HEADER TRANSCRIPTION 01-MAR-13 4JGM
TITLE CRYSTAL STRUCTURE OF RELB DOUBLE MUTANTS: Y300F/I335V
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRANSCRIPTION FACTOR RELB;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: DIMERIZATION DOMAIN;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090
KEYWDS INTERTWINED DIMER, SIDE-BY SIDE DIMER, TRANSCRIPTION FACTOR,
KEYWDS 2 TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR D.B.HUANG,D.VU,G.GHOSH
REVDAT 2 20-SEP-23 4JGM 1 SEQADV
REVDAT 1 15-JAN-14 4JGM 0
JRNL AUTH D.VU,D.B.HUANG,A.VEMU,G.GHOSH
JRNL TITL A STRUCTURAL BASIS FOR SELECTIVE DIMERIZATION BY NF-KAPPA B
JRNL TITL 2 RELB.
JRNL REF J.MOL.BIOL. V. 425 1934 2013
JRNL REFN ISSN 0022-2836
JRNL PMID 23485337
JRNL DOI 10.1016/J.JMB.2013.02.020
REMARK 2
REMARK 2 RESOLUTION. 3.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.3
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.43
REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 104419.630
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.8
REMARK 3 NUMBER OF REFLECTIONS : 3061
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) : 0.211
REMARK 3 FREE R VALUE : 0.292
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200
REMARK 3 FREE R VALUE TEST SET COUNT : 158
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.023
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) : 3.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.70
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 356
REMARK 3 BIN R VALUE (WORKING SET) : 0.2550
REMARK 3 BIN FREE R VALUE : 0.2640
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 19
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.061
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 867
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 54
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.30
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 10.43000
REMARK 3 B22 (A**2) : 10.43000
REMARK 3 B33 (A**2) : -20.86000
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 COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33
REMARK 3 ESD FROM SIGMAA (A) : 0.43
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.44
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.42
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.500
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.00
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.990
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) : 1.550 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.850 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.880 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.160 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.36
REMARK 3 BSOL : 82.37
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 : DNA-RNA_REP.PARAM
REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 4 : ION.PARAM
REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM
REMARK 3 PARAMETER FILE 6 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
REMARK 3 TOPOLOGY FILE 4 : ION.TOP
REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP
REMARK 3 TOPOLOGY FILE 6 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
REMARK 4
REMARK 4 4JGM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-13.
REMARK 100 THE DEPOSITION ID IS D_1000078020.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 02-JUL-11
REMARK 200 TEMPERATURE (KELVIN) : 200
REMARK 200 PH : 5.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 19-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.1
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3061
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.08800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.17
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5
REMARK 200 DATA REDUNDANCY IN SHELL : 3.40
REMARK 200 R MERGE FOR SHELL (I) : 0.51000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MERLOT
REMARK 200 STARTING MODEL: PDB ENTRY 1ZK9
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 62.87
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4000, PH 5.6, VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 277K
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 21.76667
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 43.53333
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 43.53333
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 21.76667
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
REMARK 350 TOTAL BURIED SURFACE AREA: 1250 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11750 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 43.53333
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 VAL A 270 136.75 -35.22
REMARK 500 ARG A 272 67.33 -156.79
REMARK 500 HIS A 275 -160.96 -101.83
REMARK 500 ARG A 285 162.37 179.59
REMARK 500 ILE A 311 146.23 -171.65
REMARK 500 ARG A 333 37.67 23.40
REMARK 500 VAL A 355 -158.43 -105.82
REMARK 500 THR A 363 -78.01 -38.67
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4JHB RELATED DB: PDB
REMARK 900 RELATED ID: 1ZK9 RELATED DB: PDB
DBREF 4JGM A 277 378 UNP Q04863 RELB_MOUSE 277 378
SEQADV 4JGM LEU A 269 UNP Q04863 EXPRESSION TAG
SEQADV 4JGM VAL A 270 UNP Q04863 EXPRESSION TAG
SEQADV 4JGM PRO A 271 UNP Q04863 EXPRESSION TAG
SEQADV 4JGM ARG A 272 UNP Q04863 EXPRESSION TAG
SEQADV 4JGM GLY A 273 UNP Q04863 EXPRESSION TAG
SEQADV 4JGM SER A 274 UNP Q04863 EXPRESSION TAG
SEQADV 4JGM HIS A 275 UNP Q04863 EXPRESSION TAG
SEQADV 4JGM MET A 276 UNP Q04863 EXPRESSION TAG
SEQADV 4JGM PHE A 300 UNP Q04863 TYR 300 ENGINEERED MUTATION
SEQADV 4JGM VAL A 335 UNP Q04863 ILE 335 ENGINEERED MUTATION
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 PHE 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 VAL 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 *54(H2 O)
SHEET 1 A 2 MET A 276 ASN A 277 0
SHEET 2 A 2 VAL A 366 CYS A 367 1 O CYS A 367 N MET A 276
SHEET 1 B 4 ILE A 283 ILE A 286 0
SHEET 2 B 4 GLU A 298 CYS A 303 -1 O LEU A 302 N ARG A 285
SHEET 3 B 4 ALA A 336 LYS A 340 -1 O PHE A 339 N LEU A 299
SHEET 4 B 4 VAL A 331 HIS A 332 -1 O HIS A 332 N ALA A 336
SHEET 1 C 5 SER A 290 PRO A 292 0
SHEET 2 C 5 LEU A 371 LEU A 376 1 O THR A 374 N GLY A 291
SHEET 3 C 5 VAL A 353 GLN A 360 -1 N VAL A 355 O PHE A 373
SHEET 4 C 5 SER A 312 THR A 317 -1 N SER A 316 O ASN A 356
SHEET 5 C 5 TRP A 320 ARG A 323 -1 O GLY A 322 N PHE A 315
CRYST1 65.940 65.940 65.300 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 0.015165 0.008756 0.000000 0.00000
SCALE2 0.000000 0.017511 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015314 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
