HEADER TRANSCRIPTION 24-SEP-01 1K1B TITLE CRYSTAL STRUCTURE OF THE ANKYRIN REPEAT DOMAIN OF BCL-3: A TITLE 2 UNIQUE MEMBER OF THE IKAPPAB PROTEIN FAMILY COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-CELL LYMPHOMA 3-ENCODED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ANKYRIN REPEAT DOMAIN; COMPND 5 SYNONYM: BCL3, BCL-3 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BCL-3, NF-KAPPAB TRANSCRIPTION FACTORS, IKAPPAB PROTEINS EXPDTA X-RAY DIFFRACTION AUTHOR F.MICHEL,M.SOLER-LOPEZ,C.PETOSA,P.CRAMER,U.SIEBENLIST, AUTHOR 2 C.W.MUELLER REVDAT 3 24-FEB-09 1K1B 1 VERSN REVDAT 2 01-APR-03 1K1B 1 JRNL REVDAT 1 21-NOV-01 1K1B 0 JRNL AUTH F.MICHEL,M.SOLER-LOPEZ,C.PETOSA,P.CRAMER, JRNL AUTH 2 U.SIEBENLIST,C.W.MULLER JRNL TITL CRYSTAL STRUCTURE OF THE ANKYRIN REPEAT DOMAIN OF JRNL TITL 2 BCL-3: A UNIQUE MEMBER OF THE IKAPPAB PROTEIN JRNL TITL 3 FAMILY. JRNL REF EMBO J. V. 20 6180 2001 JRNL REFN ISSN 0261-4189 JRNL PMID 11707390 JRNL DOI 10.1093/EMBOJ/20.22.6180 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 14542 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 709 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1717 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 198 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.76000 REMARK 3 B22 (A**2) : -1.18000 REMARK 3 B33 (A**2) : 0.91000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.17000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.196 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.615 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.007 ; 0.021 REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.004 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.091 ; 0.200 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.490 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.925 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.503 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.533 ; 4.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES LEU182 AND SER307 PRESENT REMARK 3 DOUBLE CONFORMATIONS. REMARK 4 REMARK 4 1K1B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-01. REMARK 100 THE RCSB ID CODE IS RCSB014435. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 14381 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.410 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09700 REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.68 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26000 REMARK 200 FOR SHELL : 3.150 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: 1IKN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, MES, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.45350 REMARK 290 SMTRY3 2 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: MONOMERIC 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 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 119 REMARK 465 ALA A 120 REMARK 465 THR A 121 REMARK 465 ARG A 122 REMARK 465 ALA A 123 REMARK 465 ASP A 124 REMARK 465 LYS A 353 REMARK 465 ALA A 354 REMARK 465 THR A 355 REMARK 465 ARG A 356 REMARK 465 PRO A 357 REMARK 465 ALA A 358 REMARK 465 SER A 359 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 152 CG REMARK 480 LYS A 330 NZ REMARK 480 ARG A 342 CZ NH1 NH2 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 NH1 ARG A 322 O HOH A 547 1.84 REMARK 500 O HOH A 545 O HOH A 552 1.97 REMARK 500 O HOH A 441 O HOH A 549 2.05 REMARK 500 O HOH A 536 O HOH A 554 2.12 REMARK 500 NZ LYS A 330 O ASN A 334 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 344 C ARG A 345 N 0.163 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 ASP A 128 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 GLN A 152 OE1 - CD - NE2 ANGL. DEV. = -108.0 DEGREES REMARK 500 ARG A 344 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 344 O - C - N ANGL. DEV. = -13.3 DEGREES 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 GLN A 152 0.11 SIDE_CHAIN REMARK 500 ARG A 344 0.20 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 125 -11.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K1A RELATED DB: PDB DBREF 1K1B A 119 359 UNP P20749 BCL3_HUMAN 119 359 SEQRES 1 A 241 MET ALA THR ARG ALA ASP GLU ASP GLY ASP THR PRO LEU SEQRES 2 A 241 HIS ILE ALA VAL VAL GLN GLY ASN LEU PRO ALA VAL HIS SEQRES 3 A 241 ARG LEU VAL ASN LEU PHE GLN GLN GLY GLY ARG GLU LEU SEQRES 4 A 241 ASP ILE TYR ASN ASN LEU ARG GLN THR PRO LEU HIS LEU SEQRES 5 A 241 ALA VAL ILE THR THR LEU PRO SER VAL VAL ARG LEU LEU SEQRES 6 A 241 VAL THR ALA GLY ALA SER PRO MET ALA LEU ASP ARG HIS SEQRES 7 A 241 GLY GLN THR ALA ALA HIS LEU ALA CYS GLU HIS ARG SER SEQRES 8 A 241 PRO THR CYS LEU ARG ALA LEU LEU ASP SER ALA ALA PRO SEQRES 9 A 241 GLY THR LEU ASP LEU GLU ALA ARG ASN TYR ASP GLY LEU SEQRES 10 A 241 THR ALA LEU HIS VAL ALA VAL ASN THR GLU CYS GLN GLU SEQRES 11 A 241 THR VAL GLN LEU LEU LEU GLU ARG GLY ALA ASP ILE ASP SEQRES 12 A 241 ALA VAL ASP ILE LYS SER GLY ARG SER PRO LEU ILE HIS SEQRES 13 A 241 ALA VAL GLU ASN ASN SER LEU SER MET VAL GLN LEU LEU SEQRES 14 A 241 LEU GLN HIS GLY ALA ASN VAL ASN ALA GLN MET TYR SER SEQRES 15 A 241 GLY SER SER ALA LEU HIS SER ALA SER GLY ARG GLY LEU SEQRES 16 A 241 LEU PRO LEU VAL ARG THR LEU VAL ARG SER GLY ALA ASP SEQRES 17 A 241 SER SER LEU LYS ASN CYS HIS ASN ASP THR PRO LEU MET SEQRES 18 A 241 VAL ALA ARG SER ARG ARG VAL ILE ASP ILE LEU ARG GLY SEQRES 19 A 241 LYS ALA THR ARG PRO ALA SER FORMUL 2 HOH *198(H2 O) HELIX 1 1 THR A 129 GLN A 137 1 9 HELIX 2 2 ASN A 139 GLY A 153 1 15 HELIX 3 3 THR A 166 THR A 174 1 9 HELIX 4 4 LEU A 176 ALA A 186 1 11 HELIX 5 5 THR A 199 HIS A 207 1 9 HELIX 6 6 SER A 209 ALA A 220 1 12 HELIX 7 7 THR A 236 GLU A 245 1 10 HELIX 8 8 CYS A 246 ARG A 256 1 11 HELIX 9 9 SER A 270 ASN A 278 1 9 HELIX 10 10 SER A 280 HIS A 290 1 11 HELIX 11 11 SER A 303 ARG A 311 1 9 HELIX 12 12 LEU A 313 SER A 323 1 11 HELIX 13 13 THR A 336 ALA A 341 1 6 HELIX 14 14 SER A 343 SER A 343 1 1 HELIX 15 15 ARG A 344 GLY A 352 1 9 CRYST1 31.350 50.907 59.495 90.00 102.04 90.00 P 1 21 1 2 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 0.031898 0.000000 0.006803 0.00000 SCALE2 0.000000 0.019644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017186 0.00000