HEADER HYDROLASE 27-JUL-23 8Q00 TITLE TSSM-UB-PA COMPLEX - A USP-LIKE DUB FROM B. PSEUDOMALLEI (193-430) TITLE 2 REACTED WITH UB-PA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TSSM; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: POLYUBIQUITIN-B; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA PSEUDOMALLEI; SOURCE 3 ORGANISM_TAXID: 28450; SOURCE 4 GENE: TSSM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: POPIN-K; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: UBB; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PTXB1 KEYWDS DEUBIQUITINASE, PAPAIN-FOLD, USP, HYDROLASE, UB-PA EXPDTA X-RAY DIFFRACTION AUTHOR M.UTHOFF,T.HERMANNS,K.HOFMANN,U.BAUMANN REVDAT 2 17-JAN-24 8Q00 1 JRNL REVDAT 1 13-DEC-23 8Q00 0 JRNL AUTH T.HERMANNS,M.UTHOFF,U.BAUMANN,K.HOFMANN JRNL TITL THE STRUCTURAL BASIS FOR DEUBIQUITINATION BY THE FINGERLESS JRNL TITL 2 USP-TYPE EFFECTOR TSSM. JRNL REF LIFE SCI ALLIANCE V. 7 2024 JRNL REFN ESSN 2575-1077 JRNL PMID 38170641 JRNL DOI 10.26508/LSA.202302422 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 91.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 130701 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9554 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5704 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 724 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -0.94000 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): 0.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.728 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6015 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5722 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8246 ; 1.760 ; 1.664 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13218 ; 0.579 ; 1.571 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 794 ; 6.267 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 50 ;10.686 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 946 ;13.039 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 951 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7226 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1318 ; 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): 3038 ; 2.789 ; 2.871 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3037 ; 2.789 ; 2.871 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3803 ; 3.787 ; 5.151 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3804 ; 3.787 ; 5.151 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2977 ; 4.536 ; 3.350 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2978 ; 4.536 ; 3.350 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4419 ; 6.612 ; 5.903 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6800 ; 8.062 ;34.950 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6576 ; 8.013 ;31.640 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 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 REMARK 4 REMARK 4 8Q00 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292132245. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DEFAULT REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS BUILT=20210323 REMARK 200 DATA SCALING SOFTWARE : XSCALE BUILT=20210323 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 132701 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 103.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.42 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.33500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.190 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CITRATE DIBASIC AND 22 REMARK 280 % W/V PEG 3350; 1:2, 1:1, 2:1 PROTEIN:RESERVOIR RATION; REMARK 280 CRYOPROTECTED WITH RESERVOIR + 25% ETHYLENE GLYCOL, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 -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 95.76000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.87500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.87500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.88000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.87500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.87500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 143.64000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.87500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.87500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.88000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.87500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.87500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 143.64000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 95.76000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 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 677 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 858 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 PRO A 202 REMARK 465 THR A 203 REMARK 465 HIS A 204 REMARK 465 ALA A 205 REMARK 465 ALA A 206 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 623 O HOH A 744 1.95 REMARK 500 O HOH C 760 O HOH C 825 2.00 REMARK 500 O HOH C 743 O HOH C 802 2.06 REMARK 500 O HOH A 797 O HOH A 849 2.08 REMARK 500 O HOH A 839 O HOH A 848 2.13 REMARK 500 O HOH A 922 O HOH A 924 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 O HOH A 848 O HOH B 144 4454 1.94 REMARK 500 O HOH A 867 O HOH A 867 7555 1.98 REMARK 500 O HOH A 660 O HOH D 130 6454 2.12 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 B 42 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 42 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG C 490 NE - CZ - NH1 ANGL. DEV. = -3.4 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 VAL A 225 99.07 -52.93 REMARK 500 HIS A 227 58.53 -141.13 REMARK 500 HIS A 227 76.82 73.77 REMARK 500 SER A 417 -151.41 -103.79 REMARK 500 ASP A 458 -112.82 53.44 REMARK 500 PRO C 226 176.19 -57.31 REMARK 500 ARG C 249 18.88 -143.82 REMARK 500 SER C 417 -142.55 -101.08 REMARK 500 ASP C 458 -115.04 55.77 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 337 0.09 SIDE CHAIN REMARK 500 ARG A 363 0.09 SIDE CHAIN REMARK 500 ARG B 74 0.14 SIDE CHAIN REMARK 500 ARG D 74 0.19 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 363 O REMARK 620 2 THR A 365 O 102.5 REMARK 620 3 VAL A 368 O 97.5 94.1 REMARK 620 4 ASP A 370 OD1 80.7 145.0 120.3 REMARK 620 5 HOH A 846 O 164.2 91.5 88.7 83.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG C 363 O REMARK 620 2 THR C 365 O 97.5 REMARK 620 3 VAL C 368 O 97.9 92.8 REMARK 620 4 ASP C 370 OD1 83.6 145.5 121.4 REMARK 620 5 HOH C 608 O 92.6 85.3 169.5 60.2 REMARK 620 6 HOH C 803 O 170.8 89.5 87.7 87.3 82.0 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8PZ3 RELATED DB: PDB REMARK 900 DIMER OF "APO"-TSSM WITH B1 B-STRAND SWAP IN IG-LIKE DOMAIN DBREF 8Q00 A 192 490 UNP D7SFB8 D7SFB8_BURPE 192 490 DBREF 8Q00 B 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 8Q00 C 192 490 UNP D7SFB8 D7SFB8_BURPE 192 490 DBREF 8Q00 D 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 8Q00 GLY A 191 UNP D7SFB8 EXPRESSION TAG SEQADV 8Q00 AYE B 76 UNP P0CG47 GLY 76 ENGINEERED MUTATION SEQADV 8Q00 GLY C 191 UNP D7SFB8 EXPRESSION TAG SEQADV 8Q00 AYE D 76 UNP P0CG47 GLY 76 ENGINEERED MUTATION SEQRES 1 A 300 GLY PRO PRO ALA VAL VAL ALA THR ARG VAL PRO PRO THR SEQRES 2 A 300 HIS ALA ALA LEU ARG ARG PRO THR ILE GLU LEU GLU PHE SEQRES 3 A 300 ASP ARG ALA ILE GLU PRO GLY SER VAL PRO HIS ILE VAL SEQRES 4 A 300 LEU ARG ALA ASP ASP GLY THR SER VAL ALA VAL GLY PRO SEQRES 5 A 300 LEU SER TRP LEU SER ASP ARG ARG ILE ALA PHE ALA PRO SEQRES 6 A 300 ARG LYS PRO LEU LYS SER ASN SER ARG TYR GLU ILE MET SEQRES 7 A 300 VAL PRO ALA GLY ILE ARG SER THR THR GLY GLU ARG SER SEQRES 8 A 300 THR HIS PRO LEU THR SER SER PHE ASP THR ALA PRO VAL SEQRES 9 A 300 THR PRO PRO ARG GLY LEU PRO ASN LEU ASP GLY ALA SER SEQRES 10 A 300 CYS PHE ILE ASN THR ALA LEU GLN LEU ALA VAL HIS SER SEQRES 11 A 300 SER ALA LEU ASP ASP ILE LEU SER ASN GLU ALA VAL PRO SEQRES 12 A 300 PRO ALA VAL ARG THR LEU LEU GLU ASP TYR ASP ALA ALA SEQRES 13 A 300 SER ALA ASP ALA LEU ASP ALA GLN LEU ALA ALA ALA VAL SEQRES 14 A 300 ALA ALA LEU ARG ALA THR PRO GLU VAL PRO ASP SER GLY SEQRES 15 A 300 PRO GLY GLN THR LEU GLU VAL MET GLN ALA LEU ARG MET SEQRES 16 A 300 PRO LEU TYR ASP THR SER SER ALA ASN ASN ALA LYS ASN SEQRES 17 A 300 ASN ALA ASP ALA ILE ARG HIS ALA PRO PRO ASN THR LYS SEQRES 18 A 300 ALA PHE PHE LEU ASN SER TYR PRO PRO LEU SER TYR ALA SEQRES 19 A 300 ASP LEU PRO ASN HIS ASP ARG LEU VAL ALA PHE ASP TYR SEQRES 20 A 300 SER THR GLY GLY HIS TYR VAL ALA TYR VAL LYS ARG ASP SEQRES 21 A 300 GLY ILE TRP TYR ARG ILE ASP ASP ALA GLN VAL SER ALA SEQRES 22 A 300 VAL ASN GLU GLN ASP LEU LEU ALA LEU PRO ALA PHE ASN SEQRES 23 A 300 PRO ALA ASN GLY SER VAL SER ILE GLU ILE ALA ILE TYR SEQRES 24 A 300 ARG SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY AYE SEQRES 1 C 300 GLY PRO PRO ALA VAL VAL ALA THR ARG VAL PRO PRO THR SEQRES 2 C 300 HIS ALA ALA LEU ARG ARG PRO THR ILE GLU LEU GLU PHE SEQRES 3 C 300 ASP ARG ALA ILE GLU PRO GLY SER VAL PRO HIS ILE VAL SEQRES 4 C 300 LEU ARG ALA ASP ASP GLY THR SER VAL ALA VAL GLY PRO SEQRES 5 C 300 LEU SER TRP LEU SER ASP ARG ARG ILE ALA PHE ALA PRO SEQRES 6 C 300 ARG LYS PRO LEU LYS SER ASN SER ARG TYR GLU ILE MET SEQRES 7 C 300 VAL PRO ALA GLY ILE ARG SER THR THR GLY GLU ARG SER SEQRES 8 C 300 THR HIS PRO LEU THR SER SER PHE ASP THR ALA PRO VAL SEQRES 9 C 300 THR PRO PRO ARG GLY LEU PRO ASN LEU ASP GLY ALA SER SEQRES 10 C 300 CYS PHE ILE ASN THR ALA LEU GLN LEU ALA VAL HIS SER SEQRES 11 C 300 SER ALA LEU ASP ASP ILE LEU SER ASN GLU ALA VAL PRO SEQRES 12 C 300 PRO ALA VAL ARG THR LEU LEU GLU ASP TYR ASP ALA ALA SEQRES 13 C 300 SER ALA ASP ALA LEU ASP ALA GLN LEU ALA ALA ALA VAL SEQRES 14 C 300 ALA ALA LEU ARG ALA THR PRO GLU VAL PRO ASP SER GLY SEQRES 15 C 300 PRO GLY GLN THR LEU GLU VAL MET GLN ALA LEU ARG MET SEQRES 16 C 300 PRO LEU TYR ASP THR SER SER ALA ASN ASN ALA LYS ASN SEQRES 17 C 300 ASN ALA ASP ALA ILE ARG HIS ALA PRO PRO ASN THR LYS SEQRES 18 C 300 ALA PHE PHE LEU ASN SER TYR PRO PRO LEU SER TYR ALA SEQRES 19 C 300 ASP LEU PRO ASN HIS ASP ARG LEU VAL ALA PHE ASP TYR SEQRES 20 C 300 SER THR GLY GLY HIS TYR VAL ALA TYR VAL LYS ARG ASP SEQRES 21 C 300 GLY ILE TRP TYR ARG ILE ASP ASP ALA GLN VAL SER ALA SEQRES 22 C 300 VAL ASN GLU GLN ASP LEU LEU ALA LEU PRO ALA PHE ASN SEQRES 23 C 300 PRO ALA ASN GLY SER VAL SER ILE GLU ILE ALA ILE TYR SEQRES 24 C 300 ARG SEQRES 1 D 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 D 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 D 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 D 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 D 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 D 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY AYE HET AYE B 76 4 HET AYE D 76 4 HET FLC A 501 13 HET EDO A 502 4 HET NA A 503 1 HET EDO C 501 4 HET NA C 502 1 HETNAM AYE PROP-2-EN-1-AMINE HETNAM FLC CITRATE ANION HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETSYN AYE ALLYLAMINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 AYE 2(C3 H7 N) FORMUL 5 FLC C6 H5 O7 3- FORMUL 6 EDO 2(C2 H6 O2) FORMUL 7 NA 2(NA 1+) FORMUL 10 HOH *724(H2 O) HELIX 1 AA1 GLU A 221 VAL A 225 5 5 HELIX 2 AA2 SER A 307 HIS A 319 1 13 HELIX 3 AA3 ALA A 322 SER A 328 1 7 HELIX 4 AA4 PRO A 333 ASP A 342 1 10 HELIX 5 AA5 SER A 347 ALA A 364 1 18 HELIX 6 AA6 GLN A 375 LEU A 383 1 9 HELIX 7 AA7 SER A 391 ALA A 393 5 3 HELIX 8 AA8 ASN A 398 HIS A 405 1 8 HELIX 9 AA9 SER A 422 LEU A 426 5 5 HELIX 10 AB1 ASN A 465 ALA A 471 1 7 HELIX 11 AB2 THR B 22 GLY B 35 1 14 HELIX 12 AB3 PRO B 37 ASP B 39 5 3 HELIX 13 AB4 LEU B 56 ASN B 60 5 5 HELIX 14 AB5 GLU C 221 VAL C 225 5 5 HELIX 15 AB6 SER C 307 HIS C 319 1 13 HELIX 16 AB7 ALA C 322 SER C 328 1 7 HELIX 17 AB8 PRO C 333 ASP C 342 1 10 HELIX 18 AB9 SER C 347 ALA C 364 1 18 HELIX 19 AC1 GLN C 375 LEU C 383 1 9 HELIX 20 AC2 SER C 391 ALA C 393 5 3 HELIX 21 AC3 ASN C 398 HIS C 405 1 8 HELIX 22 AC4 ASN C 428 ASP C 430 5 3 HELIX 23 AC5 ASN C 465 ALA C 471 1 7 HELIX 24 AC6 THR D 22 GLY D 35 1 14 HELIX 25 AC7 PRO D 37 ASP D 39 5 3 HELIX 26 AC8 LEU D 56 ASN D 60 5 5 SHEET 1 AA1 4 VAL A 195 ARG A 199 0 SHEET 2 AA1 4 ILE A 212 PHE A 216 -1 O GLU A 213 N ARG A 199 SHEET 3 AA1 4 ARG A 250 PHE A 253 -1 O PHE A 253 N ILE A 212 SHEET 4 AA1 4 SER A 244 SER A 247 -1 N SER A 244 O ALA A 252 SHEET 1 AA2 4 SER A 237 ALA A 239 0 SHEET 2 AA2 4 VAL A 229 ALA A 232 -1 N LEU A 230 O VAL A 238 SHEET 3 AA2 4 ARG A 264 VAL A 269 -1 O MET A 268 N VAL A 229 SHEET 4 AA2 4 LEU A 285 ASP A 290 -1 O LEU A 285 N VAL A 269 SHEET 1 AA3 7 TYR A 388 ASP A 389 0 SHEET 2 AA3 7 ALA A 412 PHE A 414 1 O PHE A 414 N TYR A 388 SHEET 3 AA3 7 ILE A 486 TYR A 489 -1 O ALA A 487 N PHE A 413 SHEET 4 AA3 7 LEU A 432 SER A 438 -1 N ALA A 434 O ILE A 488 SHEET 5 AA3 7 TYR A 443 ARG A 449 -1 O TYR A 446 N PHE A 435 SHEET 6 AA3 7 ILE A 452 ASP A 457 -1 O ILE A 456 N ALA A 445 SHEET 7 AA3 7 GLN A 460 VAL A 464 -1 O VAL A 464 N TRP A 453 SHEET 1 AA4 2 PHE A 475 ASN A 476 0 SHEET 2 AA4 2 SER A 481 VAL A 482 -1 O SER A 481 N ASN A 476 SHEET 1 AA5 5 THR B 12 GLU B 16 0 SHEET 2 AA5 5 GLN B 2 THR B 7 -1 N VAL B 5 O ILE B 13 SHEET 3 AA5 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 AA5 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 AA5 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 AA6 4 VAL C 195 ARG C 199 0 SHEET 2 AA6 4 ILE C 212 PHE C 216 -1 O GLU C 213 N ARG C 199 SHEET 3 AA6 4 ARG C 250 PHE C 253 -1 O PHE C 253 N ILE C 212 SHEET 4 AA6 4 SER C 244 SER C 247 -1 N SER C 244 O ALA C 252 SHEET 1 AA7 4 SER C 237 ALA C 239 0 SHEET 2 AA7 4 VAL C 229 ALA C 232 -1 N LEU C 230 O VAL C 238 SHEET 3 AA7 4 ARG C 264 VAL C 269 -1 O MET C 268 N VAL C 229 SHEET 4 AA7 4 LEU C 285 ASP C 290 -1 O LEU C 285 N VAL C 269 SHEET 1 AA8 7 TYR C 388 ASP C 389 0 SHEET 2 AA8 7 ALA C 412 PHE C 414 1 O ALA C 412 N TYR C 388 SHEET 3 AA8 7 ILE C 486 TYR C 489 -1 O ALA C 487 N PHE C 413 SHEET 4 AA8 7 LEU C 432 SER C 438 -1 N ALA C 434 O ILE C 488 SHEET 5 AA8 7 TYR C 443 ARG C 449 -1 O TYR C 446 N PHE C 435 SHEET 6 AA8 7 ILE C 452 ASP C 457 -1 O ILE C 456 N ALA C 445 SHEET 7 AA8 7 GLN C 460 VAL C 464 -1 O SER C 462 N ARG C 455 SHEET 1 AA9 5 THR D 12 GLU D 16 0 SHEET 2 AA9 5 GLN D 2 THR D 7 -1 N VAL D 5 O ILE D 13 SHEET 3 AA9 5 THR D 66 LEU D 71 1 O LEU D 67 N PHE D 4 SHEET 4 AA9 5 GLN D 41 PHE D 45 -1 N ARG D 42 O VAL D 70 SHEET 5 AA9 5 LYS D 48 GLN D 49 -1 O LYS D 48 N PHE D 45 LINK SG CYS A 308 C2 AYE B 76 1555 1555 1.81 LINK C GLY B 75 N1 AYE B 76 1555 1555 1.39 LINK SG CYS C 308 C2 AYE D 76 1555 1555 1.81 LINK C GLY D 75 N1 AYE D 76 1555 1555 1.44 LINK O ARG A 363 NA NA A 503 1555 1555 2.37 LINK O THR A 365 NA NA A 503 1555 1555 2.33 LINK O VAL A 368 NA NA A 503 1555 1555 2.31 LINK OD1 ASP A 370 NA NA A 503 1555 1555 2.37 LINK NA NA A 503 O HOH A 846 1555 1555 2.36 LINK O ARG C 363 NA NA C 502 1555 1555 2.38 LINK O THR C 365 NA NA C 502 1555 1555 2.32 LINK O VAL C 368 NA NA C 502 1555 1555 2.33 LINK OD1 ASP C 370 NA NA C 502 1555 1555 2.38 LINK NA NA C 502 O HOH C 608 1555 1555 2.56 LINK NA NA C 502 O HOH C 803 1555 1555 2.32 CISPEP 1 TYR A 418 PRO A 419 0 1.48 CISPEP 2 TYR C 418 PRO C 419 0 -10.51 CRYST1 103.750 103.750 191.520 90.00 90.00 90.00 P 41 21 2 16 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 0.009639 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009639 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005221 0.00000