HEADER LIGASE 06-APR-23 8SDE TITLE ELECTROSTATIC-MEDIATED TETRAMERIZATION OF THE COILED-COIL DOMAIN IN TITLE 2 TRIM29 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIPARTITE MOTIF-CONTAINING PROTEIN 29; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: COILED COIL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TRIM29; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS E3 UBIQUITIN LIGASE, UBIQUITINATION, COILED-COIL, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR X.H.LOU,Y.ZHUANG,B.B.MA,X.C.LI REVDAT 1 24-APR-24 8SDE 0 JRNL AUTH X.H.LOU,Y.ZHUANG,B.B.MA,X.C.LI JRNL TITL ELECTROSTATIC-MEDIATED TETRAMERIZATION OF THE COILED-COIL JRNL TITL 2 DOMAIN IN TRIM29 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 5394 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.267 REMARK 3 FREE R VALUE TEST SET COUNT : 392 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.27 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 342 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 19 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 744 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 86.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.30100 REMARK 3 B22 (A**2) : 2.59600 REMARK 3 B33 (A**2) : -7.89700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.339 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.255 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.274 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 758 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1009 ; 1.785 ; 1.652 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 88 ; 4.247 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 48 ;37.127 ;25.208 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 169 ;20.319 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;18.121 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 99 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 541 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 294 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 516 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 16 ; 0.076 ; 0.200 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): 355 ; 6.261 ; 6.169 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 442 ; 7.953 ; 9.224 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 402 ;10.714 ; 7.700 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 566 ;16.004 ;10.990 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 258 A 346 REMARK 3 RESIDUE RANGE : A 401 A 415 REMARK 3 RESIDUE RANGE : A 501 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): -15.2666 -8.1262 -23.6626 REMARK 3 T TENSOR REMARK 3 T11: 0.1050 T22: 0.1679 REMARK 3 T33: 0.1474 T12: 0.0044 REMARK 3 T13: -0.0004 T23: -0.0224 REMARK 3 L TENSOR REMARK 3 L11: 0.0556 L22: 0.5027 REMARK 3 L33: 12.6897 L12: 0.0076 REMARK 3 L13: 0.1946 L23: 2.4110 REMARK 3 S TENSOR REMARK 3 S11: -0.0696 S12: 0.0226 S13: 0.0001 REMARK 3 S21: 0.0446 S22: -0.0943 S23: 0.0480 REMARK 3 S31: 0.1093 S32: -0.0762 S33: 0.1639 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 NOT BEEN USED REMARK 4 REMARK 4 8SDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5400 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.31900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% GLYCEROL, 38% MPD, AND 0.1M ACETIC REMARK 280 ACID PH4.7, VAPOR DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.52500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.81500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.75500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.52500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.81500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 53.75500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.52500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 23.81500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.75500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.52500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 23.81500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.75500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -45.05000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 -45.05000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 257 REMARK 465 VAL A 347 REMARK 465 ASP A 348 DBREF 8SDE A 259 348 UNP Q8R2Q0 TRI29_MOUSE 259 348 SEQADV 8SDE GLY A 257 UNP Q8R2Q0 EXPRESSION TAG SEQADV 8SDE PRO A 258 UNP Q8R2Q0 EXPRESSION TAG SEQRES 1 A 92 GLY PRO THR VAL GLU GLU ALA LYS ALA GLU LYS GLU THR SEQRES 2 A 92 GLU LEU SER LEU GLN LYS GLU GLN LEU GLN LEU LYS ILE SEQRES 3 A 92 ILE GLU ILE GLU ASP ASP VAL GLU LYS TRP GLN LYS GLU SEQRES 4 A 92 LYS ASP ARG ILE LYS SER PHE THR THR ASN GLU LYS ALA SEQRES 5 A 92 ILE LEU GLU GLN ASN PHE ARG ASP LEU VAL ARG GLU LEU SEQRES 6 A 92 GLU LYS GLN LYS GLU GLU VAL ARG ALA ALA LEU GLU GLN SEQRES 7 A 92 ARG GLU GLN ASP ALA VAL ASP GLN VAL LYS VAL ILE VAL SEQRES 8 A 92 ASP HET GOL A 501 6 HET GOL A 502 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *15(H2 O) HELIX 1 AA1 THR A 259 GLN A 342 1 84 CRYST1 45.050 47.630 107.510 90.00 90.00 90.00 I 2 2 2 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 0.022198 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020995 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009301 0.00000