PDB Short entry for 3U21 HEADER TRANSCRIPTION REGULATION, DNA BINDING 30-SEP-11 3U21 TITLE CRYSTAL STRUCTURE OF A FRAGMENT OF NUCLEAR FACTOR RELATED TO KAPPA-B- TITLE 2 BINDING PROTEIN (RESIDUES 370-495) (NFRKB) FROM HOMO SAPIENS AT 2.18 TITLE 3 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DNA-BINDING PROTEIN R KAPPA-B, INO80 COMPLEX SUBUNIT G; COMPND 5 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: BC063280, INO80G, NFRKB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS DNA/RNA-BINDING 3-HELICAL BUNDLE, WINGED-HTH DOMAIN, STRUCTURAL KEYWDS 2 GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, PSI-BIOLOGY, TRANSCRIPTION REGULATION, DNA KEYWDS 4 BINDING PROTEIN, DNA BINDING, PARTNERSHIP FOR STEM CELL BIOLOGY, KEYWDS 5 STEMCELL EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG),PARTNERSHIP FOR STEM CELL AUTHOR 2 BIOLOGY,PARTNERSHIP FOR STEM CELL BIOLOGY (STEMCELL) REVDAT 4 01-FEB-23 3U21 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3U21 1 REMARK REVDAT 2 10-OCT-12 3U21 1 JRNL REVDAT 1 02-NOV-11 3U21 0 JRNL AUTH A.KUMAR,S.MOCKLINGHOFF,F.YUMOTO,L.JAROSZEWSKI,C.L.FARR, JRNL AUTH 2 A.GRZECHNIK,P.NGUYEN,C.X.WEICHENBERGER,H.J.CHIU,H.E.KLOCK, JRNL AUTH 3 M.A.ELSLIGER,A.M.DEACON,A.GODZIK,S.A.LESLEY,B.R.CONKLIN, JRNL AUTH 4 R.J.FLETTERICK,I.A.WILSON JRNL TITL STRUCTURE OF A NOVEL WINGED-HELIX LIKE DOMAIN FROM HUMAN JRNL TITL 2 NFRKB PROTEIN. JRNL REF PLOS ONE V. 7 43761 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22984442 JRNL DOI 10.1371/JOURNAL.PONE.0043761 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0116 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 13504 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 + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 662 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 809 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1732 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.21000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.43000 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): 0.222 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.518 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1780 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1163 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2425 ; 1.252 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2861 ; 0.866 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 214 ; 5.482 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;37.308 ;26.104 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 301 ;15.037 ;15.133 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ; 7.053 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 279 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1922 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 338 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 372 A 437 4 REMARK 3 1 B 372 B 437 4 REMARK 3 2 A 445 A 483 4 REMARK 3 2 B 445 B 483 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1360 ; 0.230 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1360 ; 2.310 ; 2.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 372 A 462 REMARK 3 RESIDUE RANGE : A 466 A 483 REMARK 3 ORIGIN FOR THE GROUP (A): 61.0380 45.3410 53.3450 REMARK 3 T TENSOR REMARK 3 T11: 0.1040 T22: 0.0908 REMARK 3 T33: 0.0800 T12: -0.0072 REMARK 3 T13: -0.0181 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 1.0635 L22: 5.4284 REMARK 3 L33: 4.0382 L12: 0.6754 REMARK 3 L13: -0.2069 L23: 0.1736 REMARK 3 S TENSOR REMARK 3 S11: -0.0925 S12: 0.0321 S13: 0.1089 REMARK 3 S21: -0.0577 S22: 0.1532 S23: -0.2375 REMARK 3 S31: -0.3529 S32: 0.0032 S33: -0.0607 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 370 B 461 REMARK 3 RESIDUE RANGE : B 464 B 483 REMARK 3 ORIGIN FOR THE GROUP (A): 48.6910 30.9920 75.4320 REMARK 3 T TENSOR REMARK 3 T11: 0.0991 T22: 0.1636 REMARK 3 T33: 0.0509 T12: 0.0091 REMARK 3 T13: -0.0305 T23: 0.0487 REMARK 3 L TENSOR REMARK 3 L11: 3.0864 L22: 2.0962 REMARK 3 L33: 4.4276 L12: 0.5889 REMARK 3 L13: -0.5343 L23: -0.3884 REMARK 3 S TENSOR REMARK 3 S11: 0.0515 S12: -0.2075 S13: -0.0591 REMARK 3 S21: 0.0171 S22: 0.1051 S23: 0.1458 REMARK 3 S31: 0.0318 S32: -0.5040 S33: -0.1566 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND REMARK 3 RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND REMARK 3 RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS REMARK 3 ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 6. SODIUM ION (NA) FROM CRYSTALLIZATION CONDITION REMARK 3 WAS MODELED. REMARK 4 REMARK 4 3U21 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837,0.97936,0.97915 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE DECEMBER 6, 2010 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13560 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 35.466 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.79600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHARP, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.09M HEPES PH 7.5, 10% GLYCEROL, REMARK 280 1.26M TRI-SODIUM CITRATE, NANODROP, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 65.41950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.47100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.47100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 98.12925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.47100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.47100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.70975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.47100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.47100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 98.12925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.47100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.47100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.70975 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 65.41950 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 300 REMARK: CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER REMARK 300 AS THE SIGNIFICANT OLIGOMERIZATION STATE. 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: 1510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 0 REMARK 465 LEU A 370 REMARK 465 GLY A 371 REMARK 465 GLN A 463 REMARK 465 SER A 464 REMARK 465 GLN A 465 REMARK 465 GLN A 484 REMARK 465 ALA A 485 REMARK 465 PHE A 486 REMARK 465 CYS A 487 REMARK 465 MLY A 488 REMARK 465 GLN A 489 REMARK 465 GLU A 490 REMARK 465 ASN A 491 REMARK 465 GLU A 492 REMARK 465 ASP A 493 REMARK 465 SER A 494 REMARK 465 SER A 495 REMARK 465 GLY B 0 REMARK 465 ALA B 440 REMARK 465 VAL B 441 REMARK 465 PRO B 442 REMARK 465 SER B 443 REMARK 465 GLY B 462 REMARK 465 GLN B 463 REMARK 465 GLN B 484 REMARK 465 ALA B 485 REMARK 465 PHE B 486 REMARK 465 CYS B 487 REMARK 465 MLY B 488 REMARK 465 GLN B 489 REMARK 465 GLU B 490 REMARK 465 ASN B 491 REMARK 465 GLU B 492 REMARK 465 ASP B 493 REMARK 465 SER B 494 REMARK 465 SER B 495 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 439 CG CD NE CZ NH1 NH2 REMARK 470 MLY A 454 CG CD CE NZ CH1 CH2 REMARK 470 ILE B 372 CG1 CG2 CD1 REMARK 470 ARG B 439 CG CD NE CZ NH1 NH2 REMARK 470 MLY B 454 CG CD CE NZ CH1 CH2 REMARK 470 GLN B 465 CG CD OE1 NE2 REMARK 470 ASP B 483 CG OD1 OD2 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 390 -47.01 75.84 REMARK 500 SER A 391 -47.25 70.91 REMARK 500 SER A 444 45.58 -98.95 REMARK 500 SER B 391 -58.79 74.11 REMARK 500 ASP B 466 -1.97 64.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 500 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 373 OD1 REMARK 620 2 ILE A 375 O 91.6 REMARK 620 3 ASN B 373 OD1 171.4 88.2 REMARK 620 4 ILE B 375 O 94.2 102.9 94.3 REMARK 620 5 HOH B 521 O 94.7 164.8 83.5 90.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 421522 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 1. THIS CONSTRUCT (RESIDUES 370-495) WAS EXPRESSED WITH AN N- REMARK 999 TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED REMARK 999 WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET REMARK 999 SEQUENCE. RESIDUE NUMBERING IS BASED ON ISOFORM 1 OF UNIPROTKB ID REMARK 999 Q6P4R8. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO REMARK 999 CRYSTALLIZATION. DBREF 3U21 A 370 495 UNP Q6P4R8 NFRKB_HUMAN 370 495 DBREF 3U21 B 370 495 UNP Q6P4R8 NFRKB_HUMAN 370 495 SEQADV 3U21 GLY A 0 UNP Q6P4R8 EXPRESSION TAG SEQADV 3U21 GLY B 0 UNP Q6P4R8 EXPRESSION TAG SEQRES 1 A 127 GLY LEU GLY ILE ASN GLU ILE SER SER SER PHE PHE SER SEQRES 2 A 127 LEU LEU LEU GLU ILE LEU LEU LEU GLU SER GLN ALA SER SEQRES 3 A 127 LEU PRO MSE LEU GLU GLU ARG VAL LEU ASP TRP GLN SER SEQRES 4 A 127 SER PRO ALA SER SER LEU ASN SER TRP PHE SER ALA ALA SEQRES 5 A 127 PRO ASN TRP ALA GLU LEU VAL LEU PRO ALA LEU GLN TYR SEQRES 6 A 127 LEU ALA GLY GLU SER ARG ALA VAL PRO SER SER PHE SER SEQRES 7 A 127 PRO PHE VAL GLU PHE MLY GLU MLY THR GLN GLN TRP MLY SEQRES 8 A 127 LEU LEU GLY GLN SER GLN ASP ASN GLU MLY GLU LEU ALA SEQRES 9 A 127 ALA LEU PHE GLN LEU TRP LEU GLU THR MLY ASP GLN ALA SEQRES 10 A 127 PHE CYS MLY GLN GLU ASN GLU ASP SER SER SEQRES 1 B 127 GLY LEU GLY ILE ASN GLU ILE SER SER SER PHE PHE SER SEQRES 2 B 127 LEU LEU LEU GLU ILE LEU LEU LEU GLU SER GLN ALA SER SEQRES 3 B 127 LEU PRO MSE LEU GLU GLU ARG VAL LEU ASP TRP GLN SER SEQRES 4 B 127 SER PRO ALA SER SER LEU ASN SER TRP PHE SER ALA ALA SEQRES 5 B 127 PRO ASN TRP ALA GLU LEU VAL LEU PRO ALA LEU GLN TYR SEQRES 6 B 127 LEU ALA GLY GLU SER ARG ALA VAL PRO SER SER PHE SER SEQRES 7 B 127 PRO PHE VAL GLU PHE MLY GLU MLY THR GLN GLN TRP MLY SEQRES 8 B 127 LEU LEU GLY GLN SER GLN ASP ASN GLU MLY GLU LEU ALA SEQRES 9 B 127 ALA LEU PHE GLN LEU TRP LEU GLU THR MLY ASP GLN ALA SEQRES 10 B 127 PHE CYS MLY GLN GLU ASN GLU ASP SER SER MODRES 3U21 MSE A 397 MET SELENOMETHIONINE MODRES 3U21 MLY A 452 LYS N-DIMETHYL-LYSINE MODRES 3U21 MLY A 454 LYS N-DIMETHYL-LYSINE MODRES 3U21 MLY A 459 LYS N-DIMETHYL-LYSINE MODRES 3U21 MLY A 469 LYS N-DIMETHYL-LYSINE MODRES 3U21 MLY A 482 LYS N-DIMETHYL-LYSINE MODRES 3U21 MSE B 397 MET SELENOMETHIONINE MODRES 3U21 MLY B 452 LYS N-DIMETHYL-LYSINE MODRES 3U21 MLY B 454 LYS N-DIMETHYL-LYSINE MODRES 3U21 MLY B 459 LYS N-DIMETHYL-LYSINE MODRES 3U21 MLY B 469 LYS N-DIMETHYL-LYSINE MODRES 3U21 MLY B 482 LYS N-DIMETHYL-LYSINE HET MSE A 397 13 HET MLY A 452 11 HET MLY A 454 5 HET MLY A 459 11 HET MLY A 469 11 HET MLY A 482 11 HET MSE B 397 8 HET MLY B 452 11 HET MLY B 454 5 HET MLY B 459 11 HET MLY B 469 11 HET MLY B 482 11 HET NA A 500 1 HETNAM MSE SELENOMETHIONINE HETNAM MLY N-DIMETHYL-LYSINE HETNAM NA SODIUM ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 1 MLY 10(C8 H18 N2 O2) FORMUL 3 NA NA 1+ FORMUL 4 HOH *25(H2 O) HELIX 1 1 SER A 378 LEU A 389 1 12 HELIX 2 2 LEU A 395 SER A 407 1 13 HELIX 3 3 SER A 408 ASN A 414 5 7 HELIX 4 4 TRP A 416 ALA A 420 5 5 HELIX 5 5 TRP A 423 GLU A 425 5 3 HELIX 6 6 LEU A 426 ALA A 435 1 10 HELIX 7 7 ASN A 467 MLY A 482 1 16 HELIX 8 8 SER B 378 SER B 391 1 14 HELIX 9 9 SER B 394 SER B 408 1 15 HELIX 10 10 PRO B 409 ASN B 414 5 6 HELIX 11 11 TRP B 416 ALA B 420 5 5 HELIX 12 12 ASN B 422 GLU B 425 5 4 HELIX 13 13 LEU B 426 ALA B 435 1 10 HELIX 14 14 ASN B 467 MLY B 482 1 16 SHEET 1 A 3 GLN A 392 SER A 394 0 SHEET 2 A 3 GLN A 457 LEU A 460 -1 O TRP A 458 N ALA A 393 SHEET 3 A 3 VAL A 449 MLY A 452 -1 N GLU A 450 O MLY A 459 SHEET 1 B 3 GLN B 392 ALA B 393 0 SHEET 2 B 3 GLN B 457 LEU B 460 -1 O TRP B 458 N ALA B 393 SHEET 3 B 3 VAL B 449 MLY B 452 -1 N GLU B 450 O MLY B 459 LINK C PRO A 396 N MSE A 397 1555 1555 1.34 LINK C MSE A 397 N LEU A 398 1555 1555 1.33 LINK C PHE A 451 N MLY A 452 1555 1555 1.33 LINK C MLY A 452 N GLU A 453 1555 1555 1.33 LINK C GLU A 453 N MLY A 454 1555 1555 1.33 LINK C MLY A 454 N THR A 455 1555 1555 1.34 LINK C TRP A 458 N MLY A 459 1555 1555 1.33 LINK C MLY A 459 N LEU A 460 1555 1555 1.33 LINK C GLU A 468 N MLY A 469 1555 1555 1.33 LINK C MLY A 469 N GLU A 470 1555 1555 1.33 LINK C THR A 481 N MLY A 482 1555 1555 1.33 LINK C MLY A 482 N ASP A 483 1555 1555 1.33 LINK C PRO B 396 N MSE B 397 1555 1555 1.33 LINK C MSE B 397 N LEU B 398 1555 1555 1.34 LINK C PHE B 451 N MLY B 452 1555 1555 1.33 LINK C MLY B 452 N GLU B 453 1555 1555 1.32 LINK C GLU B 453 N MLY B 454 1555 1555 1.33 LINK C MLY B 454 N THR B 455 1555 1555 1.33 LINK C TRP B 458 N MLY B 459 1555 1555 1.34 LINK C MLY B 459 N LEU B 460 1555 1555 1.33 LINK C GLU B 468 N MLY B 469 1555 1555 1.32 LINK C MLY B 469 N GLU B 470 1555 1555 1.32 LINK C THR B 481 N MLY B 482 1555 1555 1.33 LINK C MLY B 482 N ASP B 483 1555 1555 1.33 LINK OD1 ASN A 373 NA NA A 500 1555 1555 2.40 LINK O ILE A 375 NA NA A 500 1555 1555 2.37 LINK NA NA A 500 OD1 ASN B 373 1555 1555 2.29 LINK NA NA A 500 O ILE B 375 1555 1555 2.33 LINK NA NA A 500 O HOH B 521 1555 1555 2.27 SITE 1 AC1 5 ASN A 373 ILE A 375 ASN B 373 ILE B 375 SITE 2 AC1 5 HOH B 521 CRYST1 60.942 60.942 130.839 90.00 90.00 90.00 P 43 21 2 16 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 0.016409 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016409 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007643 0.00000