HEADER DNA BINDING PROTEIN/DNA 04-NOV-21 7VUP TITLE STRUCTURE OF NF-KB P52 HOMODIMER BOUND TO +1/-1 SWAP P-SELECTIN KB DNA TITLE 2 FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR FACTOR NF-KAPPA-B P52 SUBUNIT; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*CP*AP*AP*GP*GP*GP*GP*AP*CP*TP*CP*CP*CP*CP*CP*TP*T)-3'); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'- COMPND 12 D(*AP*AP*GP*GP*GP*GP*GP*AP*GP*TP*CP*CP*CP*CP*TP*TP*G)-3'); COMPND 13 CHAIN: D; COMPND 14 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: NFKB2, LYT10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_TAXID: 9606 KEYWDS DNA-PROTEIN COMPLEX, TRANSCRIPTION FACTOR, TRANSCRIPTION, DNA BINDING KEYWDS 2 PROTEIN, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.A.MESHCHERYAKOV,V.Y.-F.WANG REVDAT 3 29-NOV-23 7VUP 1 REMARK REVDAT 2 15-MAR-23 7VUP 1 JRNL REVDAT 1 24-NOV-21 7VUP 0 JRNL AUTH W.PAN,V.A.MESHCHERYAKOV,T.LI,Y.WANG,G.GHOSH,V.Y.WANG JRNL TITL STRUCTURES OF NF-KAPPA B P52 HOMODIMER-DNA COMPLEXES JRNL TITL 2 RATIONALIZE BINDING MECHANISMS AND TRANSCRIPTION ACTIVATION. JRNL REF ELIFE V. 12 2023 JRNL REFN ESSN 2050-084X JRNL PMID 36779700 JRNL DOI 10.7554/ELIFE.86258 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 14233 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.271 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.848 REMARK 3 FREE R VALUE TEST SET COUNT : 690 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3165 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.4810 REMARK 3 BIN FREE R VALUE SET COUNT : 167 REMARK 3 BIN FREE R VALUE : 0.4790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4668 REMARK 3 NUCLEIC ACID ATOMS : 691 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 156.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 15.98400 REMARK 3 B22 (A**2) : 2.19000 REMARK 3 B33 (A**2) : -18.17400 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.622 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.788 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 58.887 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.864 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5544 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4966 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7617 ; 1.735 ; 1.668 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11510 ; 1.328 ; 1.586 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 590 ; 7.722 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 256 ;30.020 ;21.328 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 870 ;18.325 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;14.484 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 728 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5769 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1208 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 988 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 45 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2481 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 111 ; 0.194 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.509 ; 0.200 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): 2366 ;10.762 ;16.155 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2365 ;10.764 ;16.154 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2954 ;17.231 ;24.236 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2955 ;17.229 ;24.238 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3178 ; 9.381 ;16.974 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3178 ; 9.381 ;16.974 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4663 ;15.361 ;25.233 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4664 ;15.359 ;25.234 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 34 A 329 NULL REMARK 3 2 B 34 B 329 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7VUP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1300025425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14272 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 REMARK 200 RESOLUTION RANGE LOW (A) : 46.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.58 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: PHASER REMARK 200 STARTING MODEL: 1A3Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM MALONATE, PH 4.0, 50MM REMARK 280 CSCL, 2.5% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 41.99350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.28250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.14450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.28250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.99350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.14450 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, D 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 465 CYS A 4 REMARK 465 TYR A 5 REMARK 465 ASN A 6 REMARK 465 PRO A 7 REMARK 465 GLY A 8 REMARK 465 LEU A 9 REMARK 465 ASP A 10 REMARK 465 GLY A 11 REMARK 465 ILE A 12 REMARK 465 ILE A 13 REMARK 465 GLU A 14 REMARK 465 TYR A 15 REMARK 465 ASP A 16 REMARK 465 ASP A 17 REMARK 465 PHE A 18 REMARK 465 LYS A 19 REMARK 465 LEU A 20 REMARK 465 ASN A 21 REMARK 465 SER A 22 REMARK 465 SER A 23 REMARK 465 ILE A 24 REMARK 465 VAL A 25 REMARK 465 GLU A 26 REMARK 465 PRO A 27 REMARK 465 LYS A 28 REMARK 465 GLU A 29 REMARK 465 PRO A 30 REMARK 465 ALA A 31 REMARK 465 PRO A 32 REMARK 465 GLU A 33 REMARK 465 GLU A 330 REMARK 465 ASP A 331 REMARK 465 LYS A 332 REMARK 465 GLU A 333 REMARK 465 GLU A 334 REMARK 465 VAL A 335 REMARK 465 GLN A 336 REMARK 465 ARG A 337 REMARK 465 LYS A 338 REMARK 465 ARG A 339 REMARK 465 ARG A 340 REMARK 465 LYS A 341 REMARK 465 ALA A 342 REMARK 465 LEU A 343 REMARK 465 PRO A 344 REMARK 465 THR A 345 REMARK 465 PHE A 346 REMARK 465 SER A 347 REMARK 465 GLN A 348 REMARK 465 PRO A 349 REMARK 465 PHE A 350 REMARK 465 GLY A 351 REMARK 465 GLY A 352 REMARK 465 GLY A 353 REMARK 465 SER A 354 REMARK 465 HIS A 355 REMARK 465 MET A 356 REMARK 465 GLY A 357 REMARK 465 GLY A 358 REMARK 465 GLY A 359 REMARK 465 SER A 360 REMARK 465 GLY A 361 REMARK 465 GLY A 362 REMARK 465 ALA A 363 REMARK 465 ALA A 364 REMARK 465 GLY A 365 REMARK 465 GLY A 366 REMARK 465 TYR A 367 REMARK 465 GLY A 368 REMARK 465 GLY A 369 REMARK 465 ALA A 370 REMARK 465 GLY A 371 REMARK 465 GLY A 372 REMARK 465 GLY A 373 REMARK 465 GLY A 374 REMARK 465 SER A 375 REMARK 465 LEU A 376 REMARK 465 GLY A 377 REMARK 465 PHE A 378 REMARK 465 PHE A 379 REMARK 465 PRO A 380 REMARK 465 SER A 381 REMARK 465 SER A 382 REMARK 465 LEU A 383 REMARK 465 ALA A 384 REMARK 465 TYR A 385 REMARK 465 SER A 386 REMARK 465 PRO A 387 REMARK 465 TYR A 388 REMARK 465 GLN A 389 REMARK 465 SER A 390 REMARK 465 GLY A 391 REMARK 465 ALA A 392 REMARK 465 GLY A 393 REMARK 465 PRO A 394 REMARK 465 MET A 395 REMARK 465 GLY A 396 REMARK 465 CYS A 397 REMARK 465 TYR A 398 REMARK 465 DC C 18 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 SER B 3 REMARK 465 CYS B 4 REMARK 465 TYR B 5 REMARK 465 ASN B 6 REMARK 465 PRO B 7 REMARK 465 GLY B 8 REMARK 465 LEU B 9 REMARK 465 ASP B 10 REMARK 465 GLY B 11 REMARK 465 ILE B 12 REMARK 465 ILE B 13 REMARK 465 GLU B 14 REMARK 465 TYR B 15 REMARK 465 ASP B 16 REMARK 465 ASP B 17 REMARK 465 PHE B 18 REMARK 465 LYS B 19 REMARK 465 LEU B 20 REMARK 465 ASN B 21 REMARK 465 SER B 22 REMARK 465 SER B 23 REMARK 465 ILE B 24 REMARK 465 VAL B 25 REMARK 465 GLU B 26 REMARK 465 PRO B 27 REMARK 465 LYS B 28 REMARK 465 GLU B 29 REMARK 465 PRO B 30 REMARK 465 ALA B 31 REMARK 465 PRO B 32 REMARK 465 GLU B 33 REMARK 465 GLU B 330 REMARK 465 ASP B 331 REMARK 465 LYS B 332 REMARK 465 GLU B 333 REMARK 465 GLU B 334 REMARK 465 VAL B 335 REMARK 465 GLN B 336 REMARK 465 ARG B 337 REMARK 465 LYS B 338 REMARK 465 ARG B 339 REMARK 465 ARG B 340 REMARK 465 LYS B 341 REMARK 465 ALA B 342 REMARK 465 LEU B 343 REMARK 465 PRO B 344 REMARK 465 THR B 345 REMARK 465 PHE B 346 REMARK 465 SER B 347 REMARK 465 GLN B 348 REMARK 465 PRO B 349 REMARK 465 PHE B 350 REMARK 465 GLY B 351 REMARK 465 GLY B 352 REMARK 465 GLY B 353 REMARK 465 SER B 354 REMARK 465 HIS B 355 REMARK 465 MET B 356 REMARK 465 GLY B 357 REMARK 465 GLY B 358 REMARK 465 GLY B 359 REMARK 465 SER B 360 REMARK 465 GLY B 361 REMARK 465 GLY B 362 REMARK 465 ALA B 363 REMARK 465 ALA B 364 REMARK 465 GLY B 365 REMARK 465 GLY B 366 REMARK 465 TYR B 367 REMARK 465 GLY B 368 REMARK 465 GLY B 369 REMARK 465 ALA B 370 REMARK 465 GLY B 371 REMARK 465 GLY B 372 REMARK 465 GLY B 373 REMARK 465 GLY B 374 REMARK 465 SER B 375 REMARK 465 LEU B 376 REMARK 465 GLY B 377 REMARK 465 PHE B 378 REMARK 465 PHE B 379 REMARK 465 PRO B 380 REMARK 465 SER B 381 REMARK 465 SER B 382 REMARK 465 LEU B 383 REMARK 465 ALA B 384 REMARK 465 TYR B 385 REMARK 465 SER B 386 REMARK 465 PRO B 387 REMARK 465 TYR B 388 REMARK 465 GLN B 389 REMARK 465 SER B 390 REMARK 465 GLY B 391 REMARK 465 ALA B 392 REMARK 465 GLY B 393 REMARK 465 PRO B 394 REMARK 465 MET B 395 REMARK 465 GLY B 396 REMARK 465 CYS B 397 REMARK 465 TYR B 398 REMARK 465 DG D 1 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 DA D 2 P OP1 OP2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 44 OG SER A 69 1.64 REMARK 500 O6 DG C 7 NZ LYS B 221 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 74 OD1 ASP B 128 2455 1.65 REMARK 500 NH2 ARG A 74 CG ASP B 128 2455 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 DA C 3 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG C 5 C3' - O3' - P ANGL. DEV. = -10.1 DEGREES REMARK 500 DA C 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA C 8 C3' - O3' - P ANGL. DEV. = -14.9 DEGREES REMARK 500 DG D 4 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG D 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG D 8 C3' - O3' - P ANGL. DEV. = -7.6 DEGREES REMARK 500 DA D 9 C3' - O3' - P ANGL. DEV. = -8.3 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 ASP A 36 -67.39 4.50 REMARK 500 SER A 61 64.61 -113.31 REMARK 500 ASN A 84 41.20 77.05 REMARK 500 TYR A 85 135.30 176.04 REMARK 500 ARG A 158 49.58 -107.17 REMARK 500 PRO A 223 99.39 -54.90 REMARK 500 SER A 226 -139.94 -95.85 REMARK 500 ASN A 268 16.97 47.36 REMARK 500 GLN A 284 16.66 51.22 REMARK 500 SER B 61 64.37 -112.26 REMARK 500 ASN B 84 40.77 77.08 REMARK 500 TYR B 85 135.57 175.01 REMARK 500 PRO B 101 109.47 -56.92 REMARK 500 ARG B 158 44.16 -106.72 REMARK 500 TRP B 270 114.80 -39.09 REMARK 500 GLN B 284 16.24 50.92 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VUP A 1 398 UNP Q00653 NFKB2_HUMAN 1 398 DBREF 7VUP C 1 18 PDB 7VUP 7VUP 1 18 DBREF 7VUP B 1 398 UNP Q00653 NFKB2_HUMAN 1 398 DBREF 7VUP D 1 18 PDB 7VUP 7VUP 1 18 SEQRES 1 A 398 MET GLU SER CYS TYR ASN PRO GLY LEU ASP GLY ILE ILE SEQRES 2 A 398 GLU TYR ASP ASP PHE LYS LEU ASN SER SER ILE VAL GLU SEQRES 3 A 398 PRO LYS GLU PRO ALA PRO GLU THR ALA ASP GLY PRO TYR SEQRES 4 A 398 LEU VAL ILE VAL GLU GLN PRO LYS GLN ARG GLY PHE ARG SEQRES 5 A 398 PHE ARG TYR GLY CYS GLU GLY PRO SER HIS GLY GLY LEU SEQRES 6 A 398 PRO GLY ALA SER SER GLU LYS GLY ARG LYS THR TYR PRO SEQRES 7 A 398 THR VAL LYS ILE CYS ASN TYR GLU GLY PRO ALA LYS ILE SEQRES 8 A 398 GLU VAL ASP LEU VAL THR HIS SER ASP PRO PRO ARG ALA SEQRES 9 A 398 HIS ALA HIS SER LEU VAL GLY LYS GLN CYS SER GLU LEU SEQRES 10 A 398 GLY ILE CYS ALA VAL SER VAL GLY PRO LYS ASP MET THR SEQRES 11 A 398 ALA GLN PHE ASN ASN LEU GLY VAL LEU HIS VAL THR LYS SEQRES 12 A 398 LYS ASN MET MET GLY THR MET ILE GLN LYS LEU GLN ARG SEQRES 13 A 398 GLN ARG LEU ARG SER ARG PRO GLN GLY LEU THR GLU ALA SEQRES 14 A 398 GLU GLN ARG GLU LEU GLU GLN GLU ALA LYS GLU LEU LYS SEQRES 15 A 398 LYS VAL MET ASP LEU SER ILE VAL ARG LEU ARG PHE SER SEQRES 16 A 398 ALA PHE LEU ARG ALA SER ASP GLY SER PHE SER LEU PRO SEQRES 17 A 398 LEU LYS PRO VAL ILE SER GLN PRO ILE HIS ASP SER LYS SEQRES 18 A 398 SER PRO GLY ALA SER ASN LEU LYS ILE SER ARG MET ASP SEQRES 19 A 398 LYS THR ALA GLY SER VAL ARG GLY GLY ASP GLU VAL TYR SEQRES 20 A 398 LEU LEU CYS ASP LYS VAL GLN LYS ASP ASP ILE GLU VAL SEQRES 21 A 398 ARG PHE TYR GLU ASP ASP GLU ASN GLY TRP GLN ALA PHE SEQRES 22 A 398 GLY ASP PHE SER PRO THR ASP VAL HIS LYS GLN TYR ALA SEQRES 23 A 398 ILE VAL PHE ARG THR PRO PRO TYR HIS LYS MET LYS ILE SEQRES 24 A 398 GLU ARG PRO VAL THR VAL PHE LEU GLN LEU LYS ARG LYS SEQRES 25 A 398 ARG GLY GLY ASP VAL SER ASP SER LYS GLN PHE THR TYR SEQRES 26 A 398 TYR PRO LEU VAL GLU ASP LYS GLU GLU VAL GLN ARG LYS SEQRES 27 A 398 ARG ARG LYS ALA LEU PRO THR PHE SER GLN PRO PHE GLY SEQRES 28 A 398 GLY GLY SER HIS MET GLY GLY GLY SER GLY GLY ALA ALA SEQRES 29 A 398 GLY GLY TYR GLY GLY ALA GLY GLY GLY GLY SER LEU GLY SEQRES 30 A 398 PHE PHE PRO SER SER LEU ALA TYR SER PRO TYR GLN SER SEQRES 31 A 398 GLY ALA GLY PRO MET GLY CYS TYR SEQRES 1 C 18 DC DA DA DG DG DG DG DA DC DT DC DC DC SEQRES 2 C 18 DC DC DT DT DC SEQRES 1 B 398 MET GLU SER CYS TYR ASN PRO GLY LEU ASP GLY ILE ILE SEQRES 2 B 398 GLU TYR ASP ASP PHE LYS LEU ASN SER SER ILE VAL GLU SEQRES 3 B 398 PRO LYS GLU PRO ALA PRO GLU THR ALA ASP GLY PRO TYR SEQRES 4 B 398 LEU VAL ILE VAL GLU GLN PRO LYS GLN ARG GLY PHE ARG SEQRES 5 B 398 PHE ARG TYR GLY CYS GLU GLY PRO SER HIS GLY GLY LEU SEQRES 6 B 398 PRO GLY ALA SER SER GLU LYS GLY ARG LYS THR TYR PRO SEQRES 7 B 398 THR VAL LYS ILE CYS ASN TYR GLU GLY PRO ALA LYS ILE SEQRES 8 B 398 GLU VAL ASP LEU VAL THR HIS SER ASP PRO PRO ARG ALA SEQRES 9 B 398 HIS ALA HIS SER LEU VAL GLY LYS GLN CYS SER GLU LEU SEQRES 10 B 398 GLY ILE CYS ALA VAL SER VAL GLY PRO LYS ASP MET THR SEQRES 11 B 398 ALA GLN PHE ASN ASN LEU GLY VAL LEU HIS VAL THR LYS SEQRES 12 B 398 LYS ASN MET MET GLY THR MET ILE GLN LYS LEU GLN ARG SEQRES 13 B 398 GLN ARG LEU ARG SER ARG PRO GLN GLY LEU THR GLU ALA SEQRES 14 B 398 GLU GLN ARG GLU LEU GLU GLN GLU ALA LYS GLU LEU LYS SEQRES 15 B 398 LYS VAL MET ASP LEU SER ILE VAL ARG LEU ARG PHE SER SEQRES 16 B 398 ALA PHE LEU ARG ALA SER ASP GLY SER PHE SER LEU PRO SEQRES 17 B 398 LEU LYS PRO VAL ILE SER GLN PRO ILE HIS ASP SER LYS SEQRES 18 B 398 SER PRO GLY ALA SER ASN LEU LYS ILE SER ARG MET ASP SEQRES 19 B 398 LYS THR ALA GLY SER VAL ARG GLY GLY ASP GLU VAL TYR SEQRES 20 B 398 LEU LEU CYS ASP LYS VAL GLN LYS ASP ASP ILE GLU VAL SEQRES 21 B 398 ARG PHE TYR GLU ASP ASP GLU ASN GLY TRP GLN ALA PHE SEQRES 22 B 398 GLY ASP PHE SER PRO THR ASP VAL HIS LYS GLN TYR ALA SEQRES 23 B 398 ILE VAL PHE ARG THR PRO PRO TYR HIS LYS MET LYS ILE SEQRES 24 B 398 GLU ARG PRO VAL THR VAL PHE LEU GLN LEU LYS ARG LYS SEQRES 25 B 398 ARG GLY GLY ASP VAL SER ASP SER LYS GLN PHE THR TYR SEQRES 26 B 398 TYR PRO LEU VAL GLU ASP LYS GLU GLU VAL GLN ARG LYS SEQRES 27 B 398 ARG ARG LYS ALA LEU PRO THR PHE SER GLN PRO PHE GLY SEQRES 28 B 398 GLY GLY SER HIS MET GLY GLY GLY SER GLY GLY ALA ALA SEQRES 29 B 398 GLY GLY TYR GLY GLY ALA GLY GLY GLY GLY SER LEU GLY SEQRES 30 B 398 PHE PHE PRO SER SER LEU ALA TYR SER PRO TYR GLN SER SEQRES 31 B 398 GLY ALA GLY PRO MET GLY CYS TYR SEQRES 1 D 18 DG DA DA DG DG DG DG DG DA DG DT DC DC SEQRES 2 D 18 DC DC DT DT DG HELIX 1 AA1 ASN A 145 ARG A 158 1 14 HELIX 2 AA2 THR A 167 LYS A 183 1 17 HELIX 3 AA3 SER A 277 THR A 279 5 3 HELIX 4 AA4 ASN B 145 ARG B 158 1 14 HELIX 5 AA5 THR B 167 LYS B 183 1 17 HELIX 6 AA6 SER B 277 THR B 279 5 3 SHEET 1 AA1 3 TYR A 39 GLU A 44 0 SHEET 2 AA1 3 THR A 79 CYS A 83 -1 O CYS A 83 N TYR A 39 SHEET 3 AA1 3 THR A 130 GLN A 132 -1 O ALA A 131 N VAL A 80 SHEET 1 AA2 3 ARG A 54 TYR A 55 0 SHEET 2 AA2 3 GLY A 137 HIS A 140 1 O HIS A 140 N ARG A 54 SHEET 3 AA2 3 SER A 108 VAL A 110 -1 N SER A 108 O LEU A 139 SHEET 1 AA3 4 CYS A 120 VAL A 124 0 SHEET 2 AA3 4 ALA A 89 VAL A 96 -1 N ILE A 91 O VAL A 122 SHEET 3 AA3 4 ILE A 189 LEU A 198 -1 O PHE A 197 N LYS A 90 SHEET 4 AA3 4 VAL A 212 ILE A 213 -1 O VAL A 212 N PHE A 194 SHEET 1 AA4 3 LEU A 207 PRO A 208 0 SHEET 2 AA4 3 ILE A 189 LEU A 198 -1 N LEU A 198 O LEU A 207 SHEET 3 AA4 3 ILE A 217 HIS A 218 -1 O ILE A 217 N VAL A 190 SHEET 1 AA5 4 ILE A 230 MET A 233 0 SHEET 2 AA5 4 GLU A 245 CYS A 250 -1 O LEU A 249 N ARG A 232 SHEET 3 AA5 4 ALA A 286 ARG A 290 -1 O PHE A 289 N VAL A 246 SHEET 4 AA5 4 VAL A 281 HIS A 282 -1 N HIS A 282 O ALA A 286 SHEET 1 AA6 5 ALA A 237 SER A 239 0 SHEET 2 AA6 5 LYS A 321 TYR A 326 1 O THR A 324 N GLY A 238 SHEET 3 AA6 5 VAL A 303 LYS A 310 -1 N VAL A 305 O PHE A 323 SHEET 4 AA6 5 GLU A 259 TYR A 263 -1 N ARG A 261 O GLN A 308 SHEET 5 AA6 5 GLN A 271 PHE A 273 -1 O ALA A 272 N PHE A 262 SHEET 1 AA7 3 TYR B 39 GLU B 44 0 SHEET 2 AA7 3 THR B 79 CYS B 83 -1 O CYS B 83 N TYR B 39 SHEET 3 AA7 3 THR B 130 GLN B 132 -1 O ALA B 131 N VAL B 80 SHEET 1 AA8 3 ARG B 54 TYR B 55 0 SHEET 2 AA8 3 GLY B 137 HIS B 140 1 O HIS B 140 N ARG B 54 SHEET 3 AA8 3 SER B 108 VAL B 110 -1 N SER B 108 O LEU B 139 SHEET 1 AA9 4 CYS B 120 VAL B 124 0 SHEET 2 AA9 4 ALA B 89 VAL B 96 -1 N ILE B 91 O VAL B 122 SHEET 3 AA9 4 ILE B 189 LEU B 198 -1 O PHE B 197 N LYS B 90 SHEET 4 AA9 4 VAL B 212 ILE B 213 -1 O VAL B 212 N PHE B 194 SHEET 1 AB1 3 LEU B 207 PRO B 208 0 SHEET 2 AB1 3 ILE B 189 LEU B 198 -1 N LEU B 198 O LEU B 207 SHEET 3 AB1 3 ILE B 217 HIS B 218 -1 O ILE B 217 N VAL B 190 SHEET 1 AB2 4 ILE B 230 MET B 233 0 SHEET 2 AB2 4 GLU B 245 CYS B 250 -1 O LEU B 249 N ARG B 232 SHEET 3 AB2 4 ALA B 286 ARG B 290 -1 O PHE B 289 N VAL B 246 SHEET 4 AB2 4 VAL B 281 HIS B 282 -1 N HIS B 282 O ALA B 286 SHEET 1 AB3 5 ALA B 237 SER B 239 0 SHEET 2 AB3 5 LYS B 321 TYR B 326 1 O THR B 324 N GLY B 238 SHEET 3 AB3 5 VAL B 303 ARG B 311 -1 N VAL B 305 O PHE B 323 SHEET 4 AB3 5 ILE B 258 TYR B 263 -1 N ARG B 261 O GLN B 308 SHEET 5 AB3 5 GLN B 271 PHE B 273 -1 O ALA B 272 N PHE B 262 SSBOND 1 CYS A 114 CYS A 120 1555 1555 2.04 SSBOND 2 CYS B 114 CYS B 120 1555 1555 2.03 CRYST1 83.987 84.289 140.565 90.00 90.00 90.00 P 21 21 21 8 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 0.011907 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011864 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007114 0.00000