HEADER SIGNALING PROTEIN 14-JAN-16 5HKH TITLE CRYSTAL STRUCTURE OF UFM1 IN COMPLEX WITH UBA5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-FOLD MODIFIER 1; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ASP-ASN-GLU-TRP-GLY-ILE-GLU-LEU-VAL; COMPND 7 CHAIN: B; COMPND 8 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: UFM1, C13ORF20, BM-002; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.HUBER,V.DOETSCH,V.V.ROGOV,M.AKUTSU REVDAT 4 10-JAN-24 5HKH 1 REMARK REVDAT 3 16-OCT-19 5HKH 1 REMARK REVDAT 2 12-OCT-16 5HKH 1 JRNL REVDAT 1 09-MAR-16 5HKH 0 JRNL AUTH S.HABISOV,J.HUBER,Y.ICHIMURA,M.AKUTSU,N.ROGOVA,F.LOEHR, JRNL AUTH 2 D.G.MCEWAN,T.JOHANSEN,I.DIKIC,V.DOETSCH,M.KOMATSU,V.V.ROGOV, JRNL AUTH 3 V.KIRKIN JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF A NOVEL INTERACTION JRNL TITL 2 MOTIF WITHIN UFM1-ACTIVATING ENZYME 5 (UBA5) REQUIRED FOR JRNL TITL 3 BINDING TO UBIQUITIN-LIKE PROTEINS AND UFMYLATION. JRNL REF J.BIOL.CHEM. V. 291 9025 2016 JRNL REFN ESSN 1083-351X JRNL PMID 26929408 JRNL DOI 10.1074/JBC.M116.715474 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 8261 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.810 REMARK 3 FREE R VALUE TEST SET COUNT : 810 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 46.8846 - 4.6327 1.00 1300 148 0.1815 0.2307 REMARK 3 2 4.6327 - 3.6776 1.00 1268 112 0.1643 0.2032 REMARK 3 3 3.6776 - 3.2128 1.00 1224 151 0.2117 0.2729 REMARK 3 4 3.2128 - 2.9191 1.00 1219 143 0.2277 0.2779 REMARK 3 5 2.9191 - 2.7099 1.00 1200 130 0.2410 0.3364 REMARK 3 6 2.7099 - 2.5502 1.00 1240 126 0.2416 0.3051 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.010 1344 REMARK 3 ANGLE : 1.258 1828 REMARK 3 CHIRALITY : 0.076 219 REMARK 3 PLANARITY : 0.006 234 REMARK 3 DIHEDRAL : 14.445 492 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 5HKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8280 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 46.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1WXS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.01 M REMARK 280 MAGNESIUM ACETATE, 30% POLYETHYLENE GLYCOL 8000, 0.05 M SODIUM REMARK 280 CACODYLATE, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.35133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.67567 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.67567 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.35133 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 A 108 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 C -2 REMARK 465 ALA C -1 REMARK 465 MET C 0 REMARK 465 GLU C 1 REMARK 465 ARG C 81 REMARK 465 VAL C 82 REMARK 465 GLY C 83 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 34 CG CD CE NZ 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 C 25 -4.23 -57.16 REMARK 500 THR C 27 131.56 -34.81 REMARK 500 REMARK 500 REMARK: NULL DBREF 5HKH A 2 83 UNP P61960 UFM1_HUMAN 2 83 DBREF 5HKH B 338 346 PDB 5HKH 5HKH 338 346 DBREF 5HKH C 2 83 UNP P61960 UFM1_HUMAN 2 83 SEQADV 5HKH GLY A -2 UNP P61960 EXPRESSION TAG SEQADV 5HKH ALA A -1 UNP P61960 EXPRESSION TAG SEQADV 5HKH MET A 0 UNP P61960 EXPRESSION TAG SEQADV 5HKH GLU A 1 UNP P61960 EXPRESSION TAG SEQADV 5HKH GLY C -2 UNP P61960 EXPRESSION TAG SEQADV 5HKH ALA C -1 UNP P61960 EXPRESSION TAG SEQADV 5HKH MET C 0 UNP P61960 EXPRESSION TAG SEQADV 5HKH GLU C 1 UNP P61960 EXPRESSION TAG SEQRES 1 A 86 GLY ALA MET GLU SER LYS VAL SER PHE LYS ILE THR LEU SEQRES 2 A 86 THR SER ASP PRO ARG LEU PRO TYR LYS VAL LEU SER VAL SEQRES 3 A 86 PRO GLU SER THR PRO PHE THR ALA VAL LEU LYS PHE ALA SEQRES 4 A 86 ALA GLU GLU PHE LYS VAL PRO ALA ALA THR SER ALA ILE SEQRES 5 A 86 ILE THR ASN ASP GLY ILE GLY ILE ASN PRO ALA GLN THR SEQRES 6 A 86 ALA GLY ASN VAL PHE LEU LYS HIS GLY SER GLU LEU ARG SEQRES 7 A 86 ILE ILE PRO ARG ASP ARG VAL GLY SEQRES 1 B 9 ASP ASN GLU TRP GLY ILE GLU LEU VAL SEQRES 1 C 86 GLY ALA MET GLU SER LYS VAL SER PHE LYS ILE THR LEU SEQRES 2 C 86 THR SER ASP PRO ARG LEU PRO TYR LYS VAL LEU SER VAL SEQRES 3 C 86 PRO GLU SER THR PRO PHE THR ALA VAL LEU LYS PHE ALA SEQRES 4 C 86 ALA GLU GLU PHE LYS VAL PRO ALA ALA THR SER ALA ILE SEQRES 5 C 86 ILE THR ASN ASP GLY ILE GLY ILE ASN PRO ALA GLN THR SEQRES 6 C 86 ALA GLY ASN VAL PHE LEU LYS HIS GLY SER GLU LEU ARG SEQRES 7 C 86 ILE ILE PRO ARG ASP ARG VAL GLY FORMUL 4 HOH *25(H2 O) HELIX 1 AA1 PRO A 28 PHE A 40 1 13 HELIX 2 AA2 THR A 62 GLY A 71 1 10 HELIX 3 AA3 PRO C 28 LYS C 41 1 14 HELIX 4 AA4 THR C 62 GLY C 71 1 10 SHEET 1 AA1 5 ALA A 48 THR A 51 0 SHEET 2 AA1 5 GLU A 73 ILE A 77 -1 O ILE A 77 N ALA A 48 SHEET 3 AA1 5 LYS A 3 THR A 9 1 N THR A 9 O ILE A 76 SHEET 4 AA1 5 TYR A 18 PRO A 24 -1 O VAL A 23 N VAL A 4 SHEET 5 AA1 5 GLU B 344 LEU B 345 -1 O GLU B 344 N SER A 22 SHEET 1 AA2 4 TYR C 18 PRO C 24 0 SHEET 2 AA2 4 LYS C 3 THR C 9 -1 N ILE C 8 O LYS C 19 SHEET 3 AA2 4 GLU C 73 ILE C 77 1 O LEU C 74 N THR C 9 SHEET 4 AA2 4 ALA C 48 THR C 51 -1 N ALA C 48 O ILE C 77 CRYST1 82.656 82.656 62.027 90.00 90.00 120.00 P 32 2 1 12 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 0.012098 0.006985 0.000000 0.00000 SCALE2 0.000000 0.013970 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016122 0.00000