HEADER HYDROLASE/PROTEIN BINDING 30-JUL-14 3WXE TITLE CRYSTAL STRUCTURE OF CYLD USP DOMAIN (C596S) IN COMPLEX WITH MET1- TITLE 2 LINKED DIUBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: USP DOMAIN, UNP RESIDUES 578-780, LINKER, 850-951; COMPND 5 SYNONYM: CYLD PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: M1-LINKED DIUBIQUITIN; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRA FISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: CYLD, CYLDA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOLDI; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: UBC; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET26B KEYWDS UBIQUITIN PROTEASE, HYDROLASE-PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.SATO,S.FUKAI REVDAT 3 01-JAN-20 3WXE 1 JRNL SEQADV REVDAT 2 16-AUG-17 3WXE 1 SOURCE REMARK REVDAT 1 11-FEB-15 3WXE 0 JRNL AUTH Y.SATO,E.GOTO,Y.SHIBATA,Y.KUBOTA,A.YAMAGATA,S.GOTO-ITO, JRNL AUTH 2 K.KUBOTA,J.INOUE,M.TAKEKAWA,F.TOKUNAGA,S.FUKAI JRNL TITL STRUCTURES OF CYLD USP WITH MET1- OR LYS63-LINKED JRNL TITL 2 DIUBIQUITIN REVEAL MECHANISMS FOR DUAL SPECIFICITY. JRNL REF NAT.STRUCT.MOL.BIOL. V. 22 222 2015 JRNL REFN ESSN 1545-9985 JRNL PMID 25686088 JRNL DOI 10.1038/NSMB.2970 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 14287 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 766 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 962 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3617 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.00000 REMARK 3 B22 (A**2) : -1.20000 REMARK 3 B33 (A**2) : -0.91000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.45000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.322 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.263 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.355 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3684 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3587 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4965 ; 1.600 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8286 ; 0.855 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 446 ; 6.020 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;37.270 ;24.647 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 702 ;17.828 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;18.156 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 558 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4083 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 810 ; 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): 1793 ; 3.306 ; 3.366 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1792 ; 3.305 ; 3.363 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2236 ; 5.364 ; 5.037 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2237 ; 5.363 ; 5.039 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1891 ; 4.264 ; 3.786 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1891 ; 4.263 ; 3.787 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2729 ; 6.439 ; 5.501 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4014 ; 9.021 ;26.381 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4006 ; 9.015 ;26.383 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 : 2 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 577 A 885 REMARK 3 ORIGIN FOR THE GROUP (A): 15.4387 2.2356 19.6070 REMARK 3 T TENSOR REMARK 3 T11: 0.1613 T22: 0.1241 REMARK 3 T33: 0.0620 T12: -0.0263 REMARK 3 T13: 0.0609 T23: -0.0288 REMARK 3 L TENSOR REMARK 3 L11: 0.1198 L22: 1.5197 REMARK 3 L33: 0.5112 L12: -0.2120 REMARK 3 L13: -0.0906 L23: -0.1252 REMARK 3 S TENSOR REMARK 3 S11: 0.0280 S12: 0.0730 S13: -0.0467 REMARK 3 S21: 0.2620 S22: -0.1347 S23: 0.1927 REMARK 3 S31: -0.0181 S32: 0.0311 S33: 0.1067 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 148 REMARK 3 ORIGIN FOR THE GROUP (A): 7.7501 -3.0518 2.1088 REMARK 3 T TENSOR REMARK 3 T11: 0.1220 T22: 0.1367 REMARK 3 T33: 0.1322 T12: 0.0941 REMARK 3 T13: -0.0190 T23: -0.0165 REMARK 3 L TENSOR REMARK 3 L11: 3.2501 L22: 1.0159 REMARK 3 L33: 0.9532 L12: -0.7429 REMARK 3 L13: -1.6849 L23: 0.2207 REMARK 3 S TENSOR REMARK 3 S11: 0.2119 S12: -0.0708 S13: -0.2677 REMARK 3 S21: -0.2757 S22: -0.2518 S23: 0.2639 REMARK 3 S31: -0.1148 S32: 0.0495 S33: 0.0398 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 3WXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000096912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU 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 : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15549 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32900 REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2VHF AND 1UBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS-HCL BUFFER, 9% PEG4000, REMARK 280 100MM MAGNESIUM CHLORIDE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 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 24.89400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 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 575 REMARK 465 HIS A 576 REMARK 465 THR A 779 REMARK 465 PRO A 780 REMARK 465 LEU A 781 REMARK 465 GLU A 782 REMARK 465 GLY A 783 REMARK 465 GLY A 784 REMARK 465 PRO A 785 REMARK 465 HIS A 786 REMARK 465 LYS A 886 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 LEU B 145 O HOH B 207 2.17 REMARK 500 OD1 ASP A 676 OH TYR A 873 2.19 REMARK 500 O HOH A 933 O HOH A 935 2.19 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 658 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 658 NE - CZ - NH2 ANGL. DEV. = -5.2 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 TYR A 593 72.67 56.74 REMARK 500 ILE A 639 -68.80 -122.87 REMARK 500 SER A 672 -40.38 -131.35 REMARK 500 THR A 799 -46.59 -136.65 REMARK 500 GLU B 64 14.91 57.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 716 LYS A 717 -149.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WXF RELATED DB: PDB REMARK 900 RELATED ID: 3WXG RELATED DB: PDB DBREF 3WXE A 578 780 UNP E7FEV5 E7FEV5_DANRE 578 780 DBREF 3WXE A 785 886 UNP E7FEV5 E7FEV5_DANRE 850 951 DBREF 3WXE B 1 148 UNP P0CG48 UBC_HUMAN 1 148 SEQADV 3WXE SER A 575 UNP E7FEV5 EXPRESSION TAG SEQADV 3WXE HIS A 576 UNP E7FEV5 EXPRESSION TAG SEQADV 3WXE MET A 577 UNP E7FEV5 EXPRESSION TAG SEQADV 3WXE SER A 596 UNP E7FEV5 CYS 596 ENGINEERED MUTATION SEQADV 3WXE LEU A 781 UNP E7FEV5 LINKER SEQADV 3WXE GLU A 782 UNP E7FEV5 LINKER SEQADV 3WXE GLY A 783 UNP E7FEV5 LINKER SEQADV 3WXE GLY A 784 UNP E7FEV5 LINKER SEQRES 1 A 312 SER HIS MET GLY LEU GLU VAL MET VAL GLY LYS LYS LYS SEQRES 2 A 312 GLY ILE GLN GLY HIS TYR ASN SER SER TYR LEU ASP SER SEQRES 3 A 312 THR LEU PHE CYS LEU PHE SER PHE SER SER VAL LEU ASP SEQRES 4 A 312 THR VAL LEU LEU ARG PRO ARG SER LYS THR ASP VAL GLU SEQRES 5 A 312 TYR TYR LYS GLU THR GLN GLU LEU LEU ARG THR GLU ILE SEQRES 6 A 312 VAL ASN PRO LEU ARG ILE HIS GLY TYR VAL CYS ALA THR SEQRES 7 A 312 LYS ILE MET LYS LEU ARG ARG ILE LEU GLU LYS VAL GLU SEQRES 8 A 312 ALA ALA SER GLY PHE THR SER GLU GLU LYS ASP PRO GLU SEQRES 9 A 312 GLU PHE LEU ASN ILE LEU PHE HIS HIS ILE LEU ARG VAL SEQRES 10 A 312 ASP PRO LEU LEU ARG LEU ARG SER ALA GLY GLN LYS VAL SEQRES 11 A 312 GLN ASP CYS TYR PHE TYR GLN ILE PHE MET ASP LYS LYS SEQRES 12 A 312 ASP LYS VAL MET VAL PRO THR SER GLN GLN LEU LEU GLU SEQRES 13 A 312 TRP SER PHE ILE ASN SER ASP LEU LYS PHE ALA GLU ALA SEQRES 14 A 312 PRO SER CYS LEU ILE ILE GLN MET PRO ARG PHE GLY LYS SEQRES 15 A 312 ASP PHE LYS MET PHE ASN LYS ILE PHE PRO SER LEU GLU SEQRES 16 A 312 LEU ASP ILE THR ASP LEU LEU ASP ASP THR PRO LEU GLU SEQRES 17 A 312 GLY GLY PRO HIS GLN GLN MET GLU LEU PHE ALA VAL LEU SEQRES 18 A 312 CYS ILE GLU THR SER HIS TYR VAL ALA PHE VAL LYS TYR SEQRES 19 A 312 GLY SER ALA ASP SER ALA TRP LEU PHE PHE ASP SER MET SEQRES 20 A 312 ALA ASP ARG ASP GLY GLY GLN ASN GLY PHE ASN ILE PRO SEQRES 21 A 312 GLN VAL SER ARG CYS PRO GLU VAL GLY GLU TYR LEU LYS SEQRES 22 A 312 MET THR PRO GLU GLU LEU HIS ALA LEU ASP PRO LYS ASN SEQRES 23 A 312 ILE GLN GLY TYR ALA ARG ARG LEU LEU CYS ASP ALA TYR SEQRES 24 A 312 MET CYS MET TYR GLN SER PRO THR MET SER LEU TYR LYS SEQRES 1 B 148 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 148 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 148 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 148 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 148 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 148 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY MET GLN SEQRES 7 B 148 ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE THR LEU SEQRES 8 B 148 GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL LYS ALA SEQRES 9 B 148 LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP GLN GLN SEQRES 10 B 148 ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP GLY ARG SEQRES 11 B 148 THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER THR LEU SEQRES 12 B 148 HIS LEU VAL LEU ARG FORMUL 3 HOH *47(H2 O) HELIX 1 1 SER A 595 SER A 607 1 13 HELIX 2 2 ASP A 613 ARG A 618 1 6 HELIX 3 3 TYR A 627 GLU A 638 1 12 HELIX 4 4 ILE A 639 GLY A 647 1 9 HELIX 5 5 CYS A 650 GLU A 665 1 16 HELIX 6 6 ASP A 676 HIS A 687 1 12 HELIX 7 7 THR A 724 SER A 736 1 13 HELIX 8 8 THR A 773 LEU A 776 5 4 HELIX 9 9 PRO A 840 LEU A 846 1 7 HELIX 10 10 THR A 849 ALA A 855 1 7 HELIX 11 11 ASP A 857 ILE A 861 5 5 HELIX 12 12 GLN A 862 GLY A 863 5 2 HELIX 13 13 TYR A 864 ASP A 871 1 8 HELIX 14 14 THR B 22 GLY B 35 1 14 HELIX 15 15 PRO B 37 ASP B 39 5 3 HELIX 16 16 LEU B 56 ASN B 60 5 5 HELIX 17 17 THR B 98 GLY B 111 1 14 HELIX 18 18 PRO B 113 ASP B 115 5 3 HELIX 19 19 LEU B 132 ASN B 136 5 5 SHEET 1 A 8 GLY A 584 LYS A 585 0 SHEET 2 A 8 PHE A 831 ARG A 838 -1 O VAL A 836 N GLY A 584 SHEET 3 A 8 TRP A 815 ASP A 825 -1 N ASP A 825 O PHE A 831 SHEET 4 A 8 TYR A 802 LYS A 807 -1 N ALA A 804 O PHE A 818 SHEET 5 A 8 GLN A 788 ILE A 797 -1 N CYS A 796 O VAL A 803 SHEET 6 A 8 ALA A 872 GLN A 878 -1 O GLN A 878 N GLU A 790 SHEET 7 A 8 CYS A 746 GLN A 750 -1 N LEU A 747 O TYR A 877 SHEET 8 A 8 TYR A 710 GLN A 711 1 N TYR A 710 O GLN A 750 SHEET 1 B 6 GLY A 584 LYS A 585 0 SHEET 2 B 6 PHE A 831 ARG A 838 -1 O VAL A 836 N GLY A 584 SHEET 3 B 6 TRP A 815 ASP A 825 -1 N ASP A 825 O PHE A 831 SHEET 4 B 6 TYR A 802 LYS A 807 -1 N ALA A 804 O PHE A 818 SHEET 5 B 6 GLN A 788 ILE A 797 -1 N CYS A 796 O VAL A 803 SHEET 6 B 6 GLU A 769 ASP A 771 -1 N LEU A 770 O MET A 789 SHEET 1 C 2 GLY A 588 ILE A 589 0 SHEET 2 C 2 TYR A 648 VAL A 649 1 O VAL A 649 N GLY A 588 SHEET 1 D 3 GLN A 705 CYS A 707 0 SHEET 2 D 3 LEU A 695 SER A 699 -1 N LEU A 695 O CYS A 707 SHEET 3 D 3 LEU A 738 PHE A 740 -1 O LYS A 739 N ARG A 698 SHEET 1 E 4 THR B 12 LEU B 15 0 SHEET 2 E 4 ILE B 3 THR B 7 -1 N VAL B 5 O ILE B 13 SHEET 3 E 4 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 E 4 GLN B 41 ILE B 44 -1 N ILE B 44 O HIS B 68 SHEET 1 F 5 THR B 88 VAL B 93 0 SHEET 2 F 5 MET B 77 LYS B 82 -1 N MET B 77 O VAL B 93 SHEET 3 F 5 THR B 142 LEU B 147 1 O LEU B 143 N PHE B 80 SHEET 4 F 5 GLN B 117 PHE B 121 -1 N ILE B 120 O HIS B 144 SHEET 5 F 5 LYS B 124 GLN B 125 -1 O LYS B 124 N PHE B 121 CRYST1 64.676 49.788 71.003 90.00 102.69 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 0.015462 0.000000 0.003482 0.00000 SCALE2 0.000000 0.020085 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014437 0.00000 MASTER 356 0 0 19 28 0 0 6 0 0 0 36 END