HEADER TRANSCRIPTION 19-SEP-18 6MI4 TITLE STRUCTURE OF THE I65M MUTANT OF NEMO(51-112) WITH N- AND C-TERMINAL TITLE 2 COILED-COIL ADAPTORS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NF-KB ESSENTIAL MODULATOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: ROSETTA 2 DE3; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS COILED COIL, SCAFFOLDING, NF-KB PATHWAY, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.PELLEGRINI,A.H.BARCZEWSKI,D.F.MIERKE,M.J.RAGUSA REVDAT 4 15-NOV-23 6MI4 1 REMARK REVDAT 3 11-OCT-23 6MI4 1 REMARK REVDAT 2 11-DEC-19 6MI4 1 REMARK REVDAT 1 07-AUG-19 6MI4 0 JRNL AUTH A.H.BARCZEWSKI,M.J.RAGUSA,D.F.MIERKE,M.PELLEGRINI JRNL TITL THE IKK-BINDING DOMAIN OF NEMO IS AN IRREGULAR COILED COIL JRNL TITL 2 WITH A DYNAMIC BINDING INTERFACE. JRNL REF SCI REP V. 9 2950 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 30814588 JRNL DOI 10.1038/S41598-019-39588-2 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 10821 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 542 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 38.2902 - 3.9675 0.98 2653 141 0.2152 0.2211 REMARK 3 2 3.9675 - 3.1496 0.99 2554 134 0.2552 0.3219 REMARK 3 3 3.1496 - 2.7516 0.99 2567 134 0.2919 0.3801 REMARK 3 4 2.7516 - 2.5001 0.98 2505 133 0.3162 0.3850 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.57 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6MI4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000236542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979329 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10941 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 38.286 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.12370 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.77020 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.380 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: 3BRV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.0, 5.8% PGA-LM, 5.45% REMARK 280 PEG 20,000 MOTHER LIQUOR IN MRC2 96 WELL SITTING DROP PLATES., REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 17.06200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 19 REMARK 465 ARG B 142 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 A 141 -58.86 -154.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6MI3 RELATED DB: PDB REMARK 900 SAME PROTEIN, WITHOUT I65M MUTATION DBREF 6MI4 A 19 142 PDB 6MI4 6MI4 19 142 DBREF 6MI4 B 19 142 PDB 6MI4 6MI4 19 142 SEQRES 1 A 124 GLY SER TRP SER VAL LYS GLU LEU GLU ASP LYS ASN GLU SEQRES 2 A 124 GLU LEU LEU SER GLU ILE ALA HIS LEU LYS ASN GLU VAL SEQRES 3 A 124 ALA ARG LEU LYS LYS LEU LEU GLN ARG CYS LEU ALA ALA SEQRES 4 A 124 ASN GLN GLU LEU ARG ASP ALA MSE ARG GLN SER ASN GLN SEQRES 5 A 124 ILE LEU ARG GLU ARG ALA GLU GLU LEU LEU HIS PHE GLN SEQRES 6 A 124 ALA SER GLN ARG GLU GLU LYS GLU PHE LEU MSE SER LYS SEQRES 7 A 124 PHE GLN GLU ALA ARG LYS LEU VAL GLU ARG LEU GLY LEU SEQRES 8 A 124 GLU LYS LEU GLU LEU GLU ASP LYS ASN GLU GLU LEU LEU SEQRES 9 A 124 SER GLU ILE ALA HIS LEU LYS ASN GLU VAL ALA ARG LEU SEQRES 10 A 124 LYS LYS LEU VAL GLY GLU ARG SEQRES 1 B 124 GLY SER TRP SER VAL LYS GLU LEU GLU ASP LYS ASN GLU SEQRES 2 B 124 GLU LEU LEU SER GLU ILE ALA HIS LEU LYS ASN GLU VAL SEQRES 3 B 124 ALA ARG LEU LYS LYS LEU LEU GLN ARG CYS LEU ALA ALA SEQRES 4 B 124 ASN GLN GLU LEU ARG ASP ALA MSE ARG GLN SER ASN GLN SEQRES 5 B 124 ILE LEU ARG GLU ARG ALA GLU GLU LEU LEU HIS PHE GLN SEQRES 6 B 124 ALA SER GLN ARG GLU GLU LYS GLU PHE LEU MSE SER LYS SEQRES 7 B 124 PHE GLN GLU ALA ARG LYS LEU VAL GLU ARG LEU GLY LEU SEQRES 8 B 124 GLU LYS LEU GLU LEU GLU ASP LYS ASN GLU GLU LEU LEU SEQRES 9 B 124 SER GLU ILE ALA HIS LEU LYS ASN GLU VAL ALA ARG LEU SEQRES 10 B 124 LYS LYS LEU VAL GLY GLU ARG HET MSE A 65 8 HET MSE A 94 8 HET MSE B 65 8 HET MSE B 94 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 HOH *59(H2 O) HELIX 1 AA1 SER A 22 GLY A 140 1 119 HELIX 2 AA2 SER B 22 GLY B 140 1 119 LINK C ALA A 64 N MSE A 65 1555 1555 1.33 LINK C MSE A 65 N ARG A 66 1555 1555 1.34 LINK C LEU A 93 N MSE A 94 1555 1555 1.33 LINK C MSE A 94 N SER A 95 1555 1555 1.34 LINK C ALA B 64 N MSE B 65 1555 1555 1.33 LINK C MSE B 65 N ARG B 66 1555 1555 1.34 LINK C LEU B 93 N MSE B 94 1555 1555 1.33 LINK C MSE B 94 N SER B 95 1555 1555 1.34 CRYST1 64.407 34.124 77.416 90.00 113.89 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 0.015526 0.000000 0.006876 0.00000 SCALE2 0.000000 0.029305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014127 0.00000