PDB Short entry for 5QIX HEADER HYDROLASE/HYDROLASE INHIBITOR 10-AUG-18 5QIX TITLE COVALENT FRAGMENT GROUP DEPOSITION -- CRYSTAL STRUCTURE OF OUTB2 IN TITLE 2 COMPLEX WITH PCM-0103007 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN THIOESTERASE OTUB2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME OTUB2,OTU DOMAIN-CONTAINING COMPND 5 UBIQUITIN ALDEHYDE-BINDING PROTEIN 2,OTUBAIN-2,UBIQUITIN-SPECIFIC- COMPND 6 PROCESSING PROTEASE OTUB2; COMPND 7 EC: 3.4.19.12; COMPND 8 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: OTUB2, C14ORF137, OTB2, OTU2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, XCHEMEXPLORER, PROTEASE KEYWDS 2 OTUB2, DEUBIQUITINATING ENZYME OTUB2, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.SETHI,A.DOUANGAMATH,E.RESNICK,A.R.BRADLEY,P.COLLINS,J.BRANDAO-NETO, AUTHOR 2 R.TALON,T.KROJER,C.BOUNTRA,C.H.ARROWSMITH,A.EDWARDS,N.LONDON,F.VON AUTHOR 3 DELFT REVDAT 1 18-DEC-19 5QIX 0 JRNL AUTH R.SETHI,A.DOUANGAMATH,E.RESNICK,A.R.BRADLEY,P.COLLINS, JRNL AUTH 2 J.BRANDAO-NETO,R.TALON,T.KROJER,C.BOUNTRA,C.H.ARROWSMITH, JRNL AUTH 3 A.EDWARDS,N.LONDON,F.VON DELFT JRNL TITL COVALENT FRAGMENT GROUP DEPOSITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 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) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 46522 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) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2189 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) : 1.39 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3309 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1820 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.40000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.075 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1929 ; 0.020 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 1734 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2592 ; 2.084 ; 1.662 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4054 ; 1.113 ; 1.667 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 237 ;12.456 ; 5.148 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;32.362 ;21.560 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 332 ;12.544 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;19.625 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 249 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2233 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 392 ; 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): 904 ; 2.206 ; 1.105 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 905 ; 2.205 ; 1.105 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1133 ; 2.819 ; 1.666 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 3663 ;12.475 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 179 ;32.912 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3701 ;18.967 ; 5.000 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 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 RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5QIX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1001402006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48731 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 29.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.62100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 1TFF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG4K, 0.1M HEPES PH 7.0, 8% 2 REMARK 280 -PROPANOL, 5 MM DTT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.16700 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ASP A 155 REMARK 465 GLU A 156 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 ARG A 49 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU A 157 CG CD OE1 OE2 REMARK 470 MET A 158 CG SD CE REMARK 470 ASP A 159 CG OD1 OD2 REMARK 470 GLU A 210 CG CD OE1 OE2 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 OG SER A 116 O2 EDO A 307 1.47 REMARK 500 O1 EDO A 307 O HOH A 401 1.96 REMARK 500 O HOH A 486 O HOH A 603 2.07 REMARK 500 OE2 GLU A 107 O HOH A 402 2.10 REMARK 500 CD ARG A 38 O HOH A 430 2.14 REMARK 500 O HOH A 402 O HOH A 411 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CB MET A 158 O HOH A 549 1455 1.64 REMARK 500 O HOH A 412 O HOH A 437 1554 2.15 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 GLU A 11 CD GLU A 11 OE1 0.077 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 ARG A 30 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 38 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 77 NE - CZ - NH2 ANGL. DEV. = -4.3 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 ARG A 49 -8.42 92.07 REMARK 500 VAL A 168 -57.17 -125.30 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 20 0.09 SIDE CHAIN REMARK 500 ARG A 29 0.25 SIDE CHAIN REMARK 500 ARG A 38 0.09 SIDE CHAIN REMARK 500 ARG A 151 0.21 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 A 655 DISTANCE = 7.15 ANGSTROMS REMARK 525 HOH A 656 DISTANCE = 7.22 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue J5V A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 308 DBREF 5QIX A 6 230 UNP Q96DC9 OTUB2_HUMAN 6 230 SEQADV 5QIX ARG A 49 UNP Q96DC9 GLY 49 CONFLICT SEQRES 1 A 225 PHE ASN LEU ILE SER GLU LYS CYS ASP ILE LEU SER ILE SEQRES 2 A 225 LEU ARG ASP HIS PRO GLU ASN ARG ILE TYR ARG ARG LYS SEQRES 3 A 225 ILE GLU GLU LEU SER LYS ARG PHE THR ALA ILE ARG LYS SEQRES 4 A 225 THR LYS GLY ASP ARG ASN CYS PHE TYR ARG ALA LEU GLY SEQRES 5 A 225 TYR SER TYR LEU GLU SER LEU LEU GLY LYS SER ARG GLU SEQRES 6 A 225 ILE PHE LYS PHE LYS GLU ARG VAL LEU GLN THR PRO ASN SEQRES 7 A 225 ASP LEU LEU ALA ALA GLY PHE GLU GLU HIS LYS PHE ARG SEQRES 8 A 225 ASN PHE PHE ASN ALA PHE TYR SER VAL VAL GLU LEU VAL SEQRES 9 A 225 GLU LYS ASP GLY SER VAL SER SER LEU LEU LYS VAL PHE SEQRES 10 A 225 ASN ASP GLN SER ALA SER ASP HIS ILE VAL GLN PHE LEU SEQRES 11 A 225 ARG LEU LEU THR SER ALA PHE ILE ARG ASN ARG ALA ASP SEQRES 12 A 225 PHE PHE ARG HIS PHE ILE ASP GLU GLU MET ASP ILE LYS SEQRES 13 A 225 ASP PHE CYS THR HIS GLU VAL GLU PRO MET ALA THR GLU SEQRES 14 A 225 CYS ASP HIS ILE GLN ILE THR ALA LEU SER GLN ALA LEU SEQRES 15 A 225 SER ILE ALA LEU GLN VAL GLU TYR VAL ASP GLU MET ASP SEQRES 16 A 225 THR ALA LEU ASN HIS HIS VAL PHE PRO GLU ALA ALA THR SEQRES 17 A 225 PRO SER VAL TYR LEU LEU TYR LYS THR SER HIS TYR ASN SEQRES 18 A 225 ILE LEU TYR ALA HET J5V A 301 13 HET EDO A 302 4 HET EDO A 303 4 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET EDO A 308 4 HET UNL A 309 1 HET UNL A 310 1 HET UNL A 311 1 HETNAM J5V N-(3-PHENYLPROP-2-YN-1-YL)ACETAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM UNL UNKNOWN LIGAND HETSYN EDO ETHYLENE GLYCOL FORMUL 2 J5V C11 H11 N O FORMUL 3 EDO 7(C2 H6 O2) FORMUL 13 HOH *256(H2 O) HELIX 1 AA1 LEU A 16 HIS A 22 5 7 HELIX 2 AA2 ASN A 25 SER A 36 1 12 HELIX 3 AA3 ASN A 50 LEU A 65 1 16 HELIX 4 AA4 LYS A 67 ALA A 88 1 22 HELIX 5 AA5 GLU A 91 ASP A 112 1 22 HELIX 6 AA6 SER A 114 ASP A 124 1 11 HELIX 7 AA7 ASP A 124 ARG A 146 1 23 HELIX 8 AA8 ARG A 146 ARG A 151 1 6 HELIX 9 AA9 ASP A 159 VAL A 168 1 10 HELIX 10 AB1 ASP A 176 SER A 188 1 13 SHEET 1 AA1 6 CYS A 13 ASP A 14 0 SHEET 2 AA1 6 ALA A 41 ARG A 43 -1 O ILE A 42 N CYS A 13 SHEET 3 AA1 6 HIS A 224 TYR A 229 -1 O ILE A 227 N ARG A 43 SHEET 4 AA1 6 VAL A 216 LYS A 221 -1 N TYR A 217 O LEU A 228 SHEET 5 AA1 6 LEU A 191 TYR A 195 1 N GLU A 194 O LEU A 218 SHEET 6 AA1 6 ASN A 204 PHE A 208 -1 O PHE A 208 N LEU A 191 LINK SG CYS A 51 C J5V A 301 1555 1555 1.67 CISPEP 1 PHE A 208 PRO A 209 0 -4.86 SITE 1 AC1 9 GLY A 47 ASP A 48 ARG A 49 ASN A 50 SITE 2 AC1 9 CYS A 51 GLU A 174 THR A 222 SER A 223 SITE 3 AC1 9 HIS A 224 SITE 1 AC2 4 PHE A 6 ASN A 7 SER A 10 LYS A 44 SITE 1 AC3 7 ARG A 77 PHE A 142 GLN A 185 ALA A 186 SITE 2 AC3 7 SER A 188 HOH A 435 HOH A 489 SITE 1 AC4 1 HIS A 93 SITE 1 AC5 2 ASN A 100 HOH A 416 SITE 1 AC6 5 ARG A 29 ASN A 145 HOH A 419 HOH A 496 SITE 2 AC6 5 HOH A 577 SITE 1 AC7 7 SER A 114 SER A 116 SER A 117 LYS A 120 SITE 2 AC7 7 ASP A 159 HOH A 401 HOH A 597 SITE 1 AC8 8 LEU A 16 LEU A 19 ASN A 83 ALA A 87 SITE 2 AC8 8 HOH A 406 HOH A 438 HOH A 519 HOH A 571 CRYST1 47.554 58.334 50.333 90.00 116.38 90.00 P 1 21 1 2 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 0.021029 0.000000 0.010429 0.00000 SCALE2 0.000000 0.017143 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022177 0.00000