HEADER TRANSCRIPTION FACTOR 12-SEP-97 1BFT TITLE STRUCTURE OF NF-KB P50 HOMODIMER BOUND TO A KB SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR FACTOR NF-KAPPA-B P65; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DIMERIZATION DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090 KEYWDS TRANSCRIPTION FACTOR, NF-KB, DIMERIZATION DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR D.B.HUANG,T.HUXFORD,Y.Q.CHEN,G.GHOSH REVDAT 4 03-APR-24 1BFT 1 REMARK REVDAT 3 07-FEB-24 1BFT 1 REMARK REVDAT 2 24-FEB-09 1BFT 1 VERSN REVDAT 1 28-JAN-98 1BFT 0 JRNL AUTH D.B.HUANG,T.HUXFORD,Y.Q.CHEN,G.GHOSH JRNL TITL THE ROLE OF DNA IN THE MECHANISM OF NFKAPPAB DIMER JRNL TITL 2 FORMATION: CRYSTAL STRUCTURES OF THE DIMERIZATION DOMAINS OF JRNL TITL 3 THE P50 AND P65 SUBUNITS. JRNL REF STRUCTURE V. 5 1427 1997 JRNL REFN ISSN 0969-2126 JRNL PMID 9384558 JRNL DOI 10.1016/S0969-2126(97)00293-1 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.GHOSH,G.VAN DUYNE,S.GHOSH,P.B.SIGLER REMARK 1 TITL STRUCTURE OF NF-KAPPA B P50 HOMODIMER BOUND TO A KAPPA B REMARK 1 TITL 2 SITE REMARK 1 REF NATURE V. 373 303 1995 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 9124 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 456 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1610 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.40 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.950 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.700 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BFT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-96 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 12401 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: DIMERIZATION DOMAINS OF P50RHR/DNA COMPLEX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 52.80500 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 52.80500 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 27.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.24500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.24500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 52.80500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.75000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.24500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.80500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.75000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.24500 REMARK 290 SMTRY3 8 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 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 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 O HOH A 724 H2 HOH A 726 1.53 REMARK 500 H1 HOH A 670 O HOH A 722 1.54 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 HH21 ARG B 253 H2 HOH B 662 8556 1.33 REMARK 500 O HOH A 687 H1 HOH A 725 3655 1.54 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 ALA A 192 -118.71 51.74 REMARK 500 GLN A 247 -9.29 75.75 REMARK 500 ALA B 192 -89.83 53.20 REMARK 500 GLU B 234 128.87 -170.15 REMARK 500 SER B 261 45.84 -107.65 REMARK 500 ARG B 278 17.16 59.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BFT A 191 291 UNP Q04207 TF65_MOUSE 191 291 DBREF 1BFT B 191 291 UNP Q04207 TF65_MOUSE 191 291 SEQRES 1 A 101 THR ALA GLU LEU LYS ILE CYS ARG VAL ASN ARG ASN SER SEQRES 2 A 101 GLY SER CYS LEU GLY GLY ASP GLU ILE PHE LEU LEU CYS SEQRES 3 A 101 ASP LYS VAL GLN LYS GLU ASP ILE GLU VAL TYR PHE THR SEQRES 4 A 101 GLY PRO GLY TRP GLU ALA ARG GLY SER PHE SER GLN ALA SEQRES 5 A 101 ASP VAL HIS ARG GLN VAL ALA ILE VAL PHE ARG THR PRO SEQRES 6 A 101 PRO TYR ALA ASP PRO SER LEU GLN ALA PRO VAL ARG VAL SEQRES 7 A 101 SER MET GLN LEU ARG ARG PRO SER ASP ARG GLU LEU SER SEQRES 8 A 101 GLU PRO MET GLU PHE GLN TYR LEU PRO ASP SEQRES 1 B 101 THR ALA GLU LEU LYS ILE CYS ARG VAL ASN ARG ASN SER SEQRES 2 B 101 GLY SER CYS LEU GLY GLY ASP GLU ILE PHE LEU LEU CYS SEQRES 3 B 101 ASP LYS VAL GLN LYS GLU ASP ILE GLU VAL TYR PHE THR SEQRES 4 B 101 GLY PRO GLY TRP GLU ALA ARG GLY SER PHE SER GLN ALA SEQRES 5 B 101 ASP VAL HIS ARG GLN VAL ALA ILE VAL PHE ARG THR PRO SEQRES 6 B 101 PRO TYR ALA ASP PRO SER LEU GLN ALA PRO VAL ARG VAL SEQRES 7 B 101 SER MET GLN LEU ARG ARG PRO SER ASP ARG GLU LEU SER SEQRES 8 B 101 GLU PRO MET GLU PHE GLN TYR LEU PRO ASP FORMUL 3 HOH *89(H2 O) HELIX 1 1 LYS A 221 ASP A 223 5 3 HELIX 2 2 GLN A 241 ASP A 243 5 3 HELIX 3 3 PRO A 275 ASP A 277 5 3 HELIX 4 4 LYS B 221 ASP B 223 5 3 HELIX 5 5 GLN B 241 ASP B 243 5 3 SHEET 1 A 5 SER A 203 SER A 205 0 SHEET 2 A 5 MET A 284 LEU A 289 1 N GLN A 287 O GLY A 204 SHEET 3 A 5 VAL A 266 ARG A 273 -1 N MET A 270 O MET A 284 SHEET 4 A 5 GLU A 225 GLY A 230 -1 N THR A 229 O SER A 269 SHEET 5 A 5 TRP A 233 ARG A 236 -1 N ALA A 235 O PHE A 228 SHEET 1 B 3 ALA A 249 ARG A 253 0 SHEET 2 B 3 GLU A 211 CYS A 216 -1 N LEU A 214 O ILE A 250 SHEET 3 B 3 ILE A 196 VAL A 199 -1 N ARG A 198 O LEU A 215 SHEET 1 C 5 SER B 203 SER B 205 0 SHEET 2 C 5 MET B 284 LEU B 289 1 N GLN B 287 O GLY B 204 SHEET 3 C 5 VAL B 266 ARG B 273 -1 N MET B 270 O MET B 284 SHEET 4 C 5 GLU B 225 GLY B 230 -1 N THR B 229 O SER B 269 SHEET 5 C 5 TRP B 233 ARG B 236 -1 N ALA B 235 O PHE B 228 SHEET 1 D 3 ALA B 249 ARG B 253 0 SHEET 2 D 3 GLU B 211 CYS B 216 -1 N LEU B 214 O ILE B 250 SHEET 3 D 3 ILE B 196 VAL B 199 -1 N ARG B 198 O LEU B 215 CRYST1 55.500 74.490 105.610 90.00 90.00 90.00 C 2 2 21 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 0.018018 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009469 0.00000