HEADER HYDROLASE/PROTEIN BINDING 17-MAY-13 4KSK TITLE GUMBY/FAM105B IN COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN FAM105B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: OTU DOMAIN (UNP RESIDUES 55-352); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: POLYUBIQUITIN-C; COMPND 9 CHAIN: C, D; COMPND 10 FRAGMENT: UNP RESIDUES 76-152; COMPND 11 SYNONYM: UBIQUITIN; COMPND 12 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: FAM105B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLAMSID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PROEX; 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: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PETM30 KEYWDS OTU DOMAIN, DEUBIQUITINASE, UBIQUITIN, HYDROLASE, HYDROLASE-PROTEIN KEYWDS 2 BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.F.CECCARELLI,Y.-C.JUANG,F.SICHERI REVDAT 5 20-SEP-23 4KSK 1 REMARK SEQADV REVDAT 4 12-NOV-14 4KSK 1 AUTHOR REVDAT 3 03-JUL-13 4KSK 1 JRNL HEADER REVDAT 2 26-JUN-13 4KSK 1 JRNL REVDAT 1 05-JUN-13 4KSK 0 JRNL AUTH E.RIVKIN,S.M.ALMEIDA,D.F.CECCARELLI,Y.C.JUANG,T.A.MACLEAN, JRNL AUTH 2 T.SRIKUMAR,H.HUANG,W.H.DUNHAM,R.FUKUMURA,G.XIE,Y.GONDO, JRNL AUTH 3 B.RAUGHT,A.C.GINGRAS,F.SICHERI,S.P.CORDES JRNL TITL THE LINEAR UBIQUITIN-SPECIFIC DEUBIQUITINASE GUMBY REGULATES JRNL TITL 2 ANGIOGENESIS. JRNL REF NATURE V. 498 318 2013 JRNL REFN ISSN 0028-0836 JRNL PMID 23708998 JRNL DOI 10.1038/NATURE12296 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 28755 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1533 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1926 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 112 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5334 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.77000 REMARK 3 B22 (A**2) : 0.33000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.72000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.477 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.288 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.268 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.893 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5446 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7382 ; 1.643 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 664 ; 6.681 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 246 ;34.176 ;24.228 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 964 ;18.208 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;19.745 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 836 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4058 ; 0.008 ; 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): 3346 ; 0.734 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5393 ; 1.317 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2100 ; 2.255 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1989 ; 3.333 ; 4.500 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): 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 : 4 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 78 A 346 REMARK 3 ORIGIN FOR THE GROUP (A): -9.5930 1.3700 38.4490 REMARK 3 T TENSOR REMARK 3 T11: 0.3018 T22: 0.0780 REMARK 3 T33: 0.1895 T12: 0.0079 REMARK 3 T13: 0.2171 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 2.4101 L22: 2.0732 REMARK 3 L33: 3.5597 L12: 0.0776 REMARK 3 L13: -1.8140 L23: 0.4569 REMARK 3 S TENSOR REMARK 3 S11: -0.0298 S12: 0.3150 S13: 0.0467 REMARK 3 S21: -0.3413 S22: 0.0311 S23: -0.0144 REMARK 3 S31: -0.0108 S32: 0.0421 S33: -0.0013 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 78 B 346 REMARK 3 ORIGIN FOR THE GROUP (A): -48.5220 -19.7380 16.4330 REMARK 3 T TENSOR REMARK 3 T11: 0.3150 T22: 0.0951 REMARK 3 T33: 0.2050 T12: 0.0129 REMARK 3 T13: 0.2340 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 2.1680 L22: 2.5663 REMARK 3 L33: 2.8252 L12: -0.3933 REMARK 3 L13: -1.2131 L23: -0.8696 REMARK 3 S TENSOR REMARK 3 S11: -0.0894 S12: -0.4246 S13: 0.0329 REMARK 3 S21: 0.5232 S22: 0.1773 S23: 0.1842 REMARK 3 S31: -0.0684 S32: 0.0918 S33: -0.0878 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 73 REMARK 3 ORIGIN FOR THE GROUP (A): -72.3680 -13.1930 1.9710 REMARK 3 T TENSOR REMARK 3 T11: 0.4161 T22: 0.4291 REMARK 3 T33: 0.7718 T12: 0.0328 REMARK 3 T13: 0.1797 T23: 0.0620 REMARK 3 L TENSOR REMARK 3 L11: 3.6326 L22: 8.8506 REMARK 3 L33: 5.2505 L12: -0.4882 REMARK 3 L13: 1.1109 L23: -2.3273 REMARK 3 S TENSOR REMARK 3 S11: 0.0112 S12: 0.4468 S13: 0.2429 REMARK 3 S21: -0.7560 S22: 0.3068 S23: 1.6117 REMARK 3 S31: -0.1769 S32: -0.8801 S33: -0.3181 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 73 REMARK 3 ORIGIN FOR THE GROUP (A): 12.5960 6.8400 55.5080 REMARK 3 T TENSOR REMARK 3 T11: 0.5244 T22: 0.7559 REMARK 3 T33: 0.2299 T12: -0.1586 REMARK 3 T13: 0.2296 T23: 0.0672 REMARK 3 L TENSOR REMARK 3 L11: 6.4770 L22: 5.6917 REMARK 3 L33: 10.9663 L12: 1.9341 REMARK 3 L13: 4.2863 L23: 2.4839 REMARK 3 S TENSOR REMARK 3 S11: 0.1193 S12: -0.3099 S13: 0.2617 REMARK 3 S21: 0.7073 S22: -0.1802 S23: -0.0231 REMARK 3 S31: -0.6878 S32: 1.8003 S33: 0.0610 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4KSK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARIMAX VHF REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28755 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.16100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.61900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4KSJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS TRIS, 200 MM AMSO4, 20% REMARK 280 PEG3350, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 21.65450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 GLY A 53 REMARK 465 SER A 54 REMARK 465 MET A 55 REMARK 465 TYR A 56 REMARK 465 ARG A 57 REMARK 465 ALA A 58 REMARK 465 ALA A 59 REMARK 465 ASP A 60 REMARK 465 GLU A 61 REMARK 465 ILE A 62 REMARK 465 GLU A 63 REMARK 465 LYS A 64 REMARK 465 GLU A 65 REMARK 465 LYS A 66 REMARK 465 GLU A 67 REMARK 465 LEU A 68 REMARK 465 LEU A 69 REMARK 465 ILE A 70 REMARK 465 HIS A 71 REMARK 465 GLU A 72 REMARK 465 ARG A 73 REMARK 465 GLY A 74 REMARK 465 ALA A 75 REMARK 465 SER A 76 REMARK 465 GLU A 77 REMARK 465 GLY A 174 REMARK 465 LEU A 175 REMARK 465 LYS A 176 REMARK 465 PHE A 177 REMARK 465 ASP A 178 REMARK 465 GLY A 179 REMARK 465 LYS A 180 REMARK 465 ASN A 181 REMARK 465 GLU A 182 REMARK 465 CYS A 347 REMARK 465 GLU A 348 REMARK 465 GLU A 349 REMARK 465 THR A 350 REMARK 465 SER A 351 REMARK 465 LEU A 352 REMARK 465 GLY B 53 REMARK 465 SER B 54 REMARK 465 MET B 55 REMARK 465 TYR B 56 REMARK 465 ARG B 57 REMARK 465 ALA B 58 REMARK 465 ALA B 59 REMARK 465 ASP B 60 REMARK 465 GLU B 61 REMARK 465 ILE B 62 REMARK 465 GLU B 63 REMARK 465 LYS B 64 REMARK 465 GLU B 65 REMARK 465 LYS B 66 REMARK 465 GLU B 67 REMARK 465 LEU B 68 REMARK 465 LEU B 69 REMARK 465 ILE B 70 REMARK 465 HIS B 71 REMARK 465 GLU B 72 REMARK 465 ARG B 73 REMARK 465 GLY B 74 REMARK 465 ALA B 75 REMARK 465 SER B 76 REMARK 465 GLU B 77 REMARK 465 GLY B 174 REMARK 465 LEU B 175 REMARK 465 LYS B 176 REMARK 465 PHE B 177 REMARK 465 ASP B 178 REMARK 465 GLY B 179 REMARK 465 LYS B 180 REMARK 465 ASN B 181 REMARK 465 GLU B 182 REMARK 465 CYS B 347 REMARK 465 GLU B 348 REMARK 465 GLU B 349 REMARK 465 THR B 350 REMARK 465 SER B 351 REMARK 465 LEU B 352 REMARK 465 GLY C -3 REMARK 465 ALA C -2 REMARK 465 MET C -1 REMARK 465 GLY C 75 REMARK 465 GLY C 76 REMARK 465 GLY D -3 REMARK 465 ALA D -2 REMARK 465 MET D -1 REMARK 465 GLY D 75 REMARK 465 GLY D 76 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 LYS A 93 CG CD CE NZ REMARK 470 GLN A 101 CG CD OE1 NE2 REMARK 470 GLU A 153 CG CD OE1 OE2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 ASP A 183 CG OD1 OD2 REMARK 470 GLU A 190 CG CD OE1 OE2 REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 212 CG CD OE1 NE2 REMARK 470 GLU A 217 CG CD OE1 OE2 REMARK 470 LYS A 247 CG CD CE NZ REMARK 470 GLU A 252 CG CD OE1 OE2 REMARK 470 LYS A 325 CG CD CE NZ REMARK 470 VAL A 346 CG1 CG2 REMARK 470 LYS B 93 CG CD CE NZ REMARK 470 GLN B 101 CG CD OE1 NE2 REMARK 470 ASP B 183 CG OD1 OD2 REMARK 470 LYS B 187 CG CD CE NZ REMARK 470 GLU B 190 CG CD OE1 OE2 REMARK 470 ARG B 206 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 209 CG CD OE1 OE2 REMARK 470 GLN B 212 CG CD OE1 NE2 REMARK 470 GLU B 217 CG CD OE1 OE2 REMARK 470 LYS B 249 CG CD CE NZ REMARK 470 LYS B 251 CG CD CE NZ REMARK 470 GLU B 252 CG CD OE1 OE2 REMARK 470 LYS B 325 CG CD CE NZ REMARK 470 VAL B 346 CG1 CG2 REMARK 470 ARG C 74 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 63 CG CD CE NZ REMARK 470 ARG D 74 CG CD NE CZ NH1 NH2 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 NH2 ARG B 299 O HOH B 417 2.10 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 124 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG C 42 NE - CZ - NH2 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 GLU A 209 -40.99 -29.69 REMARK 500 PHE A 219 65.15 -109.99 REMARK 500 SER A 266 40.22 -141.69 REMARK 500 HIS A 276 -59.39 -131.91 REMARK 500 ASN A 311 33.64 -95.16 REMARK 500 ARG A 345 -98.55 156.01 REMARK 500 PRO B 152 -9.03 -59.73 REMARK 500 HIS B 276 -58.30 -129.94 REMARK 500 HIS B 282 -64.89 -120.74 REMARK 500 ARG B 345 49.79 91.42 REMARK 500 GLU C 64 -2.94 65.98 REMARK 500 ASN D 60 58.96 35.21 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 LEU C 73 ARG C 74 149.93 REMARK 500 REMARK 500 REMARK: NULL 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 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KSJ RELATED DB: PDB REMARK 900 RELATED ID: 4KSL RELATED DB: PDB DBREF 4KSK A 55 352 UNP Q96BN8 F105B_HUMAN 55 352 DBREF 4KSK B 55 352 UNP Q96BN8 F105B_HUMAN 55 352 DBREF 4KSK C 0 76 UNP P0CG48 UBC_HUMAN 76 152 DBREF 4KSK D 0 76 UNP P0CG48 UBC_HUMAN 76 152 SEQADV 4KSK GLY A 53 UNP Q96BN8 EXPRESSION TAG SEQADV 4KSK SER A 54 UNP Q96BN8 EXPRESSION TAG SEQADV 4KSK SER A 129 UNP Q96BN8 CYS 129 ENGINEERED MUTATION SEQADV 4KSK GLY B 53 UNP Q96BN8 EXPRESSION TAG SEQADV 4KSK SER B 54 UNP Q96BN8 EXPRESSION TAG SEQADV 4KSK SER B 129 UNP Q96BN8 CYS 129 ENGINEERED MUTATION SEQADV 4KSK GLY C -3 UNP P0CG48 EXPRESSION TAG SEQADV 4KSK ALA C -2 UNP P0CG48 EXPRESSION TAG SEQADV 4KSK MET C -1 UNP P0CG48 EXPRESSION TAG SEQADV 4KSK GLY D -3 UNP P0CG48 EXPRESSION TAG SEQADV 4KSK ALA D -2 UNP P0CG48 EXPRESSION TAG SEQADV 4KSK MET D -1 UNP P0CG48 EXPRESSION TAG SEQRES 1 A 300 GLY SER MET TYR ARG ALA ALA ASP GLU ILE GLU LYS GLU SEQRES 2 A 300 LYS GLU LEU LEU ILE HIS GLU ARG GLY ALA SER GLU PRO SEQRES 3 A 300 ARG LEU SER VAL ALA PRO GLU MET ASP ILE MET ASP TYR SEQRES 4 A 300 CYS LYS LYS GLU TRP ARG GLY ASN THR GLN LYS ALA THR SEQRES 5 A 300 CYS MET LYS MET GLY TYR GLU GLU VAL SER GLN LYS PHE SEQRES 6 A 300 THR SER ILE ARG ARG VAL ARG GLY ASP ASN TYR SER ALA SEQRES 7 A 300 LEU ARG ALA THR LEU PHE GLN ALA MET SER GLN ALA VAL SEQRES 8 A 300 GLY LEU PRO PRO TRP LEU GLN ASP PRO GLU LEU MET LEU SEQRES 9 A 300 LEU PRO GLU LYS LEU ILE SER LYS TYR ASN TRP ILE LYS SEQRES 10 A 300 GLN TRP LYS LEU GLY LEU LYS PHE ASP GLY LYS ASN GLU SEQRES 11 A 300 ASP LEU VAL ASP LYS ILE LYS GLU SER LEU THR LEU LEU SEQRES 12 A 300 ARG LYS LYS TRP ALA GLY LEU ALA GLU MET ARG THR ALA SEQRES 13 A 300 GLU ALA ARG GLN ILE ALA CYS ASP GLU LEU PHE THR ASN SEQRES 14 A 300 GLU ALA GLU GLU TYR SER LEU TYR GLU ALA VAL LYS PHE SEQRES 15 A 300 LEU MET LEU ASN ARG ALA ILE GLU LEU TYR ASN ASP LYS SEQRES 16 A 300 GLU LYS GLY LYS GLU VAL PRO PHE PHE SER VAL LEU LEU SEQRES 17 A 300 PHE ALA ARG ASP THR SER ASN ASP PRO GLY GLN LEU LEU SEQRES 18 A 300 ARG ASN HIS LEU ASN GLN VAL GLY HIS THR GLY GLY LEU SEQRES 19 A 300 GLU GLN VAL GLU MET PHE LEU LEU ALA TYR ALA VAL ARG SEQRES 20 A 300 HIS THR ILE GLN VAL TYR ARG LEU SER LYS TYR ASN THR SEQRES 21 A 300 GLU GLU PHE ILE THR VAL TYR PRO THR ASP PRO PRO LYS SEQRES 22 A 300 ASP TRP PRO VAL VAL THR LEU ILE ALA GLU ASP ASP ARG SEQRES 23 A 300 HIS TYR ASN ILE PRO VAL ARG VAL CYS GLU GLU THR SER SEQRES 24 A 300 LEU SEQRES 1 B 300 GLY SER MET TYR ARG ALA ALA ASP GLU ILE GLU LYS GLU SEQRES 2 B 300 LYS GLU LEU LEU ILE HIS GLU ARG GLY ALA SER GLU PRO SEQRES 3 B 300 ARG LEU SER VAL ALA PRO GLU MET ASP ILE MET ASP TYR SEQRES 4 B 300 CYS LYS LYS GLU TRP ARG GLY ASN THR GLN LYS ALA THR SEQRES 5 B 300 CYS MET LYS MET GLY TYR GLU GLU VAL SER GLN LYS PHE SEQRES 6 B 300 THR SER ILE ARG ARG VAL ARG GLY ASP ASN TYR SER ALA SEQRES 7 B 300 LEU ARG ALA THR LEU PHE GLN ALA MET SER GLN ALA VAL SEQRES 8 B 300 GLY LEU PRO PRO TRP LEU GLN ASP PRO GLU LEU MET LEU SEQRES 9 B 300 LEU PRO GLU LYS LEU ILE SER LYS TYR ASN TRP ILE LYS SEQRES 10 B 300 GLN TRP LYS LEU GLY LEU LYS PHE ASP GLY LYS ASN GLU SEQRES 11 B 300 ASP LEU VAL ASP LYS ILE LYS GLU SER LEU THR LEU LEU SEQRES 12 B 300 ARG LYS LYS TRP ALA GLY LEU ALA GLU MET ARG THR ALA SEQRES 13 B 300 GLU ALA ARG GLN ILE ALA CYS ASP GLU LEU PHE THR ASN SEQRES 14 B 300 GLU ALA GLU GLU TYR SER LEU TYR GLU ALA VAL LYS PHE SEQRES 15 B 300 LEU MET LEU ASN ARG ALA ILE GLU LEU TYR ASN ASP LYS SEQRES 16 B 300 GLU LYS GLY LYS GLU VAL PRO PHE PHE SER VAL LEU LEU SEQRES 17 B 300 PHE ALA ARG ASP THR SER ASN ASP PRO GLY GLN LEU LEU SEQRES 18 B 300 ARG ASN HIS LEU ASN GLN VAL GLY HIS THR GLY GLY LEU SEQRES 19 B 300 GLU GLN VAL GLU MET PHE LEU LEU ALA TYR ALA VAL ARG SEQRES 20 B 300 HIS THR ILE GLN VAL TYR ARG LEU SER LYS TYR ASN THR SEQRES 21 B 300 GLU GLU PHE ILE THR VAL TYR PRO THR ASP PRO PRO LYS SEQRES 22 B 300 ASP TRP PRO VAL VAL THR LEU ILE ALA GLU ASP ASP ARG SEQRES 23 B 300 HIS TYR ASN ILE PRO VAL ARG VAL CYS GLU GLU THR SER SEQRES 24 B 300 LEU SEQRES 1 C 80 GLY ALA MET GLY MET GLN ILE PHE VAL LYS THR LEU THR SEQRES 2 C 80 GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP THR SEQRES 3 C 80 ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY SEQRES 4 C 80 ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS SEQRES 5 C 80 GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE SEQRES 6 C 80 GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU ARG SEQRES 7 C 80 GLY GLY SEQRES 1 D 80 GLY ALA MET GLY MET GLN ILE PHE VAL LYS THR LEU THR SEQRES 2 D 80 GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP THR SEQRES 3 D 80 ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY SEQRES 4 D 80 ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS SEQRES 5 D 80 GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE SEQRES 6 D 80 GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU ARG SEQRES 7 D 80 GLY GLY HET SO4 A 401 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *162(H2 O) HELIX 1 1 ILE A 88 TRP A 96 1 9 HELIX 2 2 THR A 100 GLN A 115 1 16 HELIX 3 3 TYR A 128 GLN A 141 1 14 HELIX 4 4 PRO A 146 ASP A 151 1 6 HELIX 5 5 PRO A 152 MET A 155 5 4 HELIX 6 6 LEU A 156 TYR A 165 1 10 HELIX 7 7 ASN A 166 TRP A 171 5 6 HELIX 8 8 LEU A 184 ALA A 203 1 20 HELIX 9 9 THR A 207 GLU A 217 1 11 HELIX 10 10 GLU A 222 LYS A 249 1 28 HELIX 11 11 PRO A 254 ALA A 262 1 9 HELIX 12 12 ASP A 268 HIS A 276 1 9 HELIX 13 13 GLU A 287 ARG A 299 1 13 HELIX 14 14 SER A 308 TYR A 310 5 3 HELIX 15 15 THR A 312 GLU A 314 5 3 HELIX 16 16 ILE B 88 TRP B 96 1 9 HELIX 17 17 THR B 100 GLN B 115 1 16 HELIX 18 18 TYR B 128 GLN B 141 1 14 HELIX 19 19 PRO B 146 ASP B 151 1 6 HELIX 20 20 GLU B 153 MET B 155 5 3 HELIX 21 21 LEU B 156 TYR B 165 1 10 HELIX 22 22 ASN B 166 TRP B 171 5 6 HELIX 23 23 LEU B 184 ALA B 203 1 20 HELIX 24 24 THR B 207 PHE B 219 1 13 HELIX 25 25 GLU B 222 GLU B 248 1 27 HELIX 26 26 PHE B 255 PHE B 261 1 7 HELIX 27 27 ARG B 263 ASN B 267 5 5 HELIX 28 28 ASP B 268 HIS B 276 1 9 HELIX 29 29 GLU B 287 ARG B 299 1 13 HELIX 30 30 SER B 308 TYR B 310 5 3 HELIX 31 31 THR C 22 GLY C 35 1 14 HELIX 32 32 PRO C 37 GLN C 41 5 5 HELIX 33 33 LEU C 56 ASN C 60 5 5 HELIX 34 34 THR D 22 GLY D 35 1 14 HELIX 35 35 PRO D 37 GLN D 41 5 5 SHEET 1 A 6 MET A 86 ASP A 87 0 SHEET 2 A 6 PHE A 117 ARG A 121 -1 O ILE A 120 N MET A 86 SHEET 3 A 6 HIS A 339 ARG A 345 -1 O VAL A 344 N SER A 119 SHEET 4 A 6 VAL A 329 ASP A 336 -1 N ILE A 333 O ASN A 341 SHEET 5 A 6 THR A 301 ARG A 306 1 N TYR A 305 O LEU A 332 SHEET 6 A 6 ILE A 316 TYR A 319 -1 O THR A 317 N VAL A 304 SHEET 1 B 6 MET B 86 ASP B 87 0 SHEET 2 B 6 SER B 119 ARG B 121 -1 O ILE B 120 N MET B 86 SHEET 3 B 6 HIS B 339 VAL B 344 -1 O ILE B 342 N ARG B 121 SHEET 4 B 6 VAL B 329 ASP B 336 -1 N ILE B 333 O ASN B 341 SHEET 5 B 6 THR B 301 ARG B 306 1 N TYR B 305 O ALA B 334 SHEET 6 B 6 ILE B 316 TYR B 319 -1 O TYR B 319 N ILE B 302 SHEET 1 C 5 THR C 12 VAL C 17 0 SHEET 2 C 5 MET C 1 LYS C 6 -1 N ILE C 3 O LEU C 15 SHEET 3 C 5 THR C 66 LEU C 69 1 O LEU C 67 N LYS C 6 SHEET 4 C 5 LEU C 43 PHE C 45 -1 N ILE C 44 O HIS C 68 SHEET 5 C 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 D 5 THR D 12 VAL D 17 0 SHEET 2 D 5 MET D 1 THR D 7 -1 N VAL D 5 O ILE D 13 SHEET 3 D 5 SER D 65 LEU D 69 1 O SER D 65 N PHE D 4 SHEET 4 D 5 LEU D 43 PHE D 45 -1 N ILE D 44 O HIS D 68 SHEET 5 D 5 LYS D 48 GLN D 49 -1 O LYS D 48 N PHE D 45 CISPEP 1 TYR A 319 PRO A 320 0 -2.71 CISPEP 2 TYR B 319 PRO B 320 0 -6.15 SITE 1 AC1 4 ASP A 336 ASP A 337 ARG A 338 GLN D 40 CRYST1 84.273 43.309 113.918 90.00 108.28 90.00 P 1 21 1 4 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 0.011866 0.000000 0.003920 0.00000 SCALE2 0.000000 0.023090 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009245 0.00000