HEADER SIGNALING PROTEIN 26-MAY-17 5O44 TITLE CRYSTAL STRUCTURE OF UNBRANCHED MIXED TRI-UBIQUITIN CHAIN CONTAINING TITLE 2 K48 AND K63 LINKAGES. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A, E; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: POLYUBIQUITIN-B; COMPND 8 CHAIN: C, B; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: POLYUBIQUITIN-B; COMPND 13 CHAIN: D, F; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUSCA DOMESTICA; SOURCE 3 ORGANISM_COMMON: HOUSE FLY; SOURCE 4 ORGANISM_TAXID: 7370; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: UBB; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 GENE: UBB; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MIXED LINKAGE UBIQUITIN CHAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.PADALA,M.N.ISUPOV,R.WIENER REVDAT 5 17-JAN-24 5O44 1 REMARK REVDAT 4 08-MAY-19 5O44 1 REMARK LINK REVDAT 3 06-DEC-17 5O44 1 JRNL REVDAT 2 15-NOV-17 5O44 1 JRNL REVDAT 1 08-NOV-17 5O44 0 JRNL AUTH P.PADALA,N.SOUDAH,M.GILADI,Y.HAITIN,M.N.ISUPOV,R.WIENER JRNL TITL THE CRYSTAL STRUCTURE AND CONFORMATIONS OF AN UNBRANCHED JRNL TITL 2 MIXED TRI-UBIQUITIN CHAIN CONTAINING K48 AND K63 LINKAGES. JRNL REF J. MOL. BIOL. V. 429 3801 2017 JRNL REFN ESSN 1089-8638 JRNL PMID 29111344 JRNL DOI 10.1016/J.JMB.2017.10.027 REMARK 2 REMARK 2 RESOLUTION. 3.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 3.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 95.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26195 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1362 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) : 3.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.22 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1886 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.4690 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.4970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3594 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 38 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 135.2 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.72000 REMARK 3 B22 (A**2) : 4.72000 REMARK 3 B33 (A**2) : -15.31000 REMARK 3 B12 (A**2) : 2.36000 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): 0.393 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.304 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3670 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4940 ; 2.376 ; 2.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 446 ; 5.894 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;45.129 ;25.181 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 734 ;22.542 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;21.956 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 591 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2628 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1802 ;11.705 ;13.115 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2242 ;16.092 ;19.659 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1868 ;15.543 ;13.689 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): 14363 ;22.985 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 15 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 73 C 1 73 4392 0.10 0.05 REMARK 3 2 A 1 76 D 1 76 4386 0.10 0.05 REMARK 3 3 A 1 73 B 1 73 4332 0.11 0.05 REMARK 3 4 A 1 76 E 1 76 4476 0.11 0.05 REMARK 3 5 A 1 76 F 1 76 4426 0.10 0.05 REMARK 3 6 C 1 73 D 1 73 4532 0.07 0.05 REMARK 3 7 C 1 74 B 1 74 4624 0.10 0.05 REMARK 3 8 C 1 73 E 1 73 4432 0.10 0.05 REMARK 3 9 C 1 73 F 1 73 4492 0.08 0.05 REMARK 3 10 D 1 73 B 1 73 4484 0.09 0.05 REMARK 3 11 D 1 76 E 1 76 4466 0.11 0.05 REMARK 3 12 D 1 76 F 1 76 4620 0.08 0.05 REMARK 3 13 B 1 73 E 1 73 4396 0.11 0.05 REMARK 3 14 B 1 73 F 1 73 4500 0.08 0.05 REMARK 3 15 E 1 76 F 1 76 4488 0.11 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: NULL REMARK 4 REMARK 4 5O44 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200005079. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0080 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2, XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27681 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.140 REMARK 200 RESOLUTION RANGE LOW (A) : 104.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14200 REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 2.08100 REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP, DM REMARK 200 STARTING MODEL: 3B08 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 7.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3M MGSO4 AND 100MM MES MONOHYDRATE REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 139.00133 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 278.00267 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 208.50200 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 347.50333 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 69.50067 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 139.00133 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 278.00267 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 347.50333 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 208.50200 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 69.50067 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: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -388.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 BIOMT1 2 0.500000 0.866025 0.000000 55.38350 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -95.92704 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 69.50067 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, F REMARK 350 BIOMT1 3 0.500000 -0.866025 0.000000 -55.38350 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 -95.92704 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 69.50067 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 -55.38350 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 -95.92704 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 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 NZ LYS B 48 C GLY F 76 1.26 REMARK 500 NZ LYS C 48 C GLY D 76 1.28 REMARK 500 NZ LYS D 63 C GLY E 76 1.29 REMARK 500 C GLY A 76 NZ LYS F 63 1.30 REMARK 500 O GLY A 76 NZ LYS F 63 1.99 REMARK 500 NZ LYS C 48 O GLY D 76 2.04 REMARK 500 NH1 ARG A 72 O1 SO4 A 102 2.09 REMARK 500 NZ LYS D 63 O GLY E 76 2.16 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 LEU A 8 CB - CG - CD1 ANGL. DEV. = -12.6 DEGREES REMARK 500 LEU A 8 CB - CG - CD2 ANGL. DEV. = 13.7 DEGREES REMARK 500 GLU A 34 CA - CB - CG ANGL. DEV. = 13.7 DEGREES REMARK 500 LEU A 43 CB - CG - CD1 ANGL. DEV. = -11.0 DEGREES REMARK 500 LEU A 71 CA - CB - CG ANGL. DEV. = -18.4 DEGREES REMARK 500 LEU A 71 CB - CG - CD1 ANGL. DEV. = 11.3 DEGREES REMARK 500 LEU A 71 CB - CG - CD2 ANGL. DEV. = -15.9 DEGREES REMARK 500 LEU C 8 CA - CB - CG ANGL. DEV. = -16.5 DEGREES REMARK 500 LEU D 8 CA - CB - CG ANGL. DEV. = -16.0 DEGREES REMARK 500 VAL D 70 CA - CB - CG2 ANGL. DEV. = 10.9 DEGREES REMARK 500 LEU D 71 CB - CG - CD1 ANGL. DEV. = 11.7 DEGREES REMARK 500 LEU B 8 CA - CB - CG ANGL. DEV. = -14.3 DEGREES REMARK 500 ARG B 42 NE - CZ - NH1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG B 42 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 LEU E 8 CB - CG - CD2 ANGL. DEV. = 16.8 DEGREES REMARK 500 LEU E 71 CB - CG - CD2 ANGL. DEV. = -22.2 DEGREES REMARK 500 ARG F 54 CG - CD - NE ANGL. DEV. = -14.8 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 ASN A 60 28.34 82.66 REMARK 500 ASN C 60 25.25 85.43 REMARK 500 ASN D 60 29.69 81.58 REMARK 500 ASN B 60 24.72 83.84 REMARK 500 ARG B 72 -94.78 -63.42 REMARK 500 ALA E 46 50.13 36.06 REMARK 500 ASN E 60 26.84 83.27 REMARK 500 ASN F 60 26.83 83.55 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 MG E 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU E 24 OE2 REMARK 620 2 ASP E 52 OD2 69.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 E 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 E 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG E 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide LYS B 48 and GLY F REMARK 800 76 DBREF 5O44 A 1 76 UNP Q45TR8 Q45TR8_MUSDO 1 76 DBREF 5O44 C 1 74 UNP P0CG47 UBB_HUMAN 1 74 DBREF 5O44 D 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 5O44 B 1 74 UNP P0CG47 UBB_HUMAN 1 74 DBREF 5O44 E 1 76 UNP Q45TR8 Q45TR8_MUSDO 1 76 DBREF 5O44 F 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 5O44 CYS A 48 UNP Q45TR8 LYS 48 ENGINEERED MUTATION SEQADV 5O44 ARG D 48 UNP P0CG47 LYS 48 ENGINEERED MUTATION SEQADV 5O44 CYS E 48 UNP Q45TR8 LYS 48 ENGINEERED MUTATION SEQADV 5O44 ARG F 48 UNP P0CG47 LYS 48 ENGINEERED MUTATION SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY CYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 74 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 74 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 74 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 74 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 74 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 74 THR LEU HIS LEU VAL LEU ARG LEU 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 ARG 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 GLY SEQRES 1 B 74 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 74 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 74 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 74 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 74 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 74 THR LEU HIS LEU VAL LEU ARG LEU ARG SEQRES 1 E 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 E 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 E 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 E 76 GLN GLN ARG LEU ILE PHE ALA GLY CYS GLN LEU GLU ASP SEQRES 5 E 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 E 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 F 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 F 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 F 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 F 76 GLN GLN ARG LEU ILE PHE ALA GLY ARG GLN LEU GLU ASP SEQRES 5 F 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 F 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET SO4 A 101 5 HET SO4 A 102 5 HET MG A 103 1 HET SO4 C 101 5 HET SO4 C 102 5 HET MG D 101 1 HET SO4 B 101 5 HET SO4 B 102 5 HET SO4 E 101 5 HET SO4 E 102 5 HET SO4 E 103 5 HET MG E 104 1 HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION FORMUL 7 SO4 9(O4 S 2-) FORMUL 9 MG 3(MG 2+) FORMUL 19 HOH *38(H2 O) HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 GLN A 41 5 5 HELIX 3 AA3 THR C 22 GLY C 35 1 14 HELIX 4 AA4 PRO C 37 ASP C 39 5 3 HELIX 5 AA5 THR D 22 GLY D 35 1 14 HELIX 6 AA6 PRO D 37 ASP D 39 5 3 HELIX 7 AA7 THR B 22 GLY B 35 1 14 HELIX 8 AA8 PRO B 37 ASP B 39 5 3 HELIX 9 AA9 LEU B 56 ASN B 60 5 5 HELIX 10 AB1 THR E 22 GLY E 35 1 14 HELIX 11 AB2 PRO E 37 ASP E 39 5 3 HELIX 12 AB3 LEU E 56 ASN E 60 5 5 HELIX 13 AB4 THR F 22 GLY F 35 1 14 HELIX 14 AB5 PRO F 37 ASP F 39 5 3 SHEET 1 AA1 5 THR A 12 GLU A 16 0 SHEET 2 AA1 5 GLN A 2 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 AA1 5 THR A 66 LEU A 69 1 O LEU A 67 N PHE A 4 SHEET 4 AA1 5 LEU A 43 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 AA1 5 CYS A 48 GLN A 49 -1 O CYS A 48 N PHE A 45 SHEET 1 AA2 5 THR C 12 GLU C 16 0 SHEET 2 AA2 5 GLN C 2 THR C 7 -1 N VAL C 5 O ILE C 13 SHEET 3 AA2 5 THR C 66 LEU C 71 1 O LEU C 67 N PHE C 4 SHEET 4 AA2 5 GLN C 41 PHE C 45 -1 N ILE C 44 O HIS C 68 SHEET 5 AA2 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 AA3 5 THR D 12 GLU D 16 0 SHEET 2 AA3 5 GLN D 2 THR D 7 -1 N VAL D 5 O ILE D 13 SHEET 3 AA3 5 THR D 66 LEU D 71 1 O LEU D 67 N PHE D 4 SHEET 4 AA3 5 GLN D 41 PHE D 45 -1 N ILE D 44 O HIS D 68 SHEET 5 AA3 5 ARG D 48 GLN D 49 -1 O ARG D 48 N PHE D 45 SHEET 1 AA4 5 THR B 12 GLU B 16 0 SHEET 2 AA4 5 GLN B 2 THR B 7 -1 N VAL B 5 O ILE B 13 SHEET 3 AA4 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 AA4 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA4 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 AA5 5 THR E 12 GLU E 16 0 SHEET 2 AA5 5 GLN E 2 LYS E 6 -1 N VAL E 5 O ILE E 13 SHEET 3 AA5 5 THR E 66 LEU E 71 1 O LEU E 67 N PHE E 4 SHEET 4 AA5 5 GLN E 41 PHE E 45 -1 N ILE E 44 O HIS E 68 SHEET 5 AA5 5 CYS E 48 GLN E 49 -1 O CYS E 48 N PHE E 45 SHEET 1 AA6 5 THR F 12 GLU F 16 0 SHEET 2 AA6 5 GLN F 2 THR F 7 -1 N VAL F 5 O ILE F 13 SHEET 3 AA6 5 THR F 66 LEU F 71 1 O LEU F 67 N PHE F 4 SHEET 4 AA6 5 GLN F 41 PHE F 45 -1 N ILE F 44 O HIS F 68 SHEET 5 AA6 5 ARG F 48 GLN F 49 -1 O ARG F 48 N PHE F 45 LINK O GLU A 64 MG MG A 103 1555 1555 2.92 LINK OE2 GLU E 24 MG MG E 104 1555 1555 2.59 LINK OD2 ASP E 52 MG MG E 104 1555 1555 2.35 SITE 1 AC1 3 ARG A 42 ARG A 72 ARG A 74 SITE 1 AC2 5 ARG A 72 ARG E 42 GLN E 49 ARG E 72 SITE 2 AC2 5 HOH E 206 SITE 1 AC3 2 GLU A 64 THR A 66 SITE 1 AC4 3 ARG C 42 GLN C 49 ARG D 42 SITE 1 AC5 2 ARG C 54 LYS F 11 SITE 1 AC6 3 THR D 55 SER D 57 ASP D 58 SITE 1 AC7 4 GLN A 62 ARG B 54 ASP B 58 GLY D 10 SITE 1 AC8 6 ARG B 42 GLN B 49 ARG B 72 ARG F 42 SITE 2 AC8 6 GLN F 49 ARG F 72 SITE 1 AC9 7 ILE E 44 ALA E 46 GLY E 47 HIS E 68 SITE 2 AC9 7 PHE F 45 SER F 65 THR F 66 SITE 1 AD1 6 ILE A 44 GLY A 47 HIS A 68 SER D 65 SITE 2 AD1 6 ARG E 72 ARG E 74 SITE 1 AD2 5 LEU A 73 ARG A 74 THR E 9 GLU E 34 SITE 2 AD2 5 HOH E 201 SITE 1 AD3 4 SER D 57 GLU E 24 ASP E 39 ASP E 52 SITE 1 AD4 19 ILE B 44 PHE B 45 ALA B 46 GLY B 47 SITE 2 AD4 19 GLN B 49 LEU B 50 TYR B 59 ALA C 46 SITE 3 AD4 19 LEU D 71 ILE F 44 PHE F 45 ALA F 46 SITE 4 AD4 19 GLY F 47 GLN F 49 LEU F 50 LEU F 71 SITE 5 AD4 19 LEU F 73 ARG F 74 GLY F 75 CRYST1 110.767 110.767 417.004 90.00 90.00 120.00 P 61 2 2 24 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 0.009028 0.005212 0.000000 0.00000 SCALE2 0.000000 0.010425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002398 0.00000