HEADER LIGASE/PROTEIN BINDING 11-AUG-11 3TDU TITLE N-TERMINAL ACETYLATION ACTS AS AN AVIDITY ENHANCER WITHIN AN TITLE 2 INTERCONNECTED MULTIPROTEIN COMPLEX: STRUCTURE OF A HUMAN CUL1WHB- TITLE 3 DCN1P-ACETYLATED UBC12N COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DCN1-LIKE PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 62-259; COMPND 5 SYNONYM: DCUN1 DOMAIN-CONTAINING PROTEIN 1, DEFECTIVE IN CULLIN COMPND 6 NEDDYLATION PROTEIN 1-LIKE PROTEIN 1, SQUAMOUS CELL CARCINOMA-RELATED COMPND 7 ONCOGENE; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CULLIN-1; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: UNP RESIDUES 702-776; COMPND 13 SYNONYM: CUL-1; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: NEDD8-CONJUGATING ENZYME UBC12; COMPND 17 CHAIN: E, F; COMPND 18 FRAGMENT: UNP RESIDUES 2-15; COMPND 19 SYNONYM: NEDD8 CARRIER PROTEIN, NEDD8 PROTEIN LIGASE, UBIQUITIN- COMPND 20 CONJUGATING ENZYME E2 M; COMPND 21 EC: 6.3.2.-; COMPND 22 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: DCUN1D1, DCUN1L1, RP42, SCCRO; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: CUL1; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PGEX; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_COMMON: HUMAN; SOURCE 23 ORGANISM_TAXID: 9606 KEYWDS E2:E3, LIGASE-PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.C.SCOTT,J.K.MONDA,E.J.BENNETT,J.W.HARPER,B.A.SCHULMAN REVDAT 7 13-MAR-24 3TDU 1 REMARK REVDAT 6 13-SEP-23 3TDU 1 REMARK REVDAT 5 29-JAN-20 3TDU 1 REMARK SEQADV LINK REVDAT 4 18-APR-18 3TDU 1 REMARK REVDAT 3 08-NOV-17 3TDU 1 REMARK REVDAT 2 23-NOV-11 3TDU 1 JRNL REVDAT 1 12-OCT-11 3TDU 0 JRNL AUTH D.C.SCOTT,J.K.MONDA,E.J.BENNETT,J.W.HARPER,B.A.SCHULMAN JRNL TITL N-TERMINAL ACETYLATION ACTS AS AN AVIDITY ENHANCER WITHIN AN JRNL TITL 2 INTERCONNECTED MULTIPROTEIN COMPLEX. JRNL REF SCIENCE V. 334 674 2011 JRNL REFN ISSN 0036-8075 JRNL PMID 21940857 JRNL DOI 10.1126/SCIENCE.1209307 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 78739 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4150 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5070 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 261 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4690 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 589 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.55000 REMARK 3 B22 (A**2) : -1.48000 REMARK 3 B33 (A**2) : 0.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.39000 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): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.716 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4880 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6561 ; 0.915 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 589 ; 4.213 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 242 ;35.223 ;24.793 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 975 ;13.349 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;15.466 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 702 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3642 ; 0.004 ; 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): 2877 ; 1.620 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4648 ; 3.399 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2003 ; 4.674 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1897 ; 8.137 ; 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): 4880 ; 2.458 ; 3.000 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 60 A 252 REMARK 3 RESIDUE RANGE : A 60 A 252 REMARK 3 ORIGIN FOR THE GROUP (A): 23.1649 -4.3659 -26.5951 REMARK 3 T TENSOR REMARK 3 T11: 0.0256 T22: 0.0287 REMARK 3 T33: 0.0317 T12: -0.0013 REMARK 3 T13: -0.0065 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.0639 L22: 0.0211 REMARK 3 L33: 0.0045 L12: -0.0095 REMARK 3 L13: 0.0044 L23: -0.0157 REMARK 3 S TENSOR REMARK 3 S11: 0.0079 S12: 0.0037 S13: -0.0060 REMARK 3 S21: -0.0128 S22: -0.0064 S23: 0.0016 REMARK 3 S31: 0.0057 S32: 0.0036 S33: -0.0015 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 60 B 253 REMARK 3 RESIDUE RANGE : B 60 B 253 REMARK 3 ORIGIN FOR THE GROUP (A): 14.8880 -7.1051 4.4874 REMARK 3 T TENSOR REMARK 3 T11: 0.0191 T22: 0.0299 REMARK 3 T33: 0.0357 T12: -0.0024 REMARK 3 T13: -0.0110 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.0387 L22: 0.0063 REMARK 3 L33: 0.0675 L12: -0.0170 REMARK 3 L13: -0.0227 L23: -0.0148 REMARK 3 S TENSOR REMARK 3 S11: 0.0001 S12: 0.0067 S13: -0.0026 REMARK 3 S21: 0.0092 S22: -0.0003 S23: 0.0065 REMARK 3 S31: -0.0283 S32: -0.0105 S33: 0.0002 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 702 C 776 REMARK 3 RESIDUE RANGE : C 24 C 547 REMARK 3 ORIGIN FOR THE GROUP (A): 23.4759 26.0957 -27.8761 REMARK 3 T TENSOR REMARK 3 T11: 0.0056 T22: 0.0366 REMARK 3 T33: 0.0178 T12: -0.0021 REMARK 3 T13: -0.0036 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.1185 L22: 1.3621 REMARK 3 L33: 0.0456 L12: 0.2773 REMARK 3 L13: 0.1061 L23: 0.2244 REMARK 3 S TENSOR REMARK 3 S11: 0.0047 S12: -0.0203 S13: 0.0087 REMARK 3 S21: -0.0208 S22: -0.0105 S23: -0.0345 REMARK 3 S31: 0.0051 S32: -0.0077 S33: 0.0058 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 701 D 776 REMARK 3 RESIDUE RANGE : D 48 D 597 REMARK 3 ORIGIN FOR THE GROUP (A): 13.9925 -37.7352 4.9822 REMARK 3 T TENSOR REMARK 3 T11: 0.0216 T22: 0.0306 REMARK 3 T33: 0.0262 T12: 0.0019 REMARK 3 T13: 0.0006 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.0216 L22: 1.0133 REMARK 3 L33: 0.4132 L12: -0.2095 REMARK 3 L13: 0.1636 L23: -0.5890 REMARK 3 S TENSOR REMARK 3 S11: 0.0227 S12: 0.0054 S13: -0.0018 REMARK 3 S21: 0.0190 S22: -0.0287 S23: 0.0409 REMARK 3 S31: 0.0267 S32: 0.0268 S33: 0.0061 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3TDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78739 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.605 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : 0.41300 REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 1LDJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG1500, 0.1M MIB, PH 4.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 276K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 67.71550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.72700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.71550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.72700 REMARK 290 SMTRY3 4 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, F 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 D 145 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 GLY A 253 REMARK 465 THR A 254 REMARK 465 LYS A 255 REMARK 465 SER A 256 REMARK 465 THR A 257 REMARK 465 THR A 258 REMARK 465 VAL A 259 REMARK 465 THR B 254 REMARK 465 LYS B 255 REMARK 465 SER B 256 REMARK 465 THR B 257 REMARK 465 THR B 258 REMARK 465 VAL B 259 REMARK 465 GLY C 700 REMARK 465 SER C 701 REMARK 465 GLY D 700 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 B 171 CE REMARK 470 ASN C 702 CG OD1 ND2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 140 CD REMARK 480 GLN B 76 CB REMARK 480 ASP B 91 CA 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 ILE B 208 O HOH B 511 1.81 REMARK 500 OD1 ASN B 167 O HOH B 541 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 108 CD LYS A 108 CE 0.193 REMARK 500 GLN A 140 CD GLN A 140 OE1 0.218 REMARK 500 GLN A 140 CD GLN A 140 NE2 0.446 REMARK 500 GLN B 76 CB GLN B 76 CG 0.397 REMARK 500 ASP B 91 CA ASP B 91 CB 0.362 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 CYS B 115 16.27 81.40 REMARK 500 MET B 227 18.09 59.34 REMARK 500 LYS C 723 -55.90 72.55 REMARK 500 LEU C 775 -84.31 -100.25 REMARK 500 ASN D 702 54.81 37.88 REMARK 500 LYS D 723 -60.06 72.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 468 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH B 432 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH B 540 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH B 585 DISTANCE = 6.77 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TDI RELATED DB: PDB REMARK 900 RELATED ID: 3TDZ RELATED DB: PDB DBREF 3TDU A 62 259 UNP Q96GG9 DCNL1_HUMAN 62 259 DBREF 3TDU B 62 259 UNP Q96GG9 DCNL1_HUMAN 62 259 DBREF 3TDU C 702 776 UNP Q13616 CUL1_HUMAN 702 776 DBREF 3TDU D 702 776 UNP Q13616 CUL1_HUMAN 702 776 DBREF 3TDU E 3 16 UNP P61081 UBC12_HUMAN 2 15 DBREF 3TDU F 3 16 UNP P61081 UBC12_HUMAN 2 15 SEQADV 3TDU GLY A 60 UNP Q96GG9 EXPRESSION TAG SEQADV 3TDU SER A 61 UNP Q96GG9 EXPRESSION TAG SEQADV 3TDU GLY B 60 UNP Q96GG9 EXPRESSION TAG SEQADV 3TDU SER B 61 UNP Q96GG9 EXPRESSION TAG SEQADV 3TDU GLY C 700 UNP Q13616 EXPRESSION TAG SEQADV 3TDU SER C 701 UNP Q13616 EXPRESSION TAG SEQADV 3TDU GLY D 700 UNP Q13616 EXPRESSION TAG SEQADV 3TDU SER D 701 UNP Q13616 EXPRESSION TAG SEQADV 3TDU ACE E 1 UNP P61081 ACETYLATION SEQADV 3TDU MET E 2 UNP P61081 INITIATING METHIONINE SEQADV 3TDU ACE F 1 UNP P61081 ACETYLATION SEQADV 3TDU MET F 2 UNP P61081 INITIATING METHIONINE SEQRES 1 A 200 GLY SER ARG LYS LYS LEU GLU GLN LEU TYR ASN ARG TYR SEQRES 2 A 200 LYS ASP PRO GLN ASP GLU ASN LYS ILE GLY ILE ASP GLY SEQRES 3 A 200 ILE GLN GLN PHE CYS ASP ASP LEU ALA LEU ASP PRO ALA SEQRES 4 A 200 SER ILE SER VAL LEU ILE ILE ALA TRP LYS PHE ARG ALA SEQRES 5 A 200 ALA THR GLN CYS GLU PHE SER LYS GLN GLU PHE MET ASP SEQRES 6 A 200 GLY MET THR GLU LEU GLY CYS ASP SER ILE GLU LYS LEU SEQRES 7 A 200 LYS ALA GLN ILE PRO LYS MET GLU GLN GLU LEU LYS GLU SEQRES 8 A 200 PRO GLY ARG PHE LYS ASP PHE TYR GLN PHE THR PHE ASN SEQRES 9 A 200 PHE ALA LYS ASN PRO GLY GLN LYS GLY LEU ASP LEU GLU SEQRES 10 A 200 MET ALA ILE ALA TYR TRP ASN LEU VAL LEU ASN GLY ARG SEQRES 11 A 200 PHE LYS PHE LEU ASP LEU TRP ASN LYS PHE LEU LEU GLU SEQRES 12 A 200 HIS HIS LYS ARG SER ILE PRO LYS ASP THR TRP ASN LEU SEQRES 13 A 200 LEU LEU ASP PHE SER THR MET ILE ALA ASP ASP MET SER SEQRES 14 A 200 ASN TYR ASP GLU GLU GLY ALA TRP PRO VAL LEU ILE ASP SEQRES 15 A 200 ASP PHE VAL GLU PHE ALA ARG PRO GLN ILE ALA GLY THR SEQRES 16 A 200 LYS SER THR THR VAL SEQRES 1 B 200 GLY SER ARG LYS LYS LEU GLU GLN LEU TYR ASN ARG TYR SEQRES 2 B 200 LYS ASP PRO GLN ASP GLU ASN LYS ILE GLY ILE ASP GLY SEQRES 3 B 200 ILE GLN GLN PHE CYS ASP ASP LEU ALA LEU ASP PRO ALA SEQRES 4 B 200 SER ILE SER VAL LEU ILE ILE ALA TRP LYS PHE ARG ALA SEQRES 5 B 200 ALA THR GLN CYS GLU PHE SER LYS GLN GLU PHE MET ASP SEQRES 6 B 200 GLY MET THR GLU LEU GLY CYS ASP SER ILE GLU LYS LEU SEQRES 7 B 200 LYS ALA GLN ILE PRO LYS MET GLU GLN GLU LEU LYS GLU SEQRES 8 B 200 PRO GLY ARG PHE LYS ASP PHE TYR GLN PHE THR PHE ASN SEQRES 9 B 200 PHE ALA LYS ASN PRO GLY GLN LYS GLY LEU ASP LEU GLU SEQRES 10 B 200 MET ALA ILE ALA TYR TRP ASN LEU VAL LEU ASN GLY ARG SEQRES 11 B 200 PHE LYS PHE LEU ASP LEU TRP ASN LYS PHE LEU LEU GLU SEQRES 12 B 200 HIS HIS LYS ARG SER ILE PRO LYS ASP THR TRP ASN LEU SEQRES 13 B 200 LEU LEU ASP PHE SER THR MET ILE ALA ASP ASP MET SER SEQRES 14 B 200 ASN TYR ASP GLU GLU GLY ALA TRP PRO VAL LEU ILE ASP SEQRES 15 B 200 ASP PHE VAL GLU PHE ALA ARG PRO GLN ILE ALA GLY THR SEQRES 16 B 200 LYS SER THR THR VAL SEQRES 1 C 77 GLY SER ASN ILE GLU GLU ASP ARG LYS LEU LEU ILE GLN SEQRES 2 C 77 ALA ALA ILE VAL ARG ILE MET LYS MET ARG LYS VAL LEU SEQRES 3 C 77 LYS HIS GLN GLN LEU LEU GLY GLU VAL LEU THR GLN LEU SEQRES 4 C 77 SER SER ARG PHE LYS PRO ARG VAL PRO VAL ILE LYS LYS SEQRES 5 C 77 CYS ILE ASP ILE LEU ILE GLU LYS GLU TYR LEU GLU ARG SEQRES 6 C 77 VAL ASP GLY GLU LYS ASP THR TYR SER TYR LEU ALA SEQRES 1 D 77 GLY SER ASN ILE GLU GLU ASP ARG LYS LEU LEU ILE GLN SEQRES 2 D 77 ALA ALA ILE VAL ARG ILE MET LYS MET ARG LYS VAL LEU SEQRES 3 D 77 LYS HIS GLN GLN LEU LEU GLY GLU VAL LEU THR GLN LEU SEQRES 4 D 77 SER SER ARG PHE LYS PRO ARG VAL PRO VAL ILE LYS LYS SEQRES 5 D 77 CYS ILE ASP ILE LEU ILE GLU LYS GLU TYR LEU GLU ARG SEQRES 6 D 77 VAL ASP GLY GLU LYS ASP THR TYR SER TYR LEU ALA SEQRES 1 E 16 ACE MET ILE LYS LEU PHE SER LEU LYS GLN GLN LYS LYS SEQRES 2 E 16 GLU GLU GLU SEQRES 1 F 16 ACE MET ILE LYS LEU PHE SER LEU LYS GLN GLN LYS LYS SEQRES 2 F 16 GLU GLU GLU HET ACE E 1 3 HET ACE F 1 3 HETNAM ACE ACETYL GROUP FORMUL 5 ACE 2(C2 H4 O) FORMUL 7 HOH *589(H2 O) HELIX 1 1 SER A 61 TYR A 72 1 12 HELIX 2 2 GLY A 82 ALA A 94 1 13 HELIX 3 3 SER A 99 PHE A 109 1 11 HELIX 4 4 LYS A 119 GLY A 130 1 12 HELIX 5 5 SER A 133 GLN A 140 1 8 HELIX 6 6 GLN A 140 LEU A 148 1 9 HELIX 7 7 GLU A 150 LYS A 166 1 17 HELIX 8 8 LEU A 175 LEU A 186 1 12 HELIX 9 9 PHE A 192 HIS A 203 1 12 HELIX 10 10 PRO A 209 ILE A 223 1 15 HELIX 11 11 PRO A 237 ILE A 251 1 15 HELIX 12 12 SER B 61 LYS B 73 1 13 HELIX 13 13 GLY B 82 ALA B 94 1 13 HELIX 14 14 SER B 99 PHE B 109 1 11 HELIX 15 15 LYS B 119 GLY B 130 1 12 HELIX 16 16 SER B 133 GLN B 140 1 8 HELIX 17 17 GLN B 140 LEU B 148 1 9 HELIX 18 18 GLU B 150 LYS B 166 1 17 HELIX 19 19 LEU B 175 LEU B 186 1 12 HELIX 20 20 PHE B 192 HIS B 203 1 12 HELIX 21 21 PRO B 209 ILE B 223 1 15 HELIX 22 22 PRO B 237 ALA B 252 1 16 HELIX 23 23 ILE C 703 LYS C 723 1 21 HELIX 24 24 HIS C 727 SER C 739 1 13 HELIX 25 25 ARG C 745 LYS C 759 1 15 HELIX 26 26 ASN D 702 LYS D 723 1 22 HELIX 27 27 HIS D 727 SER D 739 1 13 HELIX 28 28 ARG D 745 LYS D 759 1 15 SHEET 1 A 3 LYS A 73 ASP A 74 0 SHEET 2 A 3 ASP A 77 ILE A 81 -1 O LYS A 80 N ASP A 74 SHEET 3 A 3 PHE A 117 SER A 118 -1 O PHE A 117 N ILE A 81 SHEET 1 B 2 LEU A 173 ASP A 174 0 SHEET 2 B 2 SER A 207 ILE A 208 -1 O ILE A 208 N LEU A 173 SHEET 1 C 2 LYS B 80 ILE B 81 0 SHEET 2 C 2 PHE B 117 SER B 118 -1 O PHE B 117 N ILE B 81 SHEET 1 D 2 LEU B 173 ASP B 174 0 SHEET 2 D 2 SER B 207 ILE B 208 -1 O ILE B 208 N LEU B 173 SHEET 1 E 3 VAL C 724 LYS C 726 0 SHEET 2 E 3 GLU C 768 TYR C 774 -1 O TYR C 772 N LEU C 725 SHEET 3 E 3 LEU C 762 VAL C 765 -1 N VAL C 765 O THR C 771 SHEET 1 F 3 VAL D 724 LYS D 726 0 SHEET 2 F 3 GLU D 768 TYR D 774 -1 O TYR D 772 N LEU D 725 SHEET 3 F 3 LEU D 762 VAL D 765 -1 N GLU D 763 O SER D 773 LINK C ACE E 1 N MET E 2 1555 1555 1.34 LINK C ACE F 1 N MET F 2 1555 1555 1.34 CISPEP 1 ALA B 252 GLY B 253 0 -2.73 CRYST1 135.431 65.454 64.182 90.00 104.73 90.00 C 1 2 1 8 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 0.007384 0.000000 0.001942 0.00000 SCALE2 0.000000 0.015278 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016110 0.00000