HEADER TRANSCRIPTION 02-MAY-05 1ZK9 TITLE NF-KB RELB FORMS AN INTERTWINED HOMODIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR RELB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DIMERIZATION DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RELB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: T7 PROMOTER; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS NF-KB, TRANSCRIPTION FACTORS, INTERTWINED DIMER, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR D.B.HUANG,D.VU,G.GHOSH REVDAT 6 23-AUG-23 1ZK9 1 SEQADV REVDAT 5 04-APR-18 1ZK9 1 REMARK REVDAT 4 13-JUL-11 1ZK9 1 VERSN REVDAT 3 24-FEB-09 1ZK9 1 VERSN REVDAT 2 27-SEP-05 1ZK9 1 JRNL REVDAT 1 10-MAY-05 1ZK9 0 JRNL AUTH D.B.HUANG,D.VU,G.GHOSH JRNL TITL NF-KAPPAB RELB FORMS AN INTERTWINED HOMODIMER. JRNL REF STRUCTURE V. 13 1365 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 16154093 JRNL DOI 10.1016/J.STR.2005.06.018 REMARK 2 REMARK 2 RESOLUTION. 2.18 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 696824.930 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.8 REMARK 3 NUMBER OF REFLECTIONS : 8178 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) : 0.195 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.200 REMARK 3 FREE R VALUE TEST SET COUNT : 509 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.32 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 897 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 61 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 869 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 103 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.93000 REMARK 3 B22 (A**2) : 5.93000 REMARK 3 B33 (A**2) : -11.87000 REMARK 3 B12 (A**2) : 6.82000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.24 REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 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) : 3.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.470 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.490 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.610 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 60.54 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000032813. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8226 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 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 (%) : 85.0 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: PDB RENTRY 1BFT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM SULFATE, REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.58000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.16000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.16000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.58000 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 9420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 43.16000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 544 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 582 LIES ON A SPECIAL POSITION. 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 310 58.63 -143.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZKA RELATED DB: PDB REMARK 900 Y300S MUTANT DBREF 1ZK9 A 277 378 UNP Q04863 RELB_MOUSE 277 378 SEQADV 1ZK9 LEU A 269 UNP Q04863 CLONING ARTIFACT SEQADV 1ZK9 VAL A 270 UNP Q04863 CLONING ARTIFACT SEQADV 1ZK9 PRO A 271 UNP Q04863 CLONING ARTIFACT SEQADV 1ZK9 ARG A 272 UNP Q04863 CLONING ARTIFACT SEQADV 1ZK9 GLY A 273 UNP Q04863 CLONING ARTIFACT SEQADV 1ZK9 SER A 274 UNP Q04863 CLONING ARTIFACT SEQADV 1ZK9 HIS A 275 UNP Q04863 CLONING ARTIFACT SEQADV 1ZK9 MET A 276 UNP Q04863 CLONING ARTIFACT SEQRES 1 A 110 LEU VAL PRO ARG GLY SER HIS MET ASN THR SER GLU LEU SEQRES 2 A 110 ARG ILE CYS ARG ILE ASN LYS GLU SER GLY PRO CYS THR SEQRES 3 A 110 GLY GLY GLU GLU LEU TYR LEU LEU CYS ASP LYS VAL GLN SEQRES 4 A 110 LYS GLU ASP ILE SER VAL VAL PHE SER THR ALA SER TRP SEQRES 5 A 110 GLU GLY ARG ALA ASP PHE SER GLN ALA ASP VAL HIS ARG SEQRES 6 A 110 GLN ILE ALA ILE VAL PHE LYS THR PRO PRO TYR GLU ASP SEQRES 7 A 110 LEU GLU ILE SER GLU PRO VAL THR VAL ASN VAL PHE LEU SEQRES 8 A 110 GLN ARG LEU THR ASP GLY VAL CYS SER GLU PRO LEU PRO SEQRES 9 A 110 PHE THR TYR LEU PRO ARG FORMUL 2 HOH *103(H2 O) HELIX 1 1 SER A 327 VAL A 331 5 5 SHEET 1 A 2 VAL A 270 ARG A 272 0 SHEET 2 A 2 HIS A 275 ASN A 277 -1 O ASN A 277 N VAL A 270 SHEET 1 B 2 ILE A 283 ILE A 286 0 SHEET 2 B 2 LEU A 301 CYS A 303 -1 O LEU A 302 N CYS A 284 SHEET 1 C 2 VAL A 314 THR A 317 0 SHEET 2 C 2 TRP A 320 ARG A 323 -1 O GLY A 322 N PHE A 315 SHEET 1 D 2 VAL A 353 VAL A 357 0 SHEET 2 D 2 LEU A 371 TYR A 375 -1 O TYR A 375 N VAL A 353 CRYST1 69.200 69.200 64.740 90.00 90.00 120.00 P 31 2 1 6 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 0.014451 0.008343 0.000000 0.00000 SCALE2 0.000000 0.016686 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015446 0.00000