HEADER SIGNALING PROTEIN 27-NOV-18 6N6S TITLE CRYSTAL STRUCTURE OF ABIN-1 UBAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TNFAIP3-INTERACTING PROTEIN 1; COMPND 3 CHAIN: B, D, A, C; COMPND 4 SYNONYM: A20-BINDING INHIBITOR OF NF-KAPPA-B ACTIVATION 1,ABIN-1,NEF- COMPND 5 ASSOCIATED FACTOR 1,NAF1,VIRION-ASSOCIATED NUCLEAR SHUTTLING PROTEIN, COMPND 6 MVAN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TNIP1, ABIN, NAF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS UBIQUITIN-BINDING DOMAIN, A20-BINDING PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.RAHIGHI,I.DIKIC,S.WAKATSUKI REVDAT 3 13-MAR-24 6N6S 1 REMARK REVDAT 2 28-AUG-19 6N6S 1 JRNL REVDAT 1 17-JUL-19 6N6S 0 JRNL AUTH L.HERHAUS,H.VAN DEN BEDEM,S.TANG,I.MASLENNIKOV,S.WAKATSUKI, JRNL AUTH 2 I.DIKIC,S.RAHIGHI JRNL TITL MOLECULAR RECOGNITION OF M1-LINKED UBIQUITIN CHAINS BY JRNL TITL 2 NATIVE AND PHOSPHORYLATED UBAN DOMAINS. JRNL REF J.MOL.BIOL. V. 431 3146 2019 JRNL REFN ESSN 1089-8638 JRNL PMID 31247202 JRNL DOI 10.1016/J.JMB.2019.06.012 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 6433 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) : 0.300 REMARK 3 R VALUE (WORKING SET) : 0.298 REMARK 3 FREE R VALUE : 0.328 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 333 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 469 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.3590 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.4430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2276 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 32 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 3.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.43000 REMARK 3 B22 (A**2) : -1.06000 REMARK 3 B33 (A**2) : -1.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.25000 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): 0.605 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.500 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.672 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.759 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.704 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2280 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2223 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3022 ; 1.269 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5221 ; 0.844 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 263 ; 5.075 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;32.668 ;26.714 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 550 ;14.459 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;11.714 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 335 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2444 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 379 ; 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): 1064 ; 0.461 ; 0.304 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1063 ; 0.461 ; 0.303 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1323 ; 0.852 ; 0.448 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1324 ; 0.852 ; 0.448 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1215 ; 0.374 ; 0.380 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1213 ; 0.366 ; 0.378 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1699 ; 0.744 ; 0.549 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2547 ; 1.808 ; 3.621 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2548 ; 1.810 ; 3.625 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 : NULL 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 6N6S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000238145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6860 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.470 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.10400 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M SODIUM MALONATE PH REMARK 280 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -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 24.28763 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.39000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.18385 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 24.28763 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.39000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 52.18385 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: B, D, A, 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 B 461 REMARK 465 SER B 462 REMARK 465 LEU B 463 REMARK 465 LYS B 529 REMARK 465 ALA B 530 REMARK 465 LYS B 531 REMARK 465 GLU B 532 REMARK 465 GLY D 461 REMARK 465 SER D 462 REMARK 465 LEU D 463 REMARK 465 GLY A 461 REMARK 465 SER A 462 REMARK 465 LEU A 463 REMARK 465 ARG A 464 REMARK 465 ALA A 530 REMARK 465 LYS A 531 REMARK 465 GLU A 532 REMARK 465 LYS C 529 REMARK 465 ALA C 530 REMARK 465 LYS C 531 REMARK 465 GLU C 532 DBREF 6N6S B 463 532 UNP Q9WUU8 TNIP1_MOUSE 463 532 DBREF 6N6S D 463 532 UNP Q9WUU8 TNIP1_MOUSE 463 532 DBREF 6N6S A 463 532 UNP Q9WUU8 TNIP1_MOUSE 463 532 DBREF 6N6S C 463 532 UNP Q9WUU8 TNIP1_MOUSE 463 532 SEQADV 6N6S GLY B 461 UNP Q9WUU8 EXPRESSION TAG SEQADV 6N6S SER B 462 UNP Q9WUU8 EXPRESSION TAG SEQADV 6N6S GLY D 461 UNP Q9WUU8 EXPRESSION TAG SEQADV 6N6S SER D 462 UNP Q9WUU8 EXPRESSION TAG SEQADV 6N6S GLY A 461 UNP Q9WUU8 EXPRESSION TAG SEQADV 6N6S SER A 462 UNP Q9WUU8 EXPRESSION TAG SEQADV 6N6S GLY C 461 UNP Q9WUU8 EXPRESSION TAG SEQADV 6N6S SER C 462 UNP Q9WUU8 EXPRESSION TAG SEQRES 1 B 72 GLY SER LEU ARG LYS GLN GLU LEU VAL THR GLN ASN GLU SEQRES 2 B 72 LEU LEU LYS GLN GLN VAL LYS ILE PHE GLU GLU ASP PHE SEQRES 3 B 72 GLN ARG GLU ARG SER ASP ARG GLU ARG MET ASN GLU GLU SEQRES 4 B 72 LYS GLU GLU LEU LYS LYS GLN VAL GLU LYS LEU GLN ALA SEQRES 5 B 72 GLN VAL THR LEU THR ASN ALA GLN LEU LYS THR LEU LYS SEQRES 6 B 72 GLU GLU GLU LYS ALA LYS GLU SEQRES 1 D 72 GLY SER LEU ARG LYS GLN GLU LEU VAL THR GLN ASN GLU SEQRES 2 D 72 LEU LEU LYS GLN GLN VAL LYS ILE PHE GLU GLU ASP PHE SEQRES 3 D 72 GLN ARG GLU ARG SER ASP ARG GLU ARG MET ASN GLU GLU SEQRES 4 D 72 LYS GLU GLU LEU LYS LYS GLN VAL GLU LYS LEU GLN ALA SEQRES 5 D 72 GLN VAL THR LEU THR ASN ALA GLN LEU LYS THR LEU LYS SEQRES 6 D 72 GLU GLU GLU LYS ALA LYS GLU SEQRES 1 A 72 GLY SER LEU ARG LYS GLN GLU LEU VAL THR GLN ASN GLU SEQRES 2 A 72 LEU LEU LYS GLN GLN VAL LYS ILE PHE GLU GLU ASP PHE SEQRES 3 A 72 GLN ARG GLU ARG SER ASP ARG GLU ARG MET ASN GLU GLU SEQRES 4 A 72 LYS GLU GLU LEU LYS LYS GLN VAL GLU LYS LEU GLN ALA SEQRES 5 A 72 GLN VAL THR LEU THR ASN ALA GLN LEU LYS THR LEU LYS SEQRES 6 A 72 GLU GLU GLU LYS ALA LYS GLU SEQRES 1 C 72 GLY SER LEU ARG LYS GLN GLU LEU VAL THR GLN ASN GLU SEQRES 2 C 72 LEU LEU LYS GLN GLN VAL LYS ILE PHE GLU GLU ASP PHE SEQRES 3 C 72 GLN ARG GLU ARG SER ASP ARG GLU ARG MET ASN GLU GLU SEQRES 4 C 72 LYS GLU GLU LEU LYS LYS GLN VAL GLU LYS LEU GLN ALA SEQRES 5 C 72 GLN VAL THR LEU THR ASN ALA GLN LEU LYS THR LEU LYS SEQRES 6 C 72 GLU GLU GLU LYS ALA LYS GLU FORMUL 5 HOH *32(H2 O) HELIX 1 AA1 ARG B 464 GLU B 527 1 64 HELIX 2 AA2 LYS D 465 GLU D 532 1 68 HELIX 3 AA3 GLN A 466 LYS A 529 1 64 HELIX 4 AA4 SER C 462 GLU C 528 1 67 CRYST1 51.290 64.780 104.403 90.00 91.49 90.00 I 1 2 1 16 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 0.019497 0.000000 0.000506 0.00000 SCALE2 0.000000 0.015437 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009581 0.00000