HEADER SIGNALING PROTEIN 13-JUL-05 2BWB TITLE CRYSTAL STRUCTURE OF THE UBA DOMAIN OF DSK2 FROM S. TITLE 2 CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE PROTEIN DSK2; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I; COMPND 4 FRAGMENT: UBA DOMAIN, RESIDUES 326-371; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: UBIQUITIN BINDING DOMAIN OF DSK2 PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_TAXID: 4932; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834(DE3)PLYSS; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX-KG KEYWDS UBIQUITIN, UBA, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.D.LOWE,N.HASAN,J.-F.TREMPE,L.FONSO,M.E.M.NOBLE, AUTHOR 2 J.A.ENDICOTT,L.N.JOHNSON,N.R.BROWN REVDAT 2 24-FEB-09 2BWB 1 VERSN REVDAT 1 25-JAN-06 2BWB 0 JRNL AUTH E.D.LOWE,N.HASAN,J.-F.TREMPE,L.FONSO,M.E.M.NOBLE, JRNL AUTH 2 J.A.ENDICOTT,L.N.JOHNSON,N.R.BROWN JRNL TITL STRUCTURES OF THE DSK2 UBL AND UBA DOMAINS AND JRNL TITL 2 THEIR COMPLEX. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 62 177 2006 JRNL REFN ISSN 0907-4449 JRNL PMID 16421449 JRNL DOI 10.1107/S0907444905037777 REMARK 2 REMARK 2 RESOLUTION. 2.3 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 101.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 22007 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) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1127 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1576 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3187 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.39 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.353 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.280 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.290 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.554 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3230 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2844 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4326 ; 1.150 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6553 ; 0.828 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 388 ; 8.997 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 214 ;39.928 ;23.738 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 539 ;19.544 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;17.230 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 433 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3758 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 743 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 696 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2734 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1514 ; 0.170 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2028 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 157 ; 0.193 ; 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): 59 ; 0.229 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 176 ; 0.243 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.205 ; 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): 2478 ; 0.357 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3055 ; 0.422 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1408 ; 0.741 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1271 ; 1.151 ; 4.500 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C D E F G H REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 328 A 370 2 REMARK 3 1 B 328 B 370 2 REMARK 3 1 C 328 C 370 2 REMARK 3 1 D 328 D 370 2 REMARK 3 1 E 328 E 370 2 REMARK 3 1 F 328 F 370 2 REMARK 3 1 G 328 G 370 2 REMARK 3 1 H 328 H 370 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 253 ; .05 ; .05 REMARK 3 TIGHT POSITIONAL 1 B (A): 253 ; .03 ; .05 REMARK 3 TIGHT POSITIONAL 1 C (A): 253 ; .04 ; .05 REMARK 3 TIGHT POSITIONAL 1 D (A): 253 ; .04 ; .05 REMARK 3 TIGHT POSITIONAL 1 E (A): 253 ; .04 ; .05 REMARK 3 TIGHT POSITIONAL 1 F (A): 253 ; .03 ; .05 REMARK 3 TIGHT POSITIONAL 1 G (A): 253 ; .03 ; .05 REMARK 3 TIGHT POSITIONAL 1 H (A): 253 ; .03 ; .05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 402 ; .82 ; .50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 402 ; .71 ; .50 REMARK 3 MEDIUM POSITIONAL 1 C (A): 402 ; .80 ; .50 REMARK 3 MEDIUM POSITIONAL 1 D (A): 402 ; .73 ; .50 REMARK 3 MEDIUM POSITIONAL 1 E (A): 402 ; .62 ; .50 REMARK 3 MEDIUM POSITIONAL 1 F (A): 402 ; .70 ; .50 REMARK 3 MEDIUM POSITIONAL 1 G (A): 402 ; .69 ; .50 REMARK 3 MEDIUM POSITIONAL 1 H (A): 402 ; .74 ; .50 REMARK 3 TIGHT THERMAL 1 A (A**2): 253 ; .06 ; .50 REMARK 3 TIGHT THERMAL 1 B (A**2): 253 ; .06 ; .50 REMARK 3 TIGHT THERMAL 1 C (A**2): 253 ; .07 ; .50 REMARK 3 TIGHT THERMAL 1 D (A**2): 253 ; .05 ; .50 REMARK 3 TIGHT THERMAL 1 E (A**2): 253 ; .10 ; .50 REMARK 3 TIGHT THERMAL 1 F (A**2): 253 ; .05 ; .50 REMARK 3 TIGHT THERMAL 1 G (A**2): 253 ; .05 ; .50 REMARK 3 TIGHT THERMAL 1 H (A**2): 253 ; .06 ; .50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 402 ; .35 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 402 ; .27 ; 2.00 REMARK 3 MEDIUM THERMAL 1 C (A**2): 402 ; .31 ; 2.00 REMARK 3 MEDIUM THERMAL 1 D (A**2): 402 ; .25 ; 2.00 REMARK 3 MEDIUM THERMAL 1 E (A**2): 402 ; .50 ; 2.00 REMARK 3 MEDIUM THERMAL 1 F (A**2): 402 ; .34 ; 2.00 REMARK 3 MEDIUM THERMAL 1 G (A**2): 402 ; .25 ; 2.00 REMARK 3 MEDIUM THERMAL 1 H (A**2): 402 ; .28 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A I REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 328 A 341 6 REMARK 3 1 I 328 I 341 6 REMARK 3 2 A 346 A 370 6 REMARK 3 2 I 346 I 370 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 2 A (A): 579 ; .74 ; 5.00 REMARK 3 LOOSE THERMAL 2 A (A**2): 579 ; 1.48 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2BWB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-05. REMARK 100 THE PDBE ID CODE IS EBI-24890. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23134 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.3 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.4 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M TRISODIUM CITRATE PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 58.15550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.03450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.15550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.03450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8, 9 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 GENERATING THE BIOMOLECULE 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMOLECULE: 5 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 BIOMOLECULE: 6 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: F 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 BIOMOLECULE: 7 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: G 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 BIOMOLECULE: 8 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: H 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 BIOMOLECULE: 9 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: I 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 LEU B 326 REMARK 465 GLY B 371 REMARK 465 LEU D 326 REMARK 465 LEU E 326 REMARK 465 GLY E 371 REMARK 465 LEU F 326 REMARK 465 GLY F 371 REMARK 465 LEU G 326 REMARK 465 LEU H 326 REMARK 465 GLY H 371 REMARK 465 LEU I 326 REMARK 465 ASP I 341 REMARK 465 MET I 342 REMARK 465 GLY I 343 REMARK 465 PHE I 344 REMARK 465 GLY I 371 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 NE2 GLN A 338 - O HOH A 2007 2.16 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 ASN E 370 CG ASN E 370 ND2 0.210 REMARK 500 ASN E 370 CG ASN E 370 OD1 0.288 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 PRO F 328 C - N - CA ANGL. DEV. = 25.4 DEGREES 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 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 GLU I 333 -56.16 -29.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 329 GLU A 330 144.99 REMARK 500 ASP F 327 PRO F 328 41.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLU A 330 24.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WR1 RELATED DB: PDB REMARK 900 THE COMPLEX STURCTURE OF DSK2P UBA WITH REMARK 900 UBIQUITIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE STRUCTURE PRESENTED IS OF THE UBA DOMAIN, RESIDUES 326- REMARK 999 371 OF THE INTACT PROTEIN DBREF 2BWB A 326 371 UNP P48510 DSK2_YEAST 326 371 DBREF 2BWB B 326 371 UNP P48510 DSK2_YEAST 326 371 DBREF 2BWB C 326 371 UNP P48510 DSK2_YEAST 326 371 DBREF 2BWB D 326 371 UNP P48510 DSK2_YEAST 326 371 DBREF 2BWB E 326 371 UNP P48510 DSK2_YEAST 326 371 DBREF 2BWB F 326 371 UNP P48510 DSK2_YEAST 326 371 DBREF 2BWB G 326 371 UNP P48510 DSK2_YEAST 326 371 DBREF 2BWB H 326 371 UNP P48510 DSK2_YEAST 326 371 DBREF 2BWB I 326 371 UNP P48510 DSK2_YEAST 326 371 SEQRES 1 A 46 LEU ASP PRO GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN SEQRES 2 A 46 LEU ASN ASP MET GLY PHE PHE ASP PHE ASP ARG ASN VAL SEQRES 3 A 46 ALA ALA LEU ARG ARG SER GLY GLY SER VAL GLN GLY ALA SEQRES 4 A 46 LEU ASP SER LEU LEU ASN GLY SEQRES 1 B 46 LEU ASP PRO GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN SEQRES 2 B 46 LEU ASN ASP MET GLY PHE PHE ASP PHE ASP ARG ASN VAL SEQRES 3 B 46 ALA ALA LEU ARG ARG SER GLY GLY SER VAL GLN GLY ALA SEQRES 4 B 46 LEU ASP SER LEU LEU ASN GLY SEQRES 1 C 46 LEU ASP PRO GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN SEQRES 2 C 46 LEU ASN ASP MET GLY PHE PHE ASP PHE ASP ARG ASN VAL SEQRES 3 C 46 ALA ALA LEU ARG ARG SER GLY GLY SER VAL GLN GLY ALA SEQRES 4 C 46 LEU ASP SER LEU LEU ASN GLY SEQRES 1 D 46 LEU ASP PRO GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN SEQRES 2 D 46 LEU ASN ASP MET GLY PHE PHE ASP PHE ASP ARG ASN VAL SEQRES 3 D 46 ALA ALA LEU ARG ARG SER GLY GLY SER VAL GLN GLY ALA SEQRES 4 D 46 LEU ASP SER LEU LEU ASN GLY SEQRES 1 E 46 LEU ASP PRO GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN SEQRES 2 E 46 LEU ASN ASP MET GLY PHE PHE ASP PHE ASP ARG ASN VAL SEQRES 3 E 46 ALA ALA LEU ARG ARG SER GLY GLY SER VAL GLN GLY ALA SEQRES 4 E 46 LEU ASP SER LEU LEU ASN GLY SEQRES 1 F 46 LEU ASP PRO GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN SEQRES 2 F 46 LEU ASN ASP MET GLY PHE PHE ASP PHE ASP ARG ASN VAL SEQRES 3 F 46 ALA ALA LEU ARG ARG SER GLY GLY SER VAL GLN GLY ALA SEQRES 4 F 46 LEU ASP SER LEU LEU ASN GLY SEQRES 1 G 46 LEU ASP PRO GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN SEQRES 2 G 46 LEU ASN ASP MET GLY PHE PHE ASP PHE ASP ARG ASN VAL SEQRES 3 G 46 ALA ALA LEU ARG ARG SER GLY GLY SER VAL GLN GLY ALA SEQRES 4 G 46 LEU ASP SER LEU LEU ASN GLY SEQRES 1 H 46 LEU ASP PRO GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN SEQRES 2 H 46 LEU ASN ASP MET GLY PHE PHE ASP PHE ASP ARG ASN VAL SEQRES 3 H 46 ALA ALA LEU ARG ARG SER GLY GLY SER VAL GLN GLY ALA SEQRES 4 H 46 LEU ASP SER LEU LEU ASN GLY SEQRES 1 I 46 LEU ASP PRO GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN SEQRES 2 I 46 LEU ASN ASP MET GLY PHE PHE ASP PHE ASP ARG ASN VAL SEQRES 3 I 46 ALA ALA LEU ARG ARG SER GLY GLY SER VAL GLN GLY ALA SEQRES 4 I 46 LEU ASP SER LEU LEU ASN GLY FORMUL 10 HOH *150(H2 O1) HELIX 1 1 ASP A 327 TYR A 332 1 6 HELIX 2 2 TYR A 332 MET A 342 1 11 HELIX 3 3 ASP A 346 GLY A 358 1 13 HELIX 4 4 SER A 360 ASN A 370 1 11 HELIX 5 5 ASP B 327 TYR B 332 1 6 HELIX 6 6 TYR B 332 MET B 342 1 11 HELIX 7 7 ASP B 346 SER B 357 1 12 HELIX 8 8 SER B 360 ASN B 370 1 11 HELIX 9 9 ASP C 327 TYR C 332 1 6 HELIX 10 10 TYR C 332 MET C 342 1 11 HELIX 11 11 ASP C 346 SER C 357 1 12 HELIX 12 12 SER C 360 ASN C 370 1 11 HELIX 13 13 ASP D 327 TYR D 332 1 6 HELIX 14 14 TYR D 332 MET D 342 1 11 HELIX 15 15 ASP D 346 GLY D 358 1 13 HELIX 16 16 SER D 360 ASN D 370 1 11 HELIX 17 17 ASP E 327 TYR E 332 1 6 HELIX 18 18 TYR E 332 MET E 342 1 11 HELIX 19 19 ASP E 346 SER E 357 1 12 HELIX 20 20 SER E 360 ASN E 370 1 11 HELIX 21 21 TYR F 332 MET F 342 1 11 HELIX 22 22 ASP F 346 SER F 357 1 12 HELIX 23 23 SER F 360 ASN F 370 1 11 HELIX 24 24 ASP G 327 TYR G 332 1 6 HELIX 25 25 TYR G 332 MET G 342 1 11 HELIX 26 26 ASP G 346 SER G 357 1 12 HELIX 27 27 SER G 360 ASN G 370 1 11 HELIX 28 28 ASP H 327 TYR H 332 1 6 HELIX 29 29 TYR H 332 MET H 342 1 11 HELIX 30 30 ASP H 346 SER H 357 1 12 HELIX 31 31 SER H 360 ASN H 370 1 11 HELIX 32 32 ASP I 327 TYR I 332 1 6 HELIX 33 33 TYR I 332 LEU I 339 1 8 HELIX 34 34 ASP I 346 SER I 357 1 12 HELIX 35 35 SER I 360 LEU I 368 1 9 CRYST1 116.311 44.069 111.525 90.00 114.87 90.00 C 1 2 1 36 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 0.008598 0.000000 0.003985 0.00000 SCALE2 0.000000 0.022692 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009883 0.00000 MTRIX1 1 0.824420 0.471130 0.313630 20.22631 1 MTRIX2 1 -0.341450 0.855970 -0.388240 -18.80769 1 MTRIX3 1 -0.451370 0.212990 0.866550 -27.27886 1 MTRIX1 2 0.353300 0.854760 0.380210 20.28533 1 MTRIX2 2 -0.423470 0.508520 -0.749720 -30.36740 1 MTRIX3 2 -0.834180 0.103870 0.541620 -63.49786 1 MTRIX1 3 -0.278860 0.933040 0.227330 3.61382 1 MTRIX2 3 -0.181590 0.181220 -0.966530 -27.32594 1 MTRIX3 3 -0.943010 -0.310810 0.118890 -98.23232 1 MTRIX1 4 0.713890 -0.063820 0.697340 81.21254 1 MTRIX2 4 0.640870 -0.341790 -0.687360 -41.14663 1 MTRIX3 4 0.282210 0.937610 -0.203100 -97.40068 1 MTRIX1 5 0.326680 0.402880 0.854960 78.56183 1 MTRIX2 5 0.939350 -0.038460 -0.340800 -6.55663 1 MTRIX3 5 -0.104420 0.914440 -0.391010 -103.46541 1 MTRIX1 6 -0.265290 0.612720 0.744440 56.53645 1 MTRIX2 6 0.918180 0.396160 0.001150 21.73804 1 MTRIX3 6 -0.294210 0.683840 -0.667690 -111.19116 1 MTRIX1 7 -0.797460 0.421990 0.431270 23.09112 1 MTRIX2 7 0.531460 0.829660 0.170920 32.64115 1 MTRIX3 7 -0.285680 0.365510 -0.885890 -111.89786 1 MTRIX1 8 -0.719900 0.618420 -0.315120 -29.08712 1 MTRIX2 8 0.247030 -0.195990 -0.948980 32.64115 1 MTRIX3 8 -0.648630 -0.761020 -0.011680 -111.89786 1