKAYA,S.V.NIKONOV, REMARK 1 AUTH 3 M.B.GARBER,T.A.MURANOVA,A.I.RYKONOVA,R.AMONS REMARK 1 TITL CRYSTAL STRUCTURE OF THE RIBOSOMAL PROTEIN S6 FROM THERMUS REMARK 1 TITL 2 THERMOPHILUS REMARK 1 REF EMBO J. V. 13 1249 1994 REMARK 1 REFN ISSN 0261-4189 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1633216.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 24922 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) : 0.247 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.600 REMARK 3 FREE R VALUE TEST SET COUNT : 896 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3859 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 150 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1638 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.10000 REMARK 3 B22 (A**2) : -1.09000 REMARK 3 B33 (A**2) : 0.00000 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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) : 0.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.720 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.690 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.120 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.48 REMARK 3 BSOL : 62.10 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.PA REMARK 3 PARAMETER FILE 2 : WATER_REP.PARA REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CQM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000009491. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0158 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24926 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.24300 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: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, SODIUM CITRATE, PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 20K, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 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+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 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 40.41900 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 40.41900 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 25.54050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.77300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.54050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.77300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.41900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.54050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.77300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.41900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.54050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.77300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ALA A 99 REMARK 465 ASN A 100 REMARK 465 ALA A 101 REMARK 465 ALA B 99 REMARK 465 ASN B 100 REMARK 465 ALA B 101 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 165 O HOH A 165 3656 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QJH RELATED DB: PDB REMARK 900 1QJH CONTAINS THE FULLY MODIFIED ALZHEIMER-LIKE VERSION OF THE REMARK 900 RIBOSOMAL PROTEIN S6. DBREF 1CQM A 1 101 UNP P23370 RS6_THETH 1 101 DBREF 1CQM B 1 101 UNP P23370 RS6_THETH 1 101 SEQADV 1CQM ALA A 41 UNP P23370 GLU 41 ENGINEERED MUTATION SEQADV 1CQM ILE A 42 UNP P23370 GLU 42 ENGINEERED MUTATION SEQADV 1CQM ALA B 41 UNP P23370 GLU 41 ENGINEERED MUTATION SEQADV 1CQM ILE B 42 UNP P23370 GLU 42 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 ALA ILE 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 LEU 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 SEQRES 1 B 101 MET ARG ARG TYR GLU VAL ASN ILE VAL LEU ASN PRO ASN SEQRES 2 B 101 LEU ASP GLN SER GLN LEU ALA LEU GLU LYS GLU ILE ILE SEQRES 3 B 101 GLN ARG ALA LEU GLU ASN TYR GLY ALA ARG VAL GLU LYS SEQRES 4 B 101 VAL ALA ILE LEU GLY LEU ARG ARG LEU ALA TYR PRO ILE SEQRES 5 B 101 ALA LYS ASP PRO GLN GLY TYR PHE LEU TRP TYR GLN VAL SEQRES 6 B 101 GLU MET PRO GLU ASP ARG VAL ASN ASP LEU ALA ARG GLU SEQRES 7 B 101 LEU ARG ILE ARG ASP ASN VAL ARG ARG VAL MET VAL VAL SEQRES 8 B 101 LYS SER GLN GLU PRO PHE LEU ALA ASN ALA FORMUL 3 HOH *156(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 ILE A 81 1 11 HELIX 4 4 ASP B 15 TYR B 33 1 19 HELIX 5 5 PRO B 68 ASP B 70 5 3 HELIX 6 6 ARG B 71 ILE B 81 1 11 SHEET 1 A 4 ARG A 36 ILE A 52 0 SHEET 2 A 4 ASP A 55 MET A 67 -1 O ASP A 55 N ILE A 52 SHEET 3 A 4 ARG A 2 LEU A 10 -1 O ARG A 2 N MET A 67 SHEET 4 A 4 VAL A 85 LYS A 92 -1 N ARG A 86 O VAL A 9 SHEET 1 B 4 ARG B 36 ILE B 52 0 SHEET 2 B 4 ASP B 55 MET B 67 -1 O ASP B 55 N ILE B 52 SHEET 3 B 4 ARG B 2 LEU B 10 -1 N ARG B 2 O MET B 67 SHEET 4 B 4 VAL B 85 LYS B 92 -1 N ARG B 86 O VAL B 9 CRYST1 51.081 105.546 80.838 90.00 90.00 90.00 C 2 2 21 16 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 0.019577 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009475 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012370 0.00000