PDB Short entry for 3DO7 HEADER TRANSCRIPTION/DNA 03-JUL-08 3DO7 TITLE X-RAY STRUCTURE OF A NF-KB P52/RELB/DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: AVIAN RETICULOENDOTHELIOSIS VIRAL (V-REL) COMPND 3 ONCOGENE RELATED B; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RHR (UNP RESIDUES 88-383); COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NUCLEAR FACTOR NF-KAPPA-B P100 SUBUNIT; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RHR (UNP RESIDUES 37-329); COMPND 11 SYNONYM: DNA-BINDING FACTOR KBF2, H2TF1, LYMPHOCYTE COMPND 12 TRANSLOCATION CHROMOSOME 10, ONCOGENE LYT-10, LYT10, COMPND 13 NUCLEAR FACTOR NF-KAPPA-B P52 SUBUNIT; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: 5'- COMPND 17 D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'; COMPND 18 CHAIN: C, D, E; COMPND 19 FRAGMENT: KAPPA B SITE; COMPND 20 ENGINEERED: YES; COMPND 21 OTHER_DETAILS: KAPPAB DNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RELB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: T7 PROMOTER; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: NFKB2, LYT10; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: T7 PROMOTER; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 21 MOL_ID: 3; SOURCE 22 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, NUCLEUS, ACTIVATOR, ALTERNATIVE KEYWDS 2 SPLICING, ANK REPEAT, CHROMOSOMAL REARRANGEMENT, CYTOPLASM, KEYWDS 3 DISEASE MUTATION, DNA-BINDING, PHOSPHOPROTEIN, KEYWDS 4 POLYMORPHISM, PROTO-ONCOGENE, TRANSCRIPTION, TRANSCRIPTION KEYWDS 5 REGULATION, UBL CONJUGATION, TRANSCRIPTION/DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.FUSCO,D.B.HUANG,D.MILLER,D.VU,G.GHOSH REVDAT 2 18-AUG-09 3DO7 1 SOURCE REVDAT 1 21-JUL-09 3DO7 0 JRNL AUTH A.FUSCO,D.B.HUANG,D.MILLER,D.VU,G.GHOSH JRNL TITL NF-KAPPPAB P52:RELB HETERODIMER USES DIFFERENT JRNL TITL 2 BINDING MODES TO RECOGNIZE DIFFERENT KAPPAB DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 3.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 53121.680 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.4 REMARK 3 NUMBER OF REFLECTIONS : 14478 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 SET) : 0.230 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 851 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.24 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 40.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1114 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 62 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4595 REMARK 3 NUCLEIC ACID ATOMS : 644 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 85.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 97.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 30.17000 REMARK 3 B22 (A**2) : -21.71000 REMARK 3 B33 (A**2) : -8.46000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.07 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.20 REMARK 3 BSOL : 10.17 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DO7 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-08. REMARK 100 THE RCSB ID CODE IS RCSB048281. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 106 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16342 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : 14.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% PEG 4000, 50 MM NACL, 0.1% BOG, REMARK 280 10 MM DTT, 10 MM NACITRATE AND 2 MM SPERMIDINE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 94.79500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 94.79500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 38.82000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.06500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.82000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.06500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 94.79500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.82000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 62.06500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 94.79500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.82000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 62.06500 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 350 REMARK 350 BIOMOLECULE: 2 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: 840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 BIOMT1 2 -1.000000 0.000000 0.000000 77.64000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 94.79500 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 DC C 12 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 ARG A 154 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 191 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 252 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 49 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 ARG B 162 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 241 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 262 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 264 CG CD OE1 OE2 REMARK 470 TYR B 294 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 296 CG CD CE NZ REMARK 470 PHE B 323 CG CD1 CD2 CE1 CE2 CZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG C 5 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG E 3 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 93 52.32 -66.21 REMARK 500 VAL A 95 26.85 -65.48 REMARK 500 PRO A 99 77.64 -21.99 REMARK 500 CYS A 100 -63.07 -160.24 REMARK 500 PRO A 101 -145.55 -72.89 REMARK 500 ARG A 102 73.27 69.51 REMARK 500 LYS A 112 122.75 -30.04 REMARK 500 GLN A 113 -82.42 -44.90 REMARK 500 SER A 126 -31.40 -149.74 REMARK 500 SER A 129 4.54 -153.42 REMARK 500 ILE A 130 134.15 -25.00 REMARK 500 GLU A 133 -59.26 -5.28 REMARK 500 SER A 134 78.51 -108.80 REMARK 500 SER A 135 -132.49 -90.90 REMARK 500 THR A 136 141.50 170.01 REMARK 500 ALA A 138 -119.88 -86.98 REMARK 500 THR A 141 -175.68 -61.05 REMARK 500 PRO A 143 97.73 -61.73 REMARK 500 ASP A 149 28.37 84.44 REMARK 500 TRP A 164 -155.58 -54.16 REMARK 500 TRP A 167 -69.62 -15.89 REMARK 500 HIS A 169 46.48 -63.38 REMARK 500 ARG A 170 161.80 -49.71 REMARK 500 PRO A 192 -80.09 -49.27 REMARK 500 HIS A 193 -86.69 -44.72 REMARK 500 VAL A 194 88.28 -48.82 REMARK 500 SER A 195 86.69 65.05 REMARK 500 ARG A 197 127.70 -174.66 REMARK 500 ASN A 201 -102.92 -108.10 REMARK 500 ASN A 202 91.31 -60.00 REMARK 500 ARG A 209 160.07 -49.31 REMARK 500 LYS A 211 24.76 -65.04 REMARK 500 GLU A 212 -55.12 -134.37 REMARK 500 ILE A 213 -72.93 0.73 REMARK 500 LEU A 223 27.34 -71.04 REMARK 500 ASP A 226 88.19 -177.79 REMARK 500 PRO A 227 6.48 -51.65 REMARK 500 TYR A 228 -0.75 -153.11 REMARK 500 ASN A 229 75.48 42.35 REMARK 500 ALA A 230 44.38 -144.98 REMARK 500 LYS A 234 86.22 66.08 REMARK 500 ASN A 235 -80.94 162.22 REMARK 500 GLN A 237 -106.43 -112.09 REMARK 500 GLU A 238 84.48 55.42 REMARK 500 ASP A 240 84.67 -65.91 REMARK 500 MET A 241 6.72 -66.05 REMARK 500 GLN A 256 -176.94 -65.12 REMARK 500 MET A 262 -158.15 -70.76 REMARK 500 PRO A 269 134.56 -10.88 REMARK 500 SER A 279 -171.19 -62.12 REMARK 500 ARG A 282 116.97 -169.43 REMARK 500 ARG A 285 160.76 173.13 REMARK 500 ASN A 287 -95.35 -48.17 REMARK 500 LEU A 301 144.38 -178.32 REMARK 500 LYS A 305 114.67 -35.60 REMARK 500 GLU A 309 24.46 -65.78 REMARK 500 ASP A 310 76.08 -176.97 REMARK 500 ILE A 311 146.14 -179.16 REMARK 500 SER A 319 -27.80 88.67 REMARK 500 GLU A 321 84.66 -156.38 REMARK 500 ALA A 324 -171.53 -50.08 REMARK 500 ARG A 333 54.54 29.06 REMARK 500 GLN A 334 9.98 53.90 REMARK 500 ILE A 335 30.63 -140.21 REMARK 500 ALA A 336 143.75 -175.65 REMARK 500 TYR A 344 -178.46 -62.13 REMARK 500 ASP A 346 81.34 53.26 REMARK 500 GLU A 348 -14.48 -146.03 REMARK 500 ILE A 349 107.82 -29.05 REMARK 500 SER A 350 -153.69 35.96 REMARK 500 GLU A 351 157.83 -44.45 REMARK 500 LEU A 362 23.71 -63.92 REMARK 500 THR A 363 -46.04 -131.12 REMARK 500 VAL A 366 116.48 -32.90 REMARK 500 ARG A 378 -155.73 48.46 REMARK 500 ASP A 379 -175.33 -61.33 REMARK 500 HIS A 380 36.71 -142.96 REMARK 500 SER A 382 -170.03 176.62 REMARK 500 PRO B 38 60.06 -64.07 REMARK 500 LEU B 65 109.43 -43.08 REMARK 500 PRO B 66 -167.13 -69.29 REMARK 500 SER B 69 32.74 -81.76 REMARK 500 LYS B 72 176.40 -54.31 REMARK 500 PRO B 78 82.01 -51.63 REMARK 500 TYR B 85 -169.86 -76.08 REMARK 500 GLU B 86 19.47 -141.27 REMARK 500 ILE B 91 87.54 -151.68 REMARK 500 ALA B 104 -152.07 -50.32 REMARK 500 GLN B 113 56.77 -92.91 REMARK 500 SER B 115 64.33 -65.24 REMARK 500 GLU B 116 -86.46 48.12 REMARK 500 LYS B 127 -66.13 -92.14 REMARK 500 ASP B 128 95.71 -58.35 REMARK 500 ASN B 134 -90.45 -61.51 REMARK 500 ASN B 135 104.12 -59.45 REMARK 500 MET B 146 -1.14 -58.42 REMARK 500 MET B 147 -86.22 -85.09 REMARK 500 THR B 149 -79.94 -71.14 REMARK 500 MET B 150 -39.29 -39.57 REMARK 500 GLN B 157 -9.72 -59.63 REMARK 500 ARG B 158 -101.73 -116.59 REMARK 500 ARG B 162 -171.06 56.79 REMARK 500 GLN B 164 -167.67 -69.35 REMARK 500 GLN B 176 -70.49 -71.52 REMARK 500 ALA B 178 -75.24 -66.56 REMARK 500 GLU B 180 29.76 -75.06 REMARK 500 LEU B 181 -23.11 -152.07 REMARK 500 VAL B 184 34.04 -148.66 REMARK 500 ASP B 186 102.89 -49.45 REMARK 500 LEU B 187 5.49 -61.06 REMARK 500 SER B 201 -170.71 49.46 REMARK 500 ASP B 202 18.28 47.27 REMARK 500 SER B 206 -12.05 177.51 REMARK 500 PRO B 208 -174.99 -55.23 REMARK 500 LEU B 209 -156.00 -152.61 REMARK 500 PRO B 216 153.93 -31.15 REMARK 500 SER B 220 4.37 -52.25 REMARK 500 SER B 222 119.98 -39.47 REMARK 500 ALA B 225 -29.95 -161.34 REMARK 500 SER B 226 -172.86 -55.13 REMARK 500 LEU B 228 78.29 -62.75 REMARK 500 ARG B 232 169.01 179.21 REMARK 500 ASP B 234 -115.61 -63.21 REMARK 500 SER B 239 -95.03 -159.15 REMARK 500 VAL B 240 -67.90 -173.13 REMARK 500 ARG B 241 -131.61 -67.55 REMARK 500 LYS B 252 127.65 -32.91 REMARK 500 LYS B 255 -5.78 -52.42 REMARK 500 ASP B 256 -152.35 -145.92 REMARK 500 ASP B 257 29.41 43.36 REMARK 500 GLU B 259 124.99 -179.59 REMARK 500 TYR B 263 -162.05 179.07 REMARK 500 GLU B 264 74.43 165.01 REMARK 500 GLU B 267 -147.97 -94.52 REMARK 500 ASN B 268 47.23 -100.32 REMARK 500 TRP B 270 120.73 152.15 REMARK 500 ALA B 272 137.13 176.02 REMARK 500 PHE B 273 -139.83 -99.48 REMARK 500 ASP B 275 105.39 -177.09 REMARK 500 THR B 279 -32.95 -25.89 REMARK 500 GLN B 284 -42.15 63.34 REMARK 500 TYR B 285 35.73 -97.51 REMARK 500 HIS B 295 34.69 -74.78 REMARK 500 ILE B 299 31.27 -72.63 REMARK 500 GLU B 300 -138.70 -70.81 REMARK 500 ARG B 301 170.27 -59.05 REMARK 500 LYS B 312 -81.60 -63.86 REMARK 500 ASP B 316 -162.18 -74.19 REMARK 500 VAL B 317 -178.02 -172.43 REMARK 500 SER B 318 -151.72 -135.66 REMARK 500 LEU B 328 153.07 -45.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG E 3 0.06 SIDE_CHAIN REMARK 500 DA E 7 0.07 SIDE_CHAIN REMARK 500 DT E 8 0.08 SIDE_CHAIN REMARK 500 DT E 9 0.06 SIDE_CHAIN REMARK 500 DC E 10 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH E 419 DISTANCE = 12.61 ANGSTROMS REMARK 525 HOH B 408 DISTANCE = 5.17 ANGSTROMS REMARK 525 HOH A 420 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH A 439 DISTANCE = 5.28 ANGSTROMS REMARK 525 HOH B 433 DISTANCE = 7.79 ANGSTROMS REMARK 525 HOH A 446 DISTANCE = 8.90 ANGSTROMS REMARK 525 HOH B 441 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH B 447 DISTANCE = 6.82 ANGSTROMS DBREF 3DO7 A 88 383 UNP Q8VE46 Q8VE46_MOUSE 88 383 DBREF 3DO7 B 37 329 UNP Q00653 NFKB2_HUMAN 37 329 DBREF 3DO7 C 2 12 PDB 3DO7 3DO7 2 12 DBREF 3DO7 D 13 23 PDB 3DO7 3DO7 13 23 DBREF 3DO7 E 2 12 PDB 3DO7 3DO7 2 12 SEQADV 3DO7 GLN A 142 UNP Q8VE46 LEU 142 CONFLICT SEQADV 3DO7 ASP B 200 UNP Q00653 ALA 200 CONFLICT SEQRES 1 A 296 SER CYS THR LEU GLY ARG LEU VAL SER PRO GLY PRO CYS SEQRES 2 A 296 PRO ARG PRO TYR LEU VAL ILE THR GLU GLN PRO LYS GLN SEQRES 3 A 296 ARG GLY MET ARG PHE ARG TYR GLU CYS GLU GLY ARG SER SEQRES 4 A 296 ALA GLY SER ILE LEU GLY GLU SER SER THR GLU ALA SER SEQRES 5 A 296 LYS THR GLN PRO ALA ILE GLU LEU ARG ASP CYS GLY GLY SEQRES 6 A 296 LEU ARG GLU VAL GLU VAL THR ALA CYS LEU VAL TRP LYS SEQRES 7 A 296 ASP TRP PRO HIS ARG VAL HIS PRO HIS SER LEU VAL GLY SEQRES 8 A 296 LYS ASP CYS THR ASP GLY VAL CYS ARG VAL ARG LEU ARG SEQRES 9 A 296 PRO HIS VAL SER PRO ARG HIS SER PHE ASN ASN LEU GLY SEQRES 10 A 296 ILE GLN CYS VAL ARG LYS LYS GLU ILE GLU ALA ALA ILE SEQRES 11 A 296 GLU ARG LYS ILE GLN LEU GLY ILE ASP PRO TYR ASN ALA SEQRES 12 A 296 GLY SER LEU LYS ASN HIS GLN GLU VAL ASP MET ASN VAL SEQRES 13 A 296 VAL ARG ILE CYS PHE GLN ALA SER TYR ARG ASP GLN GLN SEQRES 14 A 296 GLY HIS LEU HIS ARG MET ASP PRO ILE LEU SER GLU PRO SEQRES 15 A 296 VAL TYR ASP LYS LYS SER THR ASN THR SER GLU LEU ARG SEQRES 16 A 296 ILE CYS ARG ILE ASN LYS GLU SER GLY PRO CYS THR GLY SEQRES 17 A 296 GLY GLU GLU LEU TYR LEU LEU CYS ASP LYS VAL GLN LYS SEQRES 18 A 296 GLU ASP ILE SER VAL VAL PHE SER THR ALA SER TRP GLU SEQRES 19 A 296 GLY ARG ALA ASP PHE SER GLN ALA ASP VAL HIS ARG GLN SEQRES 20 A 296 ILE ALA ILE VAL PHE LYS THR PRO PRO TYR GLU ASP LEU SEQRES 21 A 296 GLU ILE SER GLU PRO VAL THR VAL ASN VAL PHE LEU GLN SEQRES 22 A 296 ARG LEU THR ASP GLY VAL CYS SER GLU PRO LEU PRO PHE SEQRES 23 A 296 THR TYR LEU PRO ARG ASP HIS ASP SER TYR SEQRES 1 B 293 GLY PRO TYR LEU VAL ILE VAL GLU GLN PRO LYS GLN ARG SEQRES 2 B 293 GLY PHE ARG PHE ARG TYR GLY CYS GLU GLY PRO SER HIS SEQRES 3 B 293 GLY GLY LEU PRO GLY ALA SER SER GLU LYS GLY ARG LYS SEQRES 4 B 293 THR TYR PRO THR VAL LYS ILE CYS ASN TYR GLU GLY PRO SEQRES 5 B 293 ALA LYS ILE GLU VAL ASP LEU VAL THR HIS SER ASP PRO SEQRES 6 B 293 PRO ARG ALA HIS ALA HIS SER LEU VAL GLY LYS GLN CYS SEQRES 7 B 293 SER GLU LEU GLY ILE CYS ALA VAL SER VAL GLY PRO LYS SEQRES 8 B 293 ASP MET THR ALA GLN PHE ASN ASN LEU GLY VAL LEU HIS SEQRES 9 B 293 VAL THR LYS LYS ASN MET MET GLY THR MET ILE GLN LYS SEQRES 10 B 293 LEU GLN ARG GLN ARG LEU ARG SER ARG PRO GLN GLY LEU SEQRES 11 B 293 THR GLU ALA GLU GLN ARG GLU LEU GLU GLN GLU ALA LYS SEQRES 12 B 293 GLU LEU LYS LYS VAL MET ASP LEU SER ILE VAL ARG LEU SEQRES 13 B 293 ARG PHE SER ALA PHE LEU ARG ASP SER ASP GLY SER PHE SEQRES 14 B 293 SER LEU PRO LEU LYS PRO VAL ILE SER GLN PRO ILE HIS SEQRES 15 B 293 ASP SER LYS SER PRO GLY ALA SER ASN LEU LYS ILE SER SEQRES 16 B 293 ARG MET ASP LYS THR ALA GLY SER VAL ARG GLY GLY ASP SEQRES 17 B 293 GLU VAL TYR LEU LEU CYS ASP LYS VAL GLN LYS ASP ASP SEQRES 18 B 293 ILE GLU VAL ARG PHE TYR GLU ASP ASP GLU ASN GLY TRP SEQRES 19 B 293 GLN ALA PHE GLY ASP PHE SER PRO THR ASP VAL HIS LYS SEQRES 20 B 293 GLN TYR ALA ILE VAL PHE ARG THR PRO PRO TYR HIS LYS SEQRES 21 B 293 MET LYS ILE GLU ARG PRO VAL THR VAL PHE LEU GLN LEU SEQRES 22 B 293 LYS ARG LYS ARG GLY GLY ASP VAL SER ASP SER LYS GLN SEQRES 23 B 293 PHE THR TYR TYR PRO LEU VAL SEQRES 1 C 11 DC DG DG DG DA DA DT DT DC DC DC SEQRES 1 D 11 DC DG DG DG DA DA DT DT DC DC DC SEQRES 1 E 11 DC DG DG DG DA DA DT DT DC DC DC FORMUL 6 HOH *49(H2 O) HELIX 1 1 GLU A 212 LEU A 223 1 12 HELIX 2 2 SER A 327 ILE A 335 5 9 HELIX 3 3 CYS B 57 GLY B 59 5 3 HELIX 4 4 ASN B 145 ARG B 158 1 14 HELIX 5 5 THR B 167 LYS B 183 1 17 HELIX 6 6 SER B 277 VAL B 281 5 5 SHEET 1 A 3 TYR A 104 ILE A 107 0 SHEET 2 A 3 ALA A 144 ARG A 148 -1 O ARG A 148 N TYR A 104 SHEET 3 A 3 ARG A 197 SER A 199 -1 O HIS A 198 N ILE A 145 SHEET 1 B 5 ARG A 114 MET A 116 0 SHEET 2 B 5 VAL A 270 ASP A 272 1 O TYR A 271 N GLY A 115 SHEET 3 B 5 VAL A 243 PHE A 248 -1 N VAL A 244 O VAL A 270 SHEET 4 B 5 ALA A 160 VAL A 163 -1 N VAL A 163 O ARG A 245 SHEET 5 B 5 VAL A 185 CYS A 186 -1 O CYS A 186 N ALA A 160 SHEET 1 C 2 SER A 175 GLY A 178 0 SHEET 2 C 2 LEU A 203 GLN A 206 -1 O GLY A 204 N VAL A 177 SHEET 1 D 2 ILE A 283 ILE A 286 0 SHEET 2 D 2 LEU A 301 CYS A 303 -1 O LEU A 302 N CYS A 284 SHEET 1 E 4 SER A 290 PRO A 292 0 SHEET 2 E 4 LEU A 371 LEU A 376 1 O THR A 374 N GLY A 291 SHEET 3 E 4 VAL A 353 GLN A 360 -1 N VAL A 357 O LEU A 371 SHEET 4 E 4 SER A 312 VAL A 314 -1 N VAL A 314 O PHE A 358 SHEET 1 F 2 GLU A 297 LEU A 299 0 SHEET 2 F 2 PHE A 339 THR A 341 -1 O THR A 341 N GLU A 297 SHEET 1 G 3 TYR B 39 VAL B 41 0 SHEET 2 G 3 THR B 79 CYS B 83 -1 O LYS B 81 N VAL B 41 SHEET 3 G 3 THR B 130 GLN B 132 -1 O ALA B 131 N VAL B 80 SHEET 1 H 3 ARG B 54 TYR B 55 0 SHEET 2 H 3 GLY B 137 HIS B 140 1 O HIS B 140 N ARG B 54 SHEET 3 H 3 LEU B 109 VAL B 110 -1 N VAL B 110 O GLY B 137 SHEET 1 I 4 CYS B 120 VAL B 124 0 SHEET 2 I 4 ALA B 89 THR B 97 -1 N VAL B 93 O CYS B 120 SHEET 3 I 4 ILE B 189 ARG B 199 -1 O SER B 195 N GLU B 92 SHEET 4 I 4 VAL B 212 ILE B 213 -1 O VAL B 212 N PHE B 194 SHEET 1 J 3 PHE B 205 LEU B 207 0 SHEET 2 J 3 ILE B 189 ARG B 199 -1 N LEU B 198 O SER B 206 SHEET 3 J 3 ILE B 217 HIS B 218 -1 O ILE B 217 N VAL B 190 SHEET 1 K 3 ARG B 232 MET B 233 0 SHEET 2 K 3 GLU B 245 LEU B 249 -1 O LEU B 249 N ARG B 232 SHEET 3 K 3 ALA B 286 ARG B 290 -1 O ILE B 287 N LEU B 248 SHEET 1 L 3 PHE B 262 TYR B 263 0 SHEET 2 L 3 VAL B 305 LEU B 307 -1 O PHE B 306 N TYR B 263 SHEET 3 L 3 LYS B 321 PHE B 323 -1 O PHE B 323 N VAL B 305 SSBOND 1 CYS A 181 CYS A 186 1555 1555 2.64 SSBOND 2 CYS B 114 CYS B 120 1555 1555 2.03 CRYST1 77.640 124.130 189.590 90.00 90.00 90.00 C 2 2 21 24 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 0.012880 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008056 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005275 0.00000