PDB Short entry for 3RD2 HEADER TRANSCRIPTION 31-MAR-11 3RD2 TITLE NIP45 SUMO-LIKE DOMAIN 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NFATC2-INTERACTING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SUMO-LIKE DOMAIN; COMPND 5 SYNONYM: 45 KDA NF-AT-INTERACTING PROTEIN, 45 KDA NFAT-INTERACTING COMPND 6 PROTEIN, NUCLEAR FACTOR OF ACTIVATED T-CELLS, CYTOPLASMIC 2- COMPND 7 INTERACTING PROTEIN; 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: NFATC2IP, NIP45; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SUMO-LIKE DOMAIN 2, PROTEIN:PROTEIN INTERACTION, UBC9, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.J.P.PERRY,A.S.ARVAI,J.A.TAINER REVDAT 3 13-SEP-23 3RD2 1 SEQADV REVDAT 2 21-SEP-11 3RD2 1 JRNL VERSN REVDAT 1 27-APR-11 3RD2 0 JRNL AUTH J.PRUDDEN,J.J.PERRY,M.NIE,A.A.VASHISHT,A.S.ARVAI,C.HITOMI, JRNL AUTH 2 G.GUENTHER,J.A.WOHLSCHLEGEL,J.A.TAINER,M.N.BODDY JRNL TITL DNA REPAIR AND GLOBAL SUMOYLATION ARE REGULATED BY DISTINCT JRNL TITL 2 UBC9 NONCOVALENT COMPLEXES. JRNL REF MOL.CELL.BIOL. V. 31 2299 2011 JRNL REFN ISSN 0270-7306 JRNL PMID 21444718 JRNL DOI 10.1128/MCB.05188-11 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6_289 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 8866 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 431 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 32.7101 - 2.3087 0.99 2922 143 0.1681 0.2006 REMARK 3 2 2.3087 - 1.8325 1.00 2883 137 0.1587 0.2081 REMARK 3 3 1.8325 - 1.6000 0.92 2630 151 0.1865 0.2598 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 : 0.35 REMARK 3 B_SOL : 40.78 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.32230 REMARK 3 B22 (A**2) : -0.04710 REMARK 3 B33 (A**2) : 0.36940 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.03610 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 : 0.005 674 REMARK 3 ANGLE : 1.023 906 REMARK 3 CHIRALITY : 0.075 95 REMARK 3 PLANARITY : 0.003 118 REMARK 3 DIHEDRAL : 13.207 255 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 3RD2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 12.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.13 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8880 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 40.6000 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 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3GOE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM 118 SULFATE, 100 MM REMARK 280 BICINE PH 9.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 273K 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 16.22300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 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 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 HIS A 339 CG ND1 CD2 CE1 NE2 DBREF 3RD2 A 345 419 UNP Q8NCF5 NF2IP_HUMAN 345 419 SEQADV 3RD2 MET A 338 UNP Q8NCF5 EXPRESSION TAG SEQADV 3RD2 HIS A 339 UNP Q8NCF5 EXPRESSION TAG SEQADV 3RD2 HIS A 340 UNP Q8NCF5 EXPRESSION TAG SEQADV 3RD2 HIS A 341 UNP Q8NCF5 EXPRESSION TAG SEQADV 3RD2 HIS A 342 UNP Q8NCF5 EXPRESSION TAG SEQADV 3RD2 HIS A 343 UNP Q8NCF5 EXPRESSION TAG SEQADV 3RD2 HIS A 344 UNP Q8NCF5 EXPRESSION TAG SEQRES 1 A 82 MET HIS HIS HIS HIS HIS HIS SER GLN GLN LEU GLN LEU SEQRES 2 A 82 ARG VAL GLN GLY LYS GLU LYS HIS GLN THR LEU GLU VAL SEQRES 3 A 82 SER LEU SER ARG ASP SER PRO LEU LYS THR LEU MET SER SEQRES 4 A 82 HIS TYR GLU GLU ALA MET GLY LEU SER GLY ARG LYS LEU SEQRES 5 A 82 SER PHE PHE PHE ASP GLY THR LYS LEU SER GLY ARG GLU SEQRES 6 A 82 LEU PRO ALA ASP LEU GLY MET GLU SER GLY ASP LEU ILE SEQRES 7 A 82 GLU VAL TRP GLY FORMUL 2 HOH *108(H2 O) HELIX 1 1 PRO A 370 GLY A 383 1 14 HELIX 2 2 LEU A 403 GLY A 408 5 6 SHEET 1 A 5 THR A 360 SER A 366 0 SHEET 2 A 5 GLN A 347 GLN A 353 -1 N LEU A 350 O VAL A 363 SHEET 3 A 5 LEU A 414 TRP A 418 1 O ILE A 415 N ARG A 351 SHEET 4 A 5 SER A 390 PHE A 393 -1 N PHE A 392 O GLU A 416 SHEET 5 A 5 THR A 396 LYS A 397 -1 O THR A 396 N PHE A 393 CRYST1 32.521 32.446 32.925 90.00 96.65 90.00 P 1 21 1 2 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 0.030749 0.000000 0.003587 0.00000 SCALE2 0.000000 0.030820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030578 0.00000