HEADER PROTEIN BINDING 27-MAY-04 1WG0 TITLE STRUCTURAL COMPARISON OF NAS6P PROTEIN STRUCTURES IN TWO DIFFERENT TITLE 2 CRYSTAL FORMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE 26S PROTEASOME REGULATORY SUBUNIT P28; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEASOME NON-ATPASE SUBUNIT 6, NAS6P; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B-NAS6P KEYWDS ANKYRIN REPEATS, GANKYRIN HOMOLOG, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS, PROTEIN KEYWDS 3 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.NAKAMURA,T.UMEHARA,A.TANAKA,M.HORIKOSHI,S.YOKOYAMA,B.PADMANABHAN, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 25-OCT-23 1WG0 1 SEQADV REVDAT 2 24-FEB-09 1WG0 1 VERSN REVDAT 1 07-JUN-05 1WG0 0 JRNL AUTH Y.NAKAMURA,T.UMEHARA,A.TANAKA,M.HORIKOSHI,S.YOKOYAMA, JRNL AUTH 2 B.PADMANABHAN JRNL TITL STRUCTURAL COMPARISON OF NAS6P PROTEIN STRUCTURES IN TWO JRNL TITL 2 DIFFERENT CRYSTAL FORMS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 8451 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 905 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.69 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 146 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1932 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.69 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.39 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WG0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023539. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8677 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.530 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19100 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: PDB ENTRY 1IXV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-20% PEG 4000, 0.1M MES, PH 6.7, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.31450 REMARK 290 SMTRY3 2 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 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: 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 ASN A 3 -13.97 94.39 REMARK 500 ASN A 13 45.32 71.21 REMARK 500 LYS A 25 88.47 -155.24 REMARK 500 ASP A 33 -165.38 -79.16 REMARK 500 ASP A 137 -169.38 -64.58 REMARK 500 LYS A 164 29.19 49.92 REMARK 500 ASN A 206 -9.91 -58.99 REMARK 500 ASP A 230 94.72 -69.81 REMARK 500 HIS A 241 -33.83 -130.22 REMARK 500 HIS A 242 121.78 92.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IXV RELATED DB: PDB REMARK 900 RELATED ID: AR_001000295.1 RELATED DB: TARGETDB DBREF 1WG0 A 1 228 UNP P50086 PSDA_YEAST 1 228 SEQADV 1WG0 VAL A 229 UNP P50086 EXPRESSION TAG SEQADV 1WG0 ASP A 230 UNP P50086 EXPRESSION TAG SEQADV 1WG0 LYS A 231 UNP P50086 EXPRESSION TAG SEQADV 1WG0 LEU A 232 UNP P50086 EXPRESSION TAG SEQADV 1WG0 ALA A 233 UNP P50086 EXPRESSION TAG SEQADV 1WG0 ALA A 234 UNP P50086 EXPRESSION TAG SEQADV 1WG0 ALA A 235 UNP P50086 EXPRESSION TAG SEQADV 1WG0 LEU A 236 UNP P50086 EXPRESSION TAG SEQADV 1WG0 GLU A 237 UNP P50086 EXPRESSION TAG SEQADV 1WG0 HIS A 238 UNP P50086 EXPRESSION TAG SEQADV 1WG0 HIS A 239 UNP P50086 EXPRESSION TAG SEQADV 1WG0 HIS A 240 UNP P50086 EXPRESSION TAG SEQADV 1WG0 HIS A 241 UNP P50086 EXPRESSION TAG SEQADV 1WG0 HIS A 242 UNP P50086 EXPRESSION TAG SEQADV 1WG0 HIS A 243 UNP P50086 EXPRESSION TAG SEQRES 1 A 243 MET SER ASN TYR PRO LEU HIS GLN ALA CYS MET GLU ASN SEQRES 2 A 243 GLU PHE PHE LYS VAL GLN GLU LEU LEU HIS SER LYS PRO SEQRES 3 A 243 SER LEU LEU LEU GLN LYS ASP GLN ASP GLY ARG ILE PRO SEQRES 4 A 243 LEU HIS TRP SER VAL SER PHE GLN ALA HIS GLU ILE THR SEQRES 5 A 243 SER PHE LEU LEU SER LYS MET GLU ASN VAL ASN LEU ASP SEQRES 6 A 243 ASP TYR PRO ASP ASP SER GLY TRP THR PRO PHE HIS ILE SEQRES 7 A 243 ALA CYS SER VAL GLY ASN LEU GLU VAL VAL LYS SER LEU SEQRES 8 A 243 TYR ASP ARG PRO LEU LYS PRO ASP LEU ASN LYS ILE THR SEQRES 9 A 243 ASN GLN GLY VAL THR CYS LEU HIS LEU ALA VAL GLY LYS SEQRES 10 A 243 LYS TRP PHE GLU VAL SER GLN PHE LEU ILE GLU ASN GLY SEQRES 11 A 243 ALA SER VAL ARG ILE LYS ASP LYS PHE ASN GLN ILE PRO SEQRES 12 A 243 LEU HIS ARG ALA ALA SER VAL GLY SER LEU LYS LEU ILE SEQRES 13 A 243 GLU LEU LEU CYS GLY LEU GLY LYS SER ALA VAL ASN TRP SEQRES 14 A 243 GLN ASP LYS GLN GLY TRP THR PRO LEU PHE HIS ALA LEU SEQRES 15 A 243 ALA GLU GLY HIS GLY ASP ALA ALA VAL LEU LEU VAL GLU SEQRES 16 A 243 LYS TYR GLY ALA GLU TYR ASP LEU VAL ASP ASN LYS GLY SEQRES 17 A 243 ALA LYS ALA GLU ASP VAL ALA LEU ASN GLU GLN VAL LYS SEQRES 18 A 243 LYS PHE PHE LEU ASN ASN VAL VAL ASP LYS LEU ALA ALA SEQRES 19 A 243 ALA LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *182(H2 O) HELIX 1 1 TYR A 4 ASN A 13 1 10 HELIX 2 2 GLU A 14 LYS A 25 1 12 HELIX 3 3 PRO A 26 GLN A 31 5 6 HELIX 4 4 ILE A 38 PHE A 46 1 9 HELIX 5 5 ALA A 48 MET A 59 1 12 HELIX 6 6 ASN A 63 TYR A 67 5 5 HELIX 7 7 THR A 74 GLY A 83 1 10 HELIX 8 8 ASN A 84 ASP A 93 1 10 HELIX 9 9 THR A 109 LYS A 117 1 9 HELIX 10 10 TRP A 119 ASN A 129 1 11 HELIX 11 11 ILE A 142 VAL A 150 1 9 HELIX 12 12 SER A 152 GLY A 161 1 10 HELIX 13 13 THR A 176 GLU A 184 1 9 HELIX 14 14 HIS A 186 GLY A 198 1 13 HELIX 15 15 LYS A 210 ALA A 215 5 6 HELIX 16 16 ASN A 217 ASN A 226 1 10 CRYST1 43.444 68.629 46.985 90.00 108.95 90.00 P 1 21 1 2 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 0.023018 0.000000 0.007903 0.00000 SCALE2 0.000000 0.014571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022503 0.00000