HEADER PROTEIN BINDING 23-JUL-25 9S2Y TITLE CRYSTAL STRUCTURE OF USP10 CATALYTIC DOMAIN (APO STATE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 10; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 10,UBIQUITIN THIOESTERASE 10, COMPND 5 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 10; 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: USP10, KIAA0190; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS USP, ISOPEPTIDASE, DEUBIQUITINASE, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.MISRA,A.VIDOV,J.VOLLRATH,I.DIKIC REVDAT 1 04-NOV-26 9S2Y 0 JRNL AUTH J.VOLLRATH,M.MISRA,V.VIDOV,U.G.MATO,T.MOSLER,R.MUKHOPADHYAY, JRNL AUTH 2 N.PAHOR,J.STUKE,M.HEINZ,B.FABIAN,O.HARTMANN, JRNL AUTH 3 G.VAN DER HEDEN VAN NOORT,G.HUMMER,P.GEURINK,M.DIEFENBACHER, JRNL AUTH 4 J.D.LANGER,I.DIKIC JRNL TITL MECHANISTIC AND STRUCTURAL INSIGHTS INTO THE UBIQUITIN JRNL TITL 2 SPECIFIC PROTEASE 10 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 40122 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2101 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2892 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 163 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2673 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 267 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.72000 REMARK 3 B22 (A**2) : 0.72000 REMARK 3 B33 (A**2) : -2.33000 REMARK 3 B12 (A**2) : 0.36000 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): 0.102 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.396 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2761 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2771 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3732 ; 1.690 ; 1.838 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6280 ; 1.011 ; 1.758 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 332 ; 6.332 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 16 ; 9.549 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 483 ;14.361 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 431 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3139 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 623 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1340 ; 3.717 ; 3.584 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1340 ; 3.715 ; 3.583 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1668 ; 5.482 ; 6.384 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1669 ; 5.492 ; 6.388 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1421 ; 5.217 ; 4.182 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1418 ; 5.179 ; 4.167 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2059 ; 7.971 ; 7.342 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 11424 ;11.491 ;45.320 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 11247 ;11.465 ;44.790 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 388 A 1715 REMARK 3 ORIGIN FOR THE GROUP (A): -37.7484 13.8434 6.8793 REMARK 3 T TENSOR REMARK 3 T11: 0.0467 T22: 0.0304 REMARK 3 T33: 0.0204 T12: 0.0107 REMARK 3 T13: 0.0023 T23: -0.0204 REMARK 3 L TENSOR REMARK 3 L11: 0.1250 L22: 0.6007 REMARK 3 L33: 0.3669 L12: 0.1735 REMARK 3 L13: -0.1284 L23: 0.0987 REMARK 3 S TENSOR REMARK 3 S11: -0.0530 S12: -0.0040 S13: 0.0030 REMARK 3 S21: -0.0664 S22: 0.0812 S23: -0.0468 REMARK 3 S31: 0.0534 S32: 0.0559 S33: -0.0282 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 9S2Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1292149476. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-24 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42256 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 76.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 40.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 9.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 (%): 53.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM SULFATE, 20% PEG 3350, REMARK 280 10% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.57500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 65.57500 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 65.57500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 65.57500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 65.57500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 65.57500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A1117 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1122 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1166 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 SER A 380 REMARK 465 MET A 381 REMARK 465 GLU A 382 REMARK 465 GLY A 383 REMARK 465 LEU A 384 REMARK 465 VAL A 385 REMARK 465 PRO A 386 REMARK 465 VAL A 387 REMARK 465 GLU A 517 REMARK 465 LYS A 518 REMARK 465 GLY A 519 REMARK 465 ARG A 520 REMARK 465 GLN A 521 REMARK 465 SER A 588 REMARK 465 GLY A 589 REMARK 465 SER A 590 REMARK 465 GLY A 591 REMARK 465 SER A 592 REMARK 465 GLY A 593 REMARK 465 SER A 594 REMARK 465 ALA A 595 REMARK 465 GLU A 692 REMARK 465 LYS A 693 REMARK 465 THR A 694 REMARK 465 GLY A 695 REMARK 465 LYS A 722 REMARK 465 ASN A 723 REMARK 465 LYS A 724 REMARK 465 ASN A 725 REMARK 465 PHE A 726 REMARK 465 LYS A 727 REMARK 465 CYS A 728 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 O HOH A 927 O HOH A 1134 2.02 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 MET A 443 CG - SD - CE ANGL. DEV. = -10.2 DEGREES REMARK 500 MET A 475 CG - SD - CE ANGL. DEV. = -11.4 DEGREES REMARK 500 ARG A 793 NE - CZ - NH2 ANGL. DEV. = -3.9 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 SER A 618 16.15 59.29 REMARK 500 LYS A 662 -60.13 -143.18 REMARK 500 ARG A 730 -0.53 84.54 REMARK 500 ASP A 767 -108.65 44.97 REMARK 500 TYR A 788 -51.11 -125.26 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 ARG A 653 0.14 SIDE CHAIN REMARK 500 ARG A 730 0.09 SIDE CHAIN 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 A1167 DISTANCE = 19.03 ANGSTROMS DBREF 9S2Y A 382 476 UNP Q14694 UBP10_HUMAN 382 476 DBREF 9S2Y A 482 547 UNP Q14694 UBP10_HUMAN 495 547 DBREF 9S2Y A 595 798 UNP Q14694 UBP10_HUMAN 595 798 SEQADV 9S2Y SER A 380 UNP Q14694 EXPRESSION TAG SEQADV 9S2Y MET A 381 UNP Q14694 EXPRESSION TAG SEQADV 9S2Y GLY A 477 UNP Q14694 LINKER SEQADV 9S2Y SER A 478 UNP Q14694 LINKER SEQADV 9S2Y GLY A 479 UNP Q14694 LINKER SEQADV 9S2Y SER A 480 UNP Q14694 LINKER SEQADV 9S2Y GLY A 481 UNP Q14694 LINKER SEQADV 9S2Y GLY A 548 UNP Q14694 LINKER SEQADV 9S2Y SER A 588 UNP Q14694 LINKER SEQADV 9S2Y GLY A 589 UNP Q14694 LINKER SEQADV 9S2Y SER A 590 UNP Q14694 LINKER SEQADV 9S2Y GLY A 591 UNP Q14694 LINKER SEQADV 9S2Y SER A 592 UNP Q14694 LINKER SEQADV 9S2Y GLY A 593 UNP Q14694 LINKER SEQADV 9S2Y SER A 594 UNP Q14694 LINKER SEQRES 1 A 367 SER MET GLU GLY LEU VAL PRO VAL SER GLU ASP PRO VAL SEQRES 2 A 367 ALA ILE LYS ILE ALA GLU LEU LEU GLU ASN VAL THR LEU SEQRES 3 A 367 ILE HIS LYS PRO VAL SER LEU GLN PRO ARG GLY LEU ILE SEQRES 4 A 367 ASN LYS GLY ASN TRP CYS TYR ILE ASN ALA THR LEU GLN SEQRES 5 A 367 ALA LEU VAL ALA CYS PRO PRO MET TYR HIS LEU MET LYS SEQRES 6 A 367 PHE ILE PRO LEU TYR SER LYS VAL GLN ARG PRO CYS THR SEQRES 7 A 367 SER THR PRO MET ILE ASP SER PHE VAL ARG LEU MET ASN SEQRES 8 A 367 GLU PHE THR ASN MET PRO GLY SER GLY SER GLY PRO GLY SEQRES 9 A 367 ALA ALA PHE GLU PRO THR TYR ILE TYR ARG LEU LEU THR SEQRES 10 A 367 VAL ASN LYS SER SER LEU SER GLU LYS GLY ARG GLN GLU SEQRES 11 A 367 ASP ALA GLU GLU TYR LEU GLY PHE ILE LEU ASN GLY LEU SEQRES 12 A 367 HIS GLU GLU MET LEU ASN LEU LYS LYS LEU LEU SER GLY SEQRES 13 A 367 SER GLY SER GLY SER GLY SER ALA ASP PHE VAL GLN THR SEQRES 14 A 367 PRO ILE THR GLY ILE PHE GLY GLY HIS ILE ARG SER VAL SEQRES 15 A 367 VAL TYR GLN GLN SER SER LYS GLU SER ALA THR LEU GLN SEQRES 16 A 367 PRO PHE PHE THR LEU GLN LEU ASP ILE GLN SER ASP LYS SEQRES 17 A 367 ILE ARG THR VAL GLN ASP ALA LEU GLU SER LEU VAL ALA SEQRES 18 A 367 ARG GLU SER VAL GLN GLY TYR THR THR LYS THR LYS GLN SEQRES 19 A 367 GLU VAL GLU ILE SER ARG ARG VAL THR LEU GLU LYS LEU SEQRES 20 A 367 PRO PRO VAL LEU VAL LEU HIS LEU LYS ARG PHE VAL TYR SEQRES 21 A 367 GLU LYS THR GLY GLY CYS GLN LYS LEU ILE LYS ASN ILE SEQRES 22 A 367 GLU TYR PRO VAL ASP LEU GLU ILE SER LYS GLU LEU LEU SEQRES 23 A 367 SER PRO GLY VAL LYS ASN LYS ASN PHE LYS CYS HIS ARG SEQRES 24 A 367 THR TYR ARG LEU PHE ALA VAL VAL TYR HIS HIS GLY ASN SEQRES 25 A 367 SER ALA THR GLY GLY HIS TYR THR THR ASP VAL PHE GLN SEQRES 26 A 367 ILE GLY LEU ASN GLY TRP LEU ARG ILE ASP ASP GLN THR SEQRES 27 A 367 VAL LYS VAL ILE ASN GLN TYR GLN VAL VAL LYS PRO THR SEQRES 28 A 367 ALA GLU ARG THR ALA TYR LEU LEU TYR TYR ARG ARG VAL SEQRES 29 A 367 ASP LEU LEU HET EDO A 801 10 HET EDO A 802 10 HET EDO A 803 10 HET EDO A 804 10 HET EDO A 805 10 HET EDO A 806 10 HET EDO A 807 10 HET SO4 A 808 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 7(C2 H6 O2) FORMUL 9 SO4 O4 S 2- FORMUL 10 HOH *267(H2 O) HELIX 1 AA1 VAL A 392 GLU A 401 1 10 HELIX 2 AA2 TRP A 423 ALA A 435 1 13 HELIX 3 AA3 CYS A 436 PHE A 445 1 10 HELIX 4 AA4 THR A 459 ASN A 470 1 12 HELIX 5 AA5 PRO A 488 VAL A 497 1 10 HELIX 6 AA6 ASP A 523 GLY A 548 1 26 HELIX 7 AA7 THR A 600 GLY A 607 1 8 HELIX 8 AA8 THR A 642 VAL A 651 1 10 HELIX 9 AA9 SER A 713 LEU A 717 5 5 HELIX 10 AB1 ASN A 774 VAL A 779 1 6 SHEET 1 AA1 2 ARG A 415 LEU A 417 0 SHEET 2 AA1 2 GLY A 483 PHE A 486 1 O PHE A 486 N GLY A 416 SHEET 1 AA2 4 SER A 619 PHE A 628 0 SHEET 2 AA2 4 GLY A 608 GLN A 616 -1 N VAL A 614 O GLU A 621 SHEET 3 AA2 4 GLU A 666 LYS A 677 -1 O THR A 674 N ARG A 611 SHEET 4 AA2 4 GLU A 654 TYR A 659 -1 N VAL A 656 O ILE A 669 SHEET 1 AA3 5 LEU A 631 LEU A 633 0 SHEET 2 AA3 5 VAL A 681 LEU A 686 1 O HIS A 685 N LEU A 633 SHEET 3 AA3 5 THR A 786 ARG A 794 -1 O LEU A 790 N LEU A 684 SHEET 4 AA3 5 THR A 731 HIS A 741 -1 N ALA A 736 O TYR A 791 SHEET 5 AA3 5 ASP A 709 GLU A 711 -1 N LEU A 710 O TYR A 732 SHEET 1 AA4 7 LEU A 631 LEU A 633 0 SHEET 2 AA4 7 VAL A 681 LEU A 686 1 O HIS A 685 N LEU A 633 SHEET 3 AA4 7 THR A 786 ARG A 794 -1 O LEU A 790 N LEU A 684 SHEET 4 AA4 7 THR A 731 HIS A 741 -1 N ALA A 736 O TYR A 791 SHEET 5 AA4 7 HIS A 749 GLN A 756 -1 O HIS A 749 N HIS A 741 SHEET 6 AA4 7 GLY A 761 ASP A 766 -1 O ILE A 765 N THR A 752 SHEET 7 AA4 7 THR A 769 ILE A 773 -1 O LYS A 771 N ARG A 764 SHEET 1 AA5 2 PHE A 689 VAL A 690 0 SHEET 2 AA5 2 GLN A 698 LYS A 699 -1 O GLN A 698 N VAL A 690 CRYST1 107.790 107.790 131.150 90.00 90.00 120.00 P 63 2 2 12 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 0.009277 0.005356 0.000000 0.00000 SCALE2 0.000000 0.010713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007625 0.00000 CONECT 5411 5412 5413 5415 5416 CONECT 5412 5411 5417 CONECT 5413 5411 5414 5418 5419 CONECT 5414 5413 5420 CONECT 5415 5411 CONECT 5416 5411 CONECT 5417 5412 CONECT 5418 5413 CONECT 5419 5413 CONECT 5420 5414 CONECT 5421 5422 5423 5425 5426 CONECT 5422 5421 5427 CONECT 5423 5421 5424 5428 5429 CONECT 5424 5423 5430 CONECT 5425 5421 CONECT 5426 5421 CONECT 5427 5422 CONECT 5428 5423 CONECT 5429 5423 CONECT 5430 5424 CONECT 5431 5432 5433 5435 5436 CONECT 5432 5431 5437 CONECT 5433 5431 5434 5438 5439 CONECT 5434 5433 5440 CONECT 5435 5431 CONECT 5436 5431 CONECT 5437 5432 CONECT 5438 5433 CONECT 5439 5433 CONECT 5440 5434 CONECT 5441 5442 5443 5445 5446 CONECT 5442 5441 5447 CONECT 5443 5441 5444 5448 5449 CONECT 5444 5443 5450 CONECT 5445 5441 CONECT 5446 5441 CONECT 5447 5442 CONECT 5448 5443 CONECT 5449 5443 CONECT 5450 5444 CONECT 5451 5452 5453 5455 5456 CONECT 5452 5451 5457 CONECT 5453 5451 5454 5458 5459 CONECT 5454 5453 5460 CONECT 5455 5451 CONECT 5456 5451 CONECT 5457 5452 CONECT 5458 5453 CONECT 5459 5453 CONECT 5460 5454 CONECT 5461 5462 5463 5465 5466 CONECT 5462 5461 5467 CONECT 5463 5461 5464 5468 5469 CONECT 5464 5463 5470 CONECT 5465 5461 CONECT 5466 5461 CONECT 5467 5462 CONECT 5468 5463 CONECT 5469 5463 CONECT 5470 5464 CONECT 5471 5472 5473 5475 5476 CONECT 5472 5471 5477 CONECT 5473 5471 5474 5478 5479 CONECT 5474 5473 5480 CONECT 5475 5471 CONECT 5476 5471 CONECT 5477 5472 CONECT 5478 5473 CONECT 5479 5473 CONECT 5480 5474 CONECT 5481 5482 5483 5484 5485 CONECT 5482 5481 CONECT 5483 5481 CONECT 5484 5481 CONECT 5485 5481 MASTER 424 0 8 10 20 0 0 6 2973 1 75 29 END