HEADER CHAPERONE/PROTEIN BINDING 07-JUN-10 3AJI TITLE STRUCTURE OF GANKYRIN-S6ATPASE PHOTO-CROSS-LINKED SITE-SPECIFICALLY, TITLE 2 AND INCOPORATED BY GENETIC CODE EXPANSION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 10; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: 26S PROTEASOME REGULATORY SUBUNIT P28, GANKYRIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEASOME (PROSOME, MACROPAIN) 26S SUBUNIT, ATPASE, 4; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: C-TERMINAL DOMAIN; COMPND 11 SYNONYM: S6C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PSMD10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 GENE: PSMC4; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GANKYRIN, S6 ATPASE, P-BENZOYL-L-PHENYLALANINE, PBPA, AMBER KEYWDS 2 SUPPRESSION, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, CHAPERONE-PROTEIN BINDING KEYWDS 4 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.SATO,S.MIMASU,A.SATO,N.HINO,K.SAKAMOTO,T.UMEHARA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 15-NOV-23 3AJI 1 REMARK REVDAT 4 01-NOV-23 3AJI 1 SEQADV LINK REVDAT 3 29-JAN-14 3AJI 1 JRNL VERSN REVDAT 2 19-JAN-11 3AJI 1 TITLE REVDAT 1 22-DEC-10 3AJI 0 JRNL AUTH S.SATO,S.MIMASU,A.SATO,N.HINO,K.SAKAMOTO,T.UMEHARA, JRNL AUTH 2 S.YOKOYAMA JRNL TITL CRYSTALLOGRAPHIC STUDY OF A SITE-SPECIFICALLY CROSS-LINKED JRNL TITL 2 PROTEIN COMPLEX WITH A GENETICALLY INCORPORATED JRNL TITL 3 PHOTOREACTIVE AMINO ACID JRNL REF BIOCHEMISTRY V. 50 250 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21128684 JRNL DOI 10.1021/BI1016183 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2665091.250 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 38604 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) : 0.171 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1914 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6083 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 347 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4668 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 327 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.13000 REMARK 3 B22 (A**2) : 4.13000 REMARK 3 B33 (A**2) : -8.27000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.032 REMARK 3 BOND ANGLES (DEGREES) : 2.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.780 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 62.45 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 : PBPA.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : PBPA.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3AJI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000029328. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-08; 24-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8 REMARK 200 BEAMLINE : BL41XU; BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : NULL; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE; RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38604 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09800 REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45400 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2DVW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 31% POLYETHYLENE GLYCOL 4000, 0.26M REMARK 280 MGCL2, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 51.58200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.78088 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.66433 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 51.58200 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 29.78088 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.66433 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 51.58200 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 29.78088 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.66433 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.56176 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 103.32867 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 59.56176 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 103.32867 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 59.56176 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 103.32867 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 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: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 A 253 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 263 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 266 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 238 LIES ON A SPECIAL POSITION. 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 GLU A 2 REMARK 465 LYS B 409 REMARK 465 ASP B 410 REMARK 465 GLU B 411 REMARK 465 GLN B 412 REMARK 465 GLU B 413 REMARK 465 HIS B 414 REMARK 465 GLU B 415 REMARK 465 PHE B 416 REMARK 465 TYR B 417 REMARK 465 LYS B 418 REMARK 465 MET C 1 REMARK 465 GLU C 2 REMARK 465 LYS D 409 REMARK 465 ASP D 410 REMARK 465 GLU D 411 REMARK 465 GLN D 412 REMARK 465 GLU D 413 REMARK 465 HIS D 414 REMARK 465 GLU D 415 REMARK 465 PHE D 416 REMARK 465 TYR D 417 REMARK 465 LYS D 418 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 OE2 GLU C 183 O HOH C 287 2.04 REMARK 500 O GLU C 205 O HOH C 365 2.08 REMARK 500 OD2 ASP B 368 OH TYR B 403 2.16 REMARK 500 O HOH C 326 O HOH C 363 2.18 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 C 312 O HOH C 369 8654 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY A 3 N GLY A 3 CA 0.111 REMARK 500 VAL A 123 CB VAL A 123 CG2 0.149 REMARK 500 ALA A 134 CA ALA A 134 CB 0.132 REMARK 500 VAL A 155 CB VAL A 155 CG1 0.130 REMARK 500 GLU A 205 CB GLU A 205 CG 0.150 REMARK 500 GLU A 205 CG GLU A 205 CD 0.101 REMARK 500 GLU A 205 CD GLU A 205 OE1 0.067 REMARK 500 GLU B 356 C GLU B 357 N 0.211 REMARK 500 ARG C 25 CG ARG C 25 CD -0.150 REMARK 500 ALA C 163 CA ALA C 163 CB 0.135 REMARK 500 GLU C 186 CB GLU C 186 CG 0.139 REMARK 500 GLU D 356 CG GLU D 356 CD -0.135 REMARK 500 GLU D 356 CD GLU D 356 OE1 0.073 REMARK 500 GLU D 356 CD GLU D 356 OE2 0.110 REMARK 500 GLU D 356 C GLU D 357 N 0.240 REMARK 500 REMARK 500 REMARK: NULL 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 CYS A 4 N - CA - C ANGL. DEV. = 17.6 DEGREES REMARK 500 MET A 9 CG - SD - CE ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 25 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 118 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 LEU A 152 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG B 338 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 GLU B 356 N - CA - C ANGL. DEV. = -17.7 DEGREES REMARK 500 GLU B 356 CA - C - N ANGL. DEV. = 13.3 DEGREES REMARK 500 GLU B 356 O - C - N ANGL. DEV. = -14.3 DEGREES REMARK 500 LEU B 385 CB - CA - C ANGL. DEV. = -11.5 DEGREES REMARK 500 ALA B 386 CB - CA - C ANGL. DEV. = 9.7 DEGREES REMARK 500 VAL B 387 N - CA - C ANGL. DEV. = 24.2 DEGREES REMARK 500 ASN B 390 N - CA - C ANGL. DEV. = 24.2 DEGREES REMARK 500 ILE C 10 CB - CG1 - CD1 ANGL. DEV. = -18.1 DEGREES REMARK 500 ARG C 25 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP C 86 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG C 118 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 SER D 355 O - C - N ANGL. DEV. = 9.8 DEGREES REMARK 500 GLU D 356 CB - CA - C ANGL. DEV. = -19.3 DEGREES REMARK 500 GLU D 356 OE1 - CD - OE2 ANGL. DEV. = -11.7 DEGREES REMARK 500 GLU D 356 CA - C - N ANGL. DEV. = 13.3 DEGREES REMARK 500 GLU D 356 O - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 ASN D 390 N - CA - C ANGL. DEV. = -28.1 DEGREES REMARK 500 ARG D 391 NE - CZ - NH1 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG D 391 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ILE D 393 N - CA - C ANGL. DEV. = -23.7 DEGREES 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 ASP A 29 92.13 -163.51 REMARK 500 ASP C 29 93.62 -160.66 REMARK 500 THR D 349 -7.72 -59.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 199 0.06 SIDE CHAIN REMARK 500 TYR B 392 0.13 SIDE CHAIN REMARK 500 TYR D 363 0.07 SIDE CHAIN REMARK 500 PHE D 399 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DVW RELATED DB: PDB REMARK 900 GANKYRIN IN COMPLEX WITH C-TERMINAL DOMAIN OF S6 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE 85TH NON-NATURAL RESIDUE IS THE PHOTO REACTED VERSION OF PBPA REMARK 999 INCOPORATED BY THE GENETIC CODE EXPANSION, AND THE 356TH RESIDUE IS REMARK 999 THE PHOTO-COVALENT-BONDED PBPA ON GLUTAMIC ACID. DBREF 3AJI A 1 231 UNP Q9Z2X2 PSD10_MOUSE 1 231 DBREF 3AJI B 337 418 UNP Q6ZWN9 Q6ZWN9_MOUSE 337 418 DBREF 3AJI C 1 231 UNP Q9Z2X2 PSD10_MOUSE 1 231 DBREF 3AJI D 337 418 UNP Q6ZWN9 Q6ZWN9_MOUSE 337 418 SEQADV 3AJI PBF A 85 UNP Q9Z2X2 ARG 85 ENGINEERED MUTATION SEQADV 3AJI MET B 336 UNP Q6ZWN9 EXPRESSION TAG SEQADV 3AJI PBF C 85 UNP Q9Z2X2 ARG 85 ENGINEERED MUTATION SEQADV 3AJI MET D 336 UNP Q6ZWN9 EXPRESSION TAG SEQRES 1 A 231 MET GLU GLY CYS VAL SER ASN ILE MET ILE CYS ASN LEU SEQRES 2 A 231 ALA TYR SER GLY LYS LEU ASP GLU LEU LYS GLU ARG ILE SEQRES 3 A 231 LEU ALA ASP LYS SER LEU ALA THR ARG THR ASP GLN ASP SEQRES 4 A 231 SER ARG THR ALA LEU HIS TRP ALA CYS SER ALA GLY HIS SEQRES 5 A 231 THR GLU ILE VAL GLU PHE LEU LEU GLN LEU GLY VAL PRO SEQRES 6 A 231 VAL ASN ASP LYS ASP ASP ALA GLY TRP SER PRO LEU HIS SEQRES 7 A 231 ILE ALA ALA SER ALA GLY PBF ASP GLU ILE VAL LYS ALA SEQRES 8 A 231 LEU LEU VAL LYS GLY ALA HIS VAL ASN ALA VAL ASN GLN SEQRES 9 A 231 ASN GLY CYS THR PRO LEU HIS TYR ALA ALA SER LYS ASN SEQRES 10 A 231 ARG HIS GLU ILE ALA VAL MET LEU LEU GLU GLY GLY ALA SEQRES 11 A 231 ASN PRO ASP ALA LYS ASP HIS TYR ASP ALA THR ALA MET SEQRES 12 A 231 HIS ARG ALA ALA ALA LYS GLY ASN LEU LYS MET VAL HIS SEQRES 13 A 231 ILE LEU LEU PHE TYR LYS ALA SER THR ASN ILE GLN ASP SEQRES 14 A 231 THR GLU GLY ASN THR PRO LEU HIS LEU ALA CYS ASP GLU SEQRES 15 A 231 GLU ARG VAL GLU GLU ALA LYS PHE LEU VAL THR GLN GLY SEQRES 16 A 231 ALA SER ILE TYR ILE GLU ASN LYS GLU GLU LYS THR PRO SEQRES 17 A 231 LEU GLN VAL ALA LYS GLY GLY LEU GLY LEU ILE LEU LYS SEQRES 18 A 231 ARG LEU ALA GLU GLY GLU GLU ALA SER MET SEQRES 1 B 83 MET ASP ARG ARG GLN LYS ARG LEU ILE PHE SER THR ILE SEQRES 2 B 83 THR SER LYS MET ASN LEU SER GLU GLU VAL ASP LEU GLU SEQRES 3 B 83 ASP TYR VAL ALA ARG PRO ASP LYS ILE SER GLY ALA ASP SEQRES 4 B 83 ILE ASN SER ILE CYS GLN GLU SER GLY MET LEU ALA VAL SEQRES 5 B 83 ARG GLU ASN ARG TYR ILE VAL LEU ALA LYS ASP PHE GLU SEQRES 6 B 83 LYS ALA TYR LYS THR VAL ILE LYS LYS ASP GLU GLN GLU SEQRES 7 B 83 HIS GLU PHE TYR LYS SEQRES 1 C 231 MET GLU GLY CYS VAL SER ASN ILE MET ILE CYS ASN LEU SEQRES 2 C 231 ALA TYR SER GLY LYS LEU ASP GLU LEU LYS GLU ARG ILE SEQRES 3 C 231 LEU ALA ASP LYS SER LEU ALA THR ARG THR ASP GLN ASP SEQRES 4 C 231 SER ARG THR ALA LEU HIS TRP ALA CYS SER ALA GLY HIS SEQRES 5 C 231 THR GLU ILE VAL GLU PHE LEU LEU GLN LEU GLY VAL PRO SEQRES 6 C 231 VAL ASN ASP LYS ASP ASP ALA GLY TRP SER PRO LEU HIS SEQRES 7 C 231 ILE ALA ALA SER ALA GLY PBF ASP GLU ILE VAL LYS ALA SEQRES 8 C 231 LEU LEU VAL LYS GLY ALA HIS VAL ASN ALA VAL ASN GLN SEQRES 9 C 231 ASN GLY CYS THR PRO LEU HIS TYR ALA ALA SER LYS ASN SEQRES 10 C 231 ARG HIS GLU ILE ALA VAL MET LEU LEU GLU GLY GLY ALA SEQRES 11 C 231 ASN PRO ASP ALA LYS ASP HIS TYR ASP ALA THR ALA MET SEQRES 12 C 231 HIS ARG ALA ALA ALA LYS GLY ASN LEU LYS MET VAL HIS SEQRES 13 C 231 ILE LEU LEU PHE TYR LYS ALA SER THR ASN ILE GLN ASP SEQRES 14 C 231 THR GLU GLY ASN THR PRO LEU HIS LEU ALA CYS ASP GLU SEQRES 15 C 231 GLU ARG VAL GLU GLU ALA LYS PHE LEU VAL THR GLN GLY SEQRES 16 C 231 ALA SER ILE TYR ILE GLU ASN LYS GLU GLU LYS THR PRO SEQRES 17 C 231 LEU GLN VAL ALA LYS GLY GLY LEU GLY LEU ILE LEU LYS SEQRES 18 C 231 ARG LEU ALA GLU GLY GLU GLU ALA SER MET SEQRES 1 D 83 MET ASP ARG ARG GLN LYS ARG LEU ILE PHE SER THR ILE SEQRES 2 D 83 THR SER LYS MET ASN LEU SER GLU GLU VAL ASP LEU GLU SEQRES 3 D 83 ASP TYR VAL ALA ARG PRO ASP LYS ILE SER GLY ALA ASP SEQRES 4 D 83 ILE ASN SER ILE CYS GLN GLU SER GLY MET LEU ALA VAL SEQRES 5 D 83 ARG GLU ASN ARG TYR ILE VAL LEU ALA LYS ASP PHE GLU SEQRES 6 D 83 LYS ALA TYR LYS THR VAL ILE LYS LYS ASP GLU GLN GLU SEQRES 7 D 83 HIS GLU PHE TYR LYS MODRES 3AJI PBF A 85 PHE PARA-(BENZOYL)-PHENYLALANINE MODRES 3AJI PBF C 85 PHE PARA-(BENZOYL)-PHENYLALANINE HET PBF A 85 18 HET PBF C 85 18 HETNAM PBF PARA-(BENZOYL)-PHENYLALANINE FORMUL 1 PBF 2(C16 H15 N O3) FORMUL 5 HOH *327(H2 O) HELIX 1 1 ILE A 8 GLY A 17 1 10 HELIX 2 2 LYS A 18 ASP A 29 1 12 HELIX 3 3 LYS A 30 ARG A 35 5 6 HELIX 4 4 THR A 42 GLY A 51 1 10 HELIX 5 5 HIS A 52 LEU A 62 1 11 HELIX 6 6 SER A 75 GLY A 84 1 10 HELIX 7 7 PBF A 85 LYS A 95 1 11 HELIX 8 8 THR A 108 LYS A 116 1 9 HELIX 9 9 ARG A 118 GLY A 128 1 11 HELIX 10 10 THR A 141 GLY A 150 1 10 HELIX 11 11 ASN A 151 TYR A 161 1 11 HELIX 12 12 THR A 174 GLU A 182 1 9 HELIX 13 13 ARG A 184 GLN A 194 1 11 HELIX 14 14 THR A 207 ALA A 212 1 6 HELIX 15 15 LYS A 213 SER A 230 1 18 HELIX 16 16 ASP B 337 SER B 350 1 14 HELIX 17 17 LEU B 360 ALA B 365 1 6 HELIX 18 18 SER B 371 LEU B 385 1 15 HELIX 19 19 ALA B 386 ARG B 388 5 3 HELIX 20 20 LEU B 395 ILE B 407 1 13 HELIX 21 21 ILE C 8 SER C 16 1 9 HELIX 22 22 LYS C 18 ASP C 29 1 12 HELIX 23 23 LYS C 30 ARG C 35 5 6 HELIX 24 24 THR C 42 GLY C 51 1 10 HELIX 25 25 HIS C 52 LEU C 62 1 11 HELIX 26 26 SER C 75 GLY C 84 1 10 HELIX 27 27 PBF C 85 LYS C 95 1 11 HELIX 28 28 THR C 108 LYS C 116 1 9 HELIX 29 29 ARG C 118 GLY C 128 1 11 HELIX 30 30 THR C 141 GLY C 150 1 10 HELIX 31 31 ASN C 151 TYR C 161 1 11 HELIX 32 32 THR C 174 GLU C 182 1 9 HELIX 33 33 ARG C 184 GLN C 194 1 11 HELIX 34 34 THR C 207 ALA C 212 1 6 HELIX 35 35 LYS C 213 SER C 230 1 18 HELIX 36 36 ASP D 337 SER D 350 1 14 HELIX 37 37 LEU D 360 ALA D 365 1 6 HELIX 38 38 SER D 371 ARG D 388 1 18 HELIX 39 39 LEU D 395 ILE D 407 1 13 LINK C GLY A 84 N PBF A 85 1555 1555 1.41 LINK C PBF A 85 N ASP A 86 1555 1555 1.30 LINK CN1 PBF A 85 CG GLU B 356 1555 1555 1.46 LINK C GLY C 84 N PBF C 85 1555 1555 1.38 LINK C PBF C 85 N ASP C 86 1555 1555 1.29 LINK CN1 PBF C 85 CG GLU D 356 1555 1555 1.34 CRYST1 103.164 103.164 154.993 90.00 90.00 120.00 H 3 18 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 0.009693 0.005596 0.000000 0.00000 SCALE2 0.000000 0.011193 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006452 0.00000