HEADER HYDROLASE 29-MAR-04 1VJV TITLE CRYSTAL STRUCTURE OF UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6 (YFR010W) TITLE 2 FROM SACCHAROMYCES CEREVISIAE AT 1.74 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 97-499; COMPND 5 SYNONYM: UBIQUITIN THIOLESTERASE 6, UBIQUITIN-SPECIFIC PROCESSING COMPND 6 PROTEASE 6, DEUBIQUITINATING ENZYME 6; COMPND 7 EC: 3.1.2.15; COMPND 8 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 GENE: UBP6, YFR010W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS YFR010W, UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6, STRUCTURAL KEYWDS 2 GENOMICS, JCSG, PSI, PROTEIN STRUCTURE INITIATIVE, JOINT CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 8 25-JAN-23 1VJV 1 SEQADV LINK REVDAT 7 04-OCT-17 1VJV 1 REMARK REVDAT 6 13-JUL-11 1VJV 1 VERSN REVDAT 5 21-JUL-09 1VJV 1 REMARK REVDAT 4 24-FEB-09 1VJV 1 VERSN REVDAT 3 28-MAR-06 1VJV 1 JRNL REVDAT 2 18-JAN-05 1VJV 1 AUTHOR KEYWDS REMARK REVDAT 1 21-SEP-04 1VJV 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6 JRNL TITL 2 (YFR010W) FROM SACCHAROMYCES CEREVISIAE AT 1.74 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 40625 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 + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2129 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 12 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.74 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4544 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 220 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2964 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 241 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 36.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.92000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : 2.59000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.624 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3063 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2725 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4119 ; 1.304 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6395 ; 0.767 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 5.866 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 450 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3349 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 601 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 545 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3127 ; 0.238 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1783 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 189 ; 0.139 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 9 ; 0.186 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 32 ; 0.294 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.165 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1833 ; 1.889 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2964 ; 3.126 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1230 ; 5.018 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1155 ; 7.490 ;11.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 103 A 343 REMARK 3 RESIDUE RANGE : A 418 A 499 REMARK 3 ORIGIN FOR THE GROUP (A): 6.8850 21.7130 22.7600 REMARK 3 T TENSOR REMARK 3 T11: 0.1090 T22: 0.0797 REMARK 3 T33: 0.0431 T12: 0.0017 REMARK 3 T13: -0.0041 T23: -0.0204 REMARK 3 L TENSOR REMARK 3 L11: 1.7387 L22: 1.0312 REMARK 3 L33: 0.7652 L12: 0.2808 REMARK 3 L13: -0.2698 L23: -0.2491 REMARK 3 S TENSOR REMARK 3 S11: 0.0581 S12: -0.0019 S13: -0.0354 REMARK 3 S21: 0.0596 S22: -0.0380 S23: -0.1391 REMARK 3 S31: -0.0327 S32: -0.0134 S33: -0.0202 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 344 A 370 REMARK 3 ORIGIN FOR THE GROUP (A): -13.2950 7.3600 23.4810 REMARK 3 T TENSOR REMARK 3 T11: 0.1445 T22: 0.1790 REMARK 3 T33: 0.1069 T12: -0.1236 REMARK 3 T13: 0.0366 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.7899 L22: 5.9251 REMARK 3 L33: 7.9764 L12: -2.1909 REMARK 3 L13: -0.3444 L23: 2.9828 REMARK 3 S TENSOR REMARK 3 S11: 0.0745 S12: 0.0468 S13: -0.2749 REMARK 3 S21: 0.0359 S22: -0.1847 S23: 0.2274 REMARK 3 S31: 0.6963 S32: -0.5621 S33: 0.1102 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 387 A 417 REMARK 3 ORIGIN FOR THE GROUP (A): -4.6620 5.9780 1.4060 REMARK 3 T TENSOR REMARK 3 T11: 0.1443 T22: 0.1409 REMARK 3 T33: 0.0564 T12: 0.0685 REMARK 3 T13: -0.0517 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 9.2697 L22: 2.5856 REMARK 3 L33: 15.3988 L12: -3.0023 REMARK 3 L13: -9.8979 L23: 5.9202 REMARK 3 S TENSOR REMARK 3 S11: 0.0511 S12: 0.1874 S13: 0.0579 REMARK 3 S21: -0.1187 S22: -0.1216 S23: -0.0141 REMARK 3 S31: 0.0123 S32: -0.1110 S33: 0.0705 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1VJV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000001931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-03; 17-JUL-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ALS; APS REMARK 200 BEAMLINE : 8.3.1; 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115870; 0.96112, REMARK 200 0.97963,0.97946 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111); REMARK 200 ROSENBAUM-ROCK DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL; WATER COOLED, SAGITALLY REMARK 200 FOCUSING 2ND CRYSTAL, ROSENBAUM- REMARK 200 ROCK VERTICAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC; APS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 4.2), CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42823 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 79.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.59400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXD, AUTOSHARP, SOLOMON REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG MME 2000, 0.03M TRIS_BASE, REMARK 280 0.07M TRIS CL , VAPOR DIFFUSION,SITTING DROP,NANODROP, REMARK 280 TEMPERATURE 277K. 21% PEG MME 2000, 0.03M TRIS_BASE, 0.07M TRIS REMARK 280 CL , VAPOR DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE 277K 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 24.61550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.16950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.72450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.16950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.61550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.72450 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 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 MSE A 85 REMARK 465 GLY A 86 REMARK 465 SER A 87 REMARK 465 ASP A 88 REMARK 465 LYS A 89 REMARK 465 ILE A 90 REMARK 465 HIS A 91 REMARK 465 HIS A 92 REMARK 465 HIS A 93 REMARK 465 HIS A 94 REMARK 465 HIS A 95 REMARK 465 HIS A 96 REMARK 465 PRO A 97 REMARK 465 GLU A 98 REMARK 465 GLN A 99 REMARK 465 GLN A 100 REMARK 465 VAL A 101 REMARK 465 GLN A 102 REMARK 465 SER A 175 REMARK 465 SER A 200 REMARK 465 GLN A 201 REMARK 465 GLY A 202 REMARK 465 GLY A 203 REMARK 465 ILE A 284 REMARK 465 GLU A 285 REMARK 465 LYS A 286 REMARK 465 ARG A 287 REMARK 465 SER A 288 REMARK 465 ASP A 289 REMARK 465 LEU A 290 REMARK 465 THR A 291 REMARK 465 GLY A 292 REMARK 465 GLU A 371 REMARK 465 ARG A 372 REMARK 465 GLU A 373 REMARK 465 ILE A 374 REMARK 465 LYS A 375 REMARK 465 ARG A 376 REMARK 465 ARG A 377 REMARK 465 LYS A 378 REMARK 465 PHE A 379 REMARK 465 ASP A 380 REMARK 465 PRO A 381 REMARK 465 SER A 382 REMARK 465 SER A 383 REMARK 465 SER A 384 REMARK 465 GLU A 385 REMARK 465 ASN A 386 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 103 OE1 NE2 REMARK 470 ASP A 247 CB CG OD1 OD2 REMARK 470 ASN A 248 CG OD1 ND2 REMARK 470 SER A 295 CB OG REMARK 470 ARG A 321 CG CD NE CZ NH1 NH2 REMARK 470 SER A 322 OG REMARK 470 THR A 323 OG1 CG2 REMARK 470 LYS A 325 CG CD CE NZ REMARK 470 LYS A 355 CE NZ REMARK 470 GLU A 366 CD OE1 OE2 REMARK 470 LYS A 370 CG CD CE NZ REMARK 470 ARG A 391 NE CZ NH1 NH2 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 MSE A 272 SE MSE A 272 CE -0.358 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 153 30.44 -99.97 REMARK 500 PRO A 181 46.89 -83.46 REMARK 500 SER A 427 -167.76 -114.85 REMARK 500 ASN A 465 76.36 -102.01 REMARK 500 ASP A 466 -114.97 57.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 355004 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 MASS SPECTROMETER DATA AND SEQUENCING THE CONSTRUCT REMARK 999 CONFIRMED THAT THE EXPRESSED PROTEIN COMPRISED AN REMARK 999 N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED BY REMARK 999 RESIDUES 97-499 OF THE PREDICTED YFR010W GENE PRODUCT. REMARK 999 CLONING ARTIFACT: THE DENSITY FOR RESIDUE 182 FROM EACH REMARK 999 MONOMER SUGGESTED THAT THIS RESIDUE WAS AN VALINE AND NOT REMARK 999 AN ISOLUCINE. SEQUENCING OF THE CONSTRUCT CONFIRMED THAT REMARK 999 RESIDUE 182 IS VALINE IN THE EXPRESSED PROTEIN. DBREF 1VJV A 97 499 UNP P43593 UBP6_YEAST 97 499 SEQADV 1VJV MSE A 85 UNP P43593 EXPRESSION TAG SEQADV 1VJV GLY A 86 UNP P43593 EXPRESSION TAG SEQADV 1VJV SER A 87 UNP P43593 EXPRESSION TAG SEQADV 1VJV ASP A 88 UNP P43593 EXPRESSION TAG SEQADV 1VJV LYS A 89 UNP P43593 EXPRESSION TAG SEQADV 1VJV ILE A 90 UNP P43593 EXPRESSION TAG SEQADV 1VJV HIS A 91 UNP P43593 EXPRESSION TAG SEQADV 1VJV HIS A 92 UNP P43593 EXPRESSION TAG SEQADV 1VJV HIS A 93 UNP P43593 EXPRESSION TAG SEQADV 1VJV HIS A 94 UNP P43593 EXPRESSION TAG SEQADV 1VJV HIS A 95 UNP P43593 EXPRESSION TAG SEQADV 1VJV HIS A 96 UNP P43593 EXPRESSION TAG SEQADV 1VJV MSE A 114 UNP P43593 MET 114 MODIFIED RESIDUE SEQADV 1VJV MSE A 136 UNP P43593 MET 136 MODIFIED RESIDUE SEQADV 1VJV MSE A 164 UNP P43593 MET 164 MODIFIED RESIDUE SEQADV 1VJV VAL A 182 UNP P43593 ILE 182 SEE REMARK 999 SEQADV 1VJV MSE A 221 UNP P43593 MET 221 MODIFIED RESIDUE SEQADV 1VJV MSE A 272 UNP P43593 MET 272 MODIFIED RESIDUE SEQADV 1VJV MSE A 344 UNP P43593 MET 344 MODIFIED RESIDUE SEQADV 1VJV MSE A 388 UNP P43593 MET 388 MODIFIED RESIDUE SEQADV 1VJV MSE A 493 UNP P43593 MET 493 MODIFIED RESIDUE SEQRES 1 A 415 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS PRO SEQRES 2 A 415 GLU GLN GLN VAL GLN GLN PHE ALA GLN LEU PRO VAL GLY SEQRES 3 A 415 PHE LYS ASN MSE GLY ASN THR CYS TYR LEU ASN ALA THR SEQRES 4 A 415 LEU GLN ALA LEU TYR ARG VAL ASN ASP LEU ARG ASP MSE SEQRES 5 A 415 ILE LEU ASN TYR ASN PRO SER GLN GLY VAL SER ASN SER SEQRES 6 A 415 GLY ALA GLN ASP GLU GLU ILE HIS LYS GLN ILE VAL ILE SEQRES 7 A 415 GLU MSE LYS ARG CYS PHE GLU ASN LEU GLN ASN LYS SER SEQRES 8 A 415 PHE LYS SER VAL LEU PRO VAL VAL LEU LEU ASN THR LEU SEQRES 9 A 415 ARG LYS CYS TYR PRO GLN PHE ALA GLU ARG ASP SER GLN SEQRES 10 A 415 GLY GLY PHE TYR LYS GLN GLN ASP ALA GLU GLU LEU PHE SEQRES 11 A 415 THR GLN LEU PHE HIS SER MSE SER ILE VAL PHE GLY ASP SEQRES 12 A 415 LYS PHE SER GLU ASP PHE ARG ILE GLN PHE LYS THR THR SEQRES 13 A 415 ILE LYS ASP THR ALA ASN ASP ASN ASP ILE THR VAL LYS SEQRES 14 A 415 GLU ASN GLU SER ASP SER LYS LEU GLN CYS HIS ILE SER SEQRES 15 A 415 GLY THR THR ASN PHE MSE ARG ASN GLY LEU LEU GLU GLY SEQRES 16 A 415 LEU ASN GLU LYS ILE GLU LYS ARG SER ASP LEU THR GLY SEQRES 17 A 415 ALA ASN SER ILE TYR SER VAL GLU LYS LYS ILE SER ARG SEQRES 18 A 415 LEU PRO LYS PHE LEU THR VAL GLN TYR VAL ARG PHE PHE SEQRES 19 A 415 TRP LYS ARG SER THR ASN LYS LYS SER LYS ILE LEU ARG SEQRES 20 A 415 LYS VAL VAL PHE PRO PHE GLN LEU ASP VAL ALA ASP MSE SEQRES 21 A 415 LEU THR PRO GLU TYR ALA ALA GLU LYS VAL LYS VAL ARG SEQRES 22 A 415 ASP GLU LEU ARG LYS VAL GLU LYS GLU LYS ASN GLU LYS SEQRES 23 A 415 GLU ARG GLU ILE LYS ARG ARG LYS PHE ASP PRO SER SER SEQRES 24 A 415 SER GLU ASN VAL MSE THR PRO ARG GLU GLN TYR GLU THR SEQRES 25 A 415 GLN VAL ALA LEU ASN GLU SER GLU LYS ASP GLN TRP LEU SEQRES 26 A 415 GLU GLU TYR LYS LYS HIS PHE PRO PRO ASN LEU GLU LYS SEQRES 27 A 415 GLY GLU ASN PRO SER CYS VAL TYR ASN LEU ILE GLY VAL SEQRES 28 A 415 ILE THR HIS GLN GLY ALA ASN SER GLU SER GLY HIS TYR SEQRES 29 A 415 GLN ALA PHE ILE ARG ASP GLU LEU ASP GLU ASN LYS TRP SEQRES 30 A 415 TYR LYS PHE ASN ASP ASP LYS VAL SER VAL VAL GLU LYS SEQRES 31 A 415 GLU LYS ILE GLU SER LEU ALA GLY GLY GLY GLU SER ASP SEQRES 32 A 415 SER ALA LEU ILE LEU MSE TYR LYS GLY PHE GLY LEU MODRES 1VJV MSE A 114 MET SELENOMETHIONINE MODRES 1VJV MSE A 136 MET SELENOMETHIONINE MODRES 1VJV MSE A 164 MET SELENOMETHIONINE MODRES 1VJV MSE A 221 MET SELENOMETHIONINE MODRES 1VJV MSE A 272 MET SELENOMETHIONINE MODRES 1VJV MSE A 344 MET SELENOMETHIONINE MODRES 1VJV MSE A 388 MET SELENOMETHIONINE MODRES 1VJV MSE A 493 MET SELENOMETHIONINE HET MSE A 114 8 HET MSE A 136 8 HET MSE A 164 8 HET MSE A 221 12 HET MSE A 272 8 HET MSE A 344 8 HET MSE A 388 8 HET MSE A 493 12 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 HOH *241(H2 O) HELIX 1 1 THR A 117 VAL A 130 1 14 HELIX 2 2 VAL A 130 ASN A 139 1 10 HELIX 3 3 ASN A 141 GLY A 145 5 5 HELIX 4 4 ASP A 153 ASN A 173 1 21 HELIX 5 5 PRO A 181 TYR A 192 1 12 HELIX 6 6 PRO A 193 GLU A 197 5 5 HELIX 7 7 ASP A 209 GLY A 226 1 18 HELIX 8 8 GLY A 226 GLU A 231 1 6 HELIX 9 9 PHE A 271 LEU A 280 1 10 HELIX 10 10 ALA A 342 LEU A 345 5 4 HELIX 11 11 THR A 346 LYS A 370 1 25 HELIX 12 12 THR A 389 LYS A 414 1 26 HELIX 13 13 GLU A 473 SER A 479 1 7 HELIX 14 14 LEU A 480 GLY A 482 5 3 SHEET 1 A 2 GLY A 110 PHE A 111 0 SHEET 2 A 2 SER A 178 VAL A 179 1 O VAL A 179 N GLY A 110 SHEET 1 B 3 ASN A 246 LYS A 253 0 SHEET 2 B 3 ILE A 235 ASP A 243 -1 N ILE A 241 O THR A 251 SHEET 3 B 3 SER A 257 ASP A 258 -1 O ASP A 258 N ILE A 235 SHEET 1 C 4 ASN A 246 LYS A 253 0 SHEET 2 C 4 ILE A 235 ASP A 243 -1 N ILE A 241 O THR A 251 SHEET 3 C 4 TYR A 297 ARG A 305 -1 O LYS A 302 N LYS A 238 SHEET 4 C 4 ASN A 281 GLU A 282 -1 N GLU A 282 O VAL A 299 SHEET 1 D 5 LEU A 261 CYS A 263 0 SHEET 2 D 5 PHE A 309 TYR A 314 1 O GLN A 313 N CYS A 263 SHEET 3 D 5 SER A 488 GLY A 496 -1 O LEU A 490 N TYR A 314 SHEET 4 D 5 VAL A 429 GLN A 439 -1 N ASN A 431 O LYS A 495 SHEET 5 D 5 GLN A 338 ASP A 340 -1 N LEU A 339 O TYR A 430 SHEET 1 E 7 LEU A 261 CYS A 263 0 SHEET 2 E 7 PHE A 309 TYR A 314 1 O GLN A 313 N CYS A 263 SHEET 3 E 7 SER A 488 GLY A 496 -1 O LEU A 490 N TYR A 314 SHEET 4 E 7 VAL A 429 GLN A 439 -1 N ASN A 431 O LYS A 495 SHEET 5 E 7 HIS A 447 ARG A 453 -1 O PHE A 451 N VAL A 435 SHEET 6 E 7 TRP A 461 ASN A 465 -1 O PHE A 464 N ALA A 450 SHEET 7 E 7 LYS A 468 VAL A 472 -1 O SER A 470 N LYS A 463 SHEET 1 F 2 PHE A 317 LYS A 320 0 SHEET 2 F 2 LYS A 325 LYS A 328 -1 O SER A 327 N PHE A 318 LINK C ASN A 113 N MSE A 114 1555 1555 1.33 LINK C MSE A 114 N GLY A 115 1555 1555 1.33 LINK C ASP A 135 N MSE A 136 1555 1555 1.34 LINK C MSE A 136 N ILE A 137 1555 1555 1.33 LINK C GLU A 163 N MSE A 164 1555 1555 1.34 LINK C MSE A 164 N LYS A 165 1555 1555 1.34 LINK C SER A 220 N MSE A 221 1555 1555 1.32 LINK C MSE A 221 N SER A 222 1555 1555 1.32 LINK C PHE A 271 N MSE A 272 1555 1555 1.31 LINK C MSE A 272 N ARG A 273 1555 1555 1.32 LINK C ASP A 343 N MSE A 344 1555 1555 1.34 LINK C MSE A 344 N LEU A 345 1555 1555 1.32 LINK C VAL A 387 N MSE A 388 1555 1555 1.33 LINK C MSE A 388 N THR A 389 1555 1555 1.33 LINK C LEU A 492 N MSE A 493 1555 1555 1.32 LINK C MSE A 493 N TYR A 494 1555 1555 1.32 CRYST1 49.231 79.449 106.339 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 0.020312 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012587 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009404 0.00000