HEADER HYDROLASE 06-FEB-24 8Y9A TITLE THE CRYSTAL STRUCTURE OF USP8 FROM BIORTUS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 8,UBIQUITIN ISOPEPTIDASE Y,HUBPY, COMPND 5 UBIQUITIN THIOESTERASE 8,UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 8; COMPND 6 EC: 3.4.19.12; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP8, KIAA0055, UBPY; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, PROTEASE, THIOL PROTEASE, CELL CYCLE, UBL CONJUGATION KEYWDS 2 PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR F.WANG,W.CHENG,Z.LV,C.JU,C.BAO REVDAT 1 06-MAR-24 8Y9A 0 JRNL AUTH F.WANG,W.CHENG,Z.LV,C.JU,C.BAO JRNL TITL THE CRYSTAL STRUCTURE OF USP8 FROM BIORTUS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 3507 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.733 REMARK 3 FREE R VALUE TEST SET COUNT : 166 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 246 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.1720 REMARK 3 BIN FREE R VALUE SET COUNT : 9 REMARK 3 BIN FREE R VALUE : 0.4060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1060 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.62000 REMARK 3 B22 (A**2) : 2.62000 REMARK 3 B33 (A**2) : -8.50000 REMARK 3 B12 (A**2) : 1.31000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.486 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.326 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.565 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.892 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1076 ; 0.002 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1030 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1438 ; 0.749 ; 1.667 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2420 ; 0.272 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 126 ; 5.519 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 8 ; 3.381 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 230 ;12.271 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 155 ; 0.036 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1183 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 197 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 265 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 93 ; 0.151 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 537 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 36 ; 0.173 ; 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 507 ; 3.454 ; 9.046 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 507 ; 3.420 ; 9.049 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 632 ; 5.307 ;13.543 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 633 ; 5.307 ;13.551 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 569 ; 3.351 ; 9.410 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 568 ; 3.345 ; 9.406 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 806 ; 5.547 ;13.961 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 807 ; 5.543 ;13.967 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8Y9A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300045207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.239850 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3507 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.82400 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.0M NA FORMATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 51.50400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 29.73585 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 31.08467 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 51.50400 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 29.73585 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 31.08467 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 51.50400 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 29.73585 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 31.08467 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 51.50400 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 29.73585 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 31.08467 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 51.50400 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 29.73585 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 31.08467 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 51.50400 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 29.73585 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 31.08467 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 59.47170 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 62.16933 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 59.47170 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 62.16933 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 59.47170 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 62.16933 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 59.47170 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 62.16933 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 59.47170 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 62.16933 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 59.47170 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 62.16933 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 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 213 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 PRO A 2 REMARK 465 ALA A 3 REMARK 465 VAL A 4 REMARK 465 ALA A 5 REMARK 465 ARG A 133 REMARK 465 LEU A 134 REMARK 465 GLN A 135 REMARK 465 GLN A 136 REMARK 465 LYS A 137 REMARK 465 ARG A 138 REMARK 465 GLN A 139 REMARK 465 GLU A 140 REMARK 465 THR A 141 REMARK 465 GLY A 142 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 203 O HOH A 207 11445 2.11 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 TYR A 12 -24.22 -140.65 REMARK 500 ARG A 54 11.83 91.78 REMARK 500 GLU A 130 -72.35 -73.50 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 227 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A 228 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A 229 DISTANCE = 8.49 ANGSTROMS DBREF 8Y9A A 1 142 UNP P40818 UBP8_HUMAN 1 142 SEQRES 1 A 142 MET PRO ALA VAL ALA SER VAL PRO LYS GLU LEU TYR LEU SEQRES 2 A 142 SER SER SER LEU LYS ASP LEU ASN LYS LYS THR GLU VAL SEQRES 3 A 142 LYS PRO GLU LYS ILE SER THR LYS SER TYR VAL HIS SER SEQRES 4 A 142 ALA LEU LYS ILE PHE LYS THR ALA GLU GLU CYS ARG LEU SEQRES 5 A 142 ASP ARG ASP GLU GLU ARG ALA TYR VAL LEU TYR MET LYS SEQRES 6 A 142 TYR VAL THR VAL TYR ASN LEU ILE LYS LYS ARG PRO ASP SEQRES 7 A 142 PHE LYS GLN GLN GLN ASP TYR PHE HIS SER ILE LEU GLY SEQRES 8 A 142 PRO GLY ASN ILE LYS LYS ALA VAL GLU GLU ALA GLU ARG SEQRES 9 A 142 LEU SER GLU SER LEU LYS LEU ARG TYR GLU GLU ALA GLU SEQRES 10 A 142 VAL ARG LYS LYS LEU GLU GLU LYS ASP ARG GLN GLU GLU SEQRES 11 A 142 ALA GLN ARG LEU GLN GLN LYS ARG GLN GLU THR GLY FORMUL 2 HOH *29(H2 O) HELIX 1 AA1 SER A 16 LYS A 22 1 7 HELIX 2 AA2 LYS A 27 ILE A 31 5 5 HELIX 3 AA3 SER A 32 ARG A 54 1 23 HELIX 4 AA4 ASP A 55 LYS A 74 1 20 HELIX 5 AA5 ARG A 76 GLN A 82 1 7 HELIX 6 AA6 GLN A 82 LEU A 90 1 9 HELIX 7 AA7 GLY A 93 GLN A 128 1 36 CRYST1 103.008 103.008 93.254 90.00 90.00 120.00 H 3 2 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 0.009708 0.005605 0.000000 0.00000 SCALE2 0.000000 0.011210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010723 0.00000 MASTER 374 0 0 7 0 0 0 6 1089 1 0 11 END