HEADER TRANSFERASE 30-MAR-12 4EFO TITLE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE DOMAIN OF HUMAN TBK1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE TBK1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UBIQUITIN-LIKE DOMAIN, UNP RESIDUE 302-383; COMPND 5 SYNONYM: NF-KAPPA-B-ACTIVATING KINASE, T2K, TANK-BINDING KINASE 1; COMPND 6 EC: 2.7.11.1; COMPND 7 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: TBK1, NAK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN LIKE DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.LI,J.LI,A.MIYAHIRA,J.SUN,Y.LIU,G.CHENG,H.LIANG REVDAT 2 20-MAR-24 4EFO 1 SEQADV REVDAT 1 27-JUN-12 4EFO 0 JRNL AUTH J.LI,J.LI,A.MIYAHIRA,J.SUN,Y.LIU,G.CHENG,H.LIANG JRNL TITL CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE DOMAIN OF HUMAN JRNL TITL 2 TBK1. JRNL REF PROTEIN CELL V. 3 383 2012 JRNL REFN ISSN 1674-800X JRNL PMID 22610919 JRNL DOI 10.1007/S13238-012-2929-1 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 19627 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1004 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.8619 - 3.3836 1.00 2722 156 0.1589 0.1717 REMARK 3 2 3.3836 - 2.6861 1.00 2662 148 0.1755 0.2205 REMARK 3 3 2.6861 - 2.3467 1.00 2690 131 0.1803 0.2229 REMARK 3 4 2.3467 - 2.1322 1.00 2660 134 0.1666 0.2157 REMARK 3 5 2.1322 - 1.9794 1.00 2656 151 0.1587 0.2120 REMARK 3 6 1.9794 - 1.8627 1.00 2627 150 0.1681 0.2118 REMARK 3 7 1.8627 - 1.7695 0.98 2606 134 0.1859 0.2556 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 43.16 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.09620 REMARK 3 B22 (A**2) : 0.94500 REMARK 3 B33 (A**2) : 3.15120 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.00240 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1434 REMARK 3 ANGLE : 1.015 1942 REMARK 3 CHIRALITY : 0.069 226 REMARK 3 PLANARITY : 0.004 241 REMARK 3 DIHEDRAL : 13.744 521 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4EFO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071558. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19650 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.769 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD 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 (%): 46.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS,0.2M NACL,21% PEG 3350, REMARK 280 PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 23.89250 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 297 REMARK 465 PRO A 387 REMARK 465 HIS A 388 REMARK 465 ARG A 389 REMARK 465 ASP A 390 REMARK 465 GLY B 297 REMARK 465 PRO B 298 REMARK 465 LEU B 299 REMARK 465 GLY B 300 REMARK 465 SER B 301 REMARK 465 THR B 302 REMARK 465 SER B 303 REMARK 465 ARG B 386 REMARK 465 PRO B 387 REMARK 465 HIS B 388 REMARK 465 ARG B 389 REMARK 465 ASP B 390 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 GLU B 362 CG CD OE1 OE2 REMARK 470 GLU B 375 CG CD OE1 OE2 REMARK 470 GLU B 385 CG CD OE1 OE2 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 OD1 ASN B 330 O HOH B 421 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 4EFO A 302 383 UNP Q9UHD2 TBK1_HUMAN 302 383 DBREF 4EFO B 302 383 UNP Q9UHD2 TBK1_HUMAN 302 383 SEQADV 4EFO GLY A 297 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO PRO A 298 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO LEU A 299 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO GLY A 300 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO SER A 301 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO LEU A 384 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO GLU A 385 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO ARG A 386 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO PRO A 387 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO HIS A 388 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO ARG A 389 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO ASP A 390 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO GLY B 297 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO PRO B 298 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO LEU B 299 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO GLY B 300 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO SER B 301 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO LEU B 384 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO GLU B 385 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO ARG B 386 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO PRO B 387 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO HIS B 388 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO ARG B 389 UNP Q9UHD2 EXPRESSION TAG SEQADV 4EFO ASP B 390 UNP Q9UHD2 EXPRESSION TAG SEQRES 1 A 94 GLY PRO LEU GLY SER THR SER ASP ILE LEU HIS ARG MET SEQRES 2 A 94 VAL ILE HIS VAL PHE SER LEU GLN GLN MET THR ALA HIS SEQRES 3 A 94 LYS ILE TYR ILE HIS SER TYR ASN THR ALA THR ILE PHE SEQRES 4 A 94 HIS GLU LEU VAL TYR LYS GLN THR LYS ILE ILE SER SER SEQRES 5 A 94 ASN GLN GLU LEU ILE TYR GLU GLY ARG ARG LEU VAL LEU SEQRES 6 A 94 GLU PRO GLY ARG LEU ALA GLN HIS PHE PRO LYS THR THR SEQRES 7 A 94 GLU GLU ASN PRO ILE PHE VAL VAL SER LEU GLU ARG PRO SEQRES 8 A 94 HIS ARG ASP SEQRES 1 B 94 GLY PRO LEU GLY SER THR SER ASP ILE LEU HIS ARG MET SEQRES 2 B 94 VAL ILE HIS VAL PHE SER LEU GLN GLN MET THR ALA HIS SEQRES 3 B 94 LYS ILE TYR ILE HIS SER TYR ASN THR ALA THR ILE PHE SEQRES 4 B 94 HIS GLU LEU VAL TYR LYS GLN THR LYS ILE ILE SER SER SEQRES 5 B 94 ASN GLN GLU LEU ILE TYR GLU GLY ARG ARG LEU VAL LEU SEQRES 6 B 94 GLU PRO GLY ARG LEU ALA GLN HIS PHE PRO LYS THR THR SEQRES 7 B 94 GLU GLU ASN PRO ILE PHE VAL VAL SER LEU GLU ARG PRO SEQRES 8 B 94 HIS ARG ASP FORMUL 3 HOH *214(H2 O) HELIX 1 1 GLY A 300 LEU A 306 5 7 HELIX 2 2 THR A 331 LYS A 344 1 14 HELIX 3 3 ILE A 346 SER A 348 5 3 HELIX 4 4 LEU A 366 PHE A 370 5 5 HELIX 5 5 ASP B 304 LEU B 306 5 3 HELIX 6 6 THR B 331 LYS B 344 1 14 HELIX 7 7 ILE B 346 SER B 348 5 3 HELIX 8 8 LEU B 366 PHE B 370 5 5 SHEET 1 A 5 THR A 320 HIS A 327 0 SHEET 2 A 5 ARG A 308 SER A 315 -1 N ILE A 311 O ILE A 324 SHEET 3 A 5 ILE A 379 SER A 383 1 O ILE A 379 N HIS A 312 SHEET 4 A 5 GLN A 350 TYR A 354 -1 N GLU A 351 O VAL A 382 SHEET 5 A 5 ARG A 357 LEU A 359 -1 O LEU A 359 N LEU A 352 SHEET 1 B 5 THR B 320 HIS B 327 0 SHEET 2 B 5 ARG B 308 SER B 315 -1 N SER B 315 O THR B 320 SHEET 3 B 5 ILE B 379 SER B 383 1 O VAL B 381 N PHE B 314 SHEET 4 B 5 GLN B 350 TYR B 354 -1 N ILE B 353 O PHE B 380 SHEET 5 B 5 ARG B 357 LEU B 359 -1 O ARG B 357 N TYR B 354 CISPEP 1 PRO A 298 LEU A 299 0 5.32 CRYST1 34.353 47.785 61.832 90.00 93.54 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 0.029110 0.000000 0.001798 0.00000 SCALE2 0.000000 0.020927 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016204 0.00000