HEADER DNA BINDING PROTEIN/DNA 12-APR-24 9BDW TITLE NF-KAPPAB RELA HOMO-DIMER BOUND TO GC-CENTRIC KAPPAB DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR P65; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 19-304; COMPND 5 SYNONYM: NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT,NUCLEAR FACTOR OF COMPND 6 KAPPA LIGHT POLYPEPTIDE GENE ENHANCER IN B-CELLS 3; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'- COMPND 10 D(P*AP*CP*TP*GP*GP*GP*AP*AP*GP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(P*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*CP*TP*TP*CP*CP*CP*AP*GP*T)-3'); COMPND 16 CHAIN: D; COMPND 17 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: RELA, NFKB3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS RELA, KAPPAB DNA, PROMOTER, TRANSCRIPTION, DNA BINDING PROTEIN, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.BISWAS,S.SHAHABI,O.V.TSODIKOV,D.HUANG,G.GHOSH REVDAT 1 24-APR-24 9BDW 0 JRNL AUTH T.BISWAS,S.SHANDY,O.V.TSODIKOV,D.HUANG,T.LI,Y.WANG,V.WANG, JRNL AUTH 2 G.GHOSH JRNL TITL TRANSIENT INTERACTIONS MODULATE AFFINITY OF NF-KAPPAB JRNL TITL 2 TRANSCRIPTION FACTORS FOR DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 56382 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2947 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) : 1.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3103 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 161 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4373 REMARK 3 NUCLEIC ACID ATOMS : 781 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 564 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.09000 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): 0.332 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.356 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5398 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4444 ; 0.011 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7488 ; 1.676 ; 1.693 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10455 ; 0.567 ; 1.561 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 549 ; 7.602 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;13.604 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 748 ;16.313 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 811 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5673 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 994 ; 0.002 ; 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): 2202 ; 3.820 ; 2.456 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2202 ; 3.821 ; 2.456 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2749 ; 4.698 ; 3.657 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2750 ; 4.708 ; 3.660 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3196 ; 6.877 ; 3.800 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3189 ; 6.860 ; 3.783 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4728 ; 9.103 ; 5.548 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6277 ; 9.386 ;49.696 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6146 ; 9.427 ;47.528 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 9806 ; 4.304 ; 3.000 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 9BDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-APR-24. REMARK 100 THE DEPOSITION ID IS D_1000282433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL 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) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60489 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.98700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 3.69600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2RAM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, MES, SPERMINE, BETA REMARK 280 -OCTYLGLUCOSIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 59.63150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.54200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 59.63150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.54200 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -127.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D 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 APPLY THE FOLLOWING TO CHAINS: A 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 45.67000 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 ASP A 294 REMARK 465 ARG A 295 REMARK 465 HIS A 296 REMARK 465 ARG A 297 REMARK 465 ILE A 298 REMARK 465 GLU A 299 REMARK 465 GLU A 300 REMARK 465 LYS A 301 REMARK 465 ARG A 302 REMARK 465 LYS A 303 REMARK 465 ARG A 304 REMARK 465 THR B 292 REMARK 465 ASP B 293 REMARK 465 ASP B 294 REMARK 465 ARG B 295 REMARK 465 HIS B 296 REMARK 465 ARG B 297 REMARK 465 ILE B 298 REMARK 465 GLU B 299 REMARK 465 GLU B 300 REMARK 465 LYS B 301 REMARK 465 ARG B 302 REMARK 465 LYS B 303 REMARK 465 ARG B 304 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 THR A 54 OG1 CG2 REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 ARG B 149 CG CD NE 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 O GLN B 29 O4 SO4 B 404 1.93 REMARK 500 O HOH C 1031 O HOH C 1040 2.11 REMARK 500 NH2 ARG A 41 O6 DG C 104 2.14 REMARK 500 CB VAL B 121 O HOH B 682 2.17 REMARK 500 O HOH A 666 O HOH A 712 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 DA C 101 P DA C 101 OP3 -0.091 REMARK 500 DA D 201 P DA D 201 OP3 -0.085 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 ARG A 84 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 33 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG B 35 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 35 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 84 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 201 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 201 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC C 102 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG C 105 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA C 107 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA D 210 O3' - P - OP2 ANGL. DEV. = 7.0 DEGREES REMARK 500 DA D 210 O5' - P - OP2 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC D 211 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 DC D 211 C5 - C4 - N4 ANGL. DEV. = 4.3 DEGREES 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 43 -3.24 81.26 REMARK 500 ASP A 53 -66.72 34.37 REMARK 500 THR A 55 76.10 145.78 REMARK 500 ASN A 138 79.44 -106.51 REMARK 500 VAL A 165 -164.34 -114.86 REMARK 500 ASP A 223 55.46 -143.94 REMARK 500 GLN A 247 -0.24 67.11 REMARK 500 THR B 54 -74.09 -83.54 REMARK 500 ASN B 139 72.87 -160.03 REMARK 500 VAL B 165 -168.21 -113.48 REMARK 500 ASP B 223 56.57 -141.01 REMARK 500 PRO B 231 104.34 -35.69 REMARK 500 PRO B 260 3.56 -66.30 REMARK 500 GLN B 263 -74.08 -44.67 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 ARG A 30 0.12 SIDE CHAIN REMARK 500 ARG A 84 0.10 SIDE CHAIN REMARK 500 ARG A 108 0.08 SIDE CHAIN REMARK 500 ARG A 133 0.10 SIDE CHAIN REMARK 500 ARG A 198 0.15 SIDE CHAIN REMARK 500 ARG A 273 0.15 SIDE CHAIN REMARK 500 ARG B 33 0.19 SIDE CHAIN REMARK 500 ARG B 35 0.18 SIDE CHAIN REMARK 500 ARG B 133 0.09 SIDE CHAIN REMARK 500 ARG B 201 0.12 SIDE CHAIN REMARK 500 ARG B 236 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 713 DISTANCE = 6.49 ANGSTROMS DBREF 9BDW A 19 304 UNP Q04207 TF65_MOUSE 19 304 DBREF 9BDW B 19 304 UNP Q04207 TF65_MOUSE 19 304 DBREF 9BDW C 101 119 PDB 9BDW 9BDW 101 119 DBREF 9BDW D 201 219 PDB 9BDW 9BDW 201 219 SEQADV 9BDW MET A 18 UNP Q04207 INITIATING METHIONINE SEQADV 9BDW MET B 18 UNP Q04207 INITIATING METHIONINE SEQRES 1 A 287 MET PRO TYR VAL GLU ILE ILE GLU GLN PRO LYS GLN ARG SEQRES 2 A 287 GLY MET ARG PHE ARG TYR LYS CYS GLU GLY ARG SER ALA SEQRES 3 A 287 GLY SER ILE PRO GLY GLU ARG SER THR ASP THR THR LYS SEQRES 4 A 287 THR HIS PRO THR ILE LYS ILE ASN GLY TYR THR GLY PRO SEQRES 5 A 287 GLY THR VAL ARG ILE SER LEU VAL THR LYS ASP PRO PRO SEQRES 6 A 287 HIS ARG PRO HIS PRO HIS GLU LEU VAL GLY LYS ASP CYS SEQRES 7 A 287 ARG ASP GLY TYR TYR GLU ALA ASP LEU CYS PRO ASP ARG SEQRES 8 A 287 SER ILE HIS SER PHE GLN ASN LEU GLY ILE GLN CYS VAL SEQRES 9 A 287 LYS LYS ARG ASP LEU GLU GLN ALA ILE SER GLN ARG ILE SEQRES 10 A 287 GLN THR ASN ASN ASN PRO PHE HIS VAL PRO ILE GLU GLU SEQRES 11 A 287 GLN ARG GLY ASP TYR ASP LEU ASN ALA VAL ARG LEU CYS SEQRES 12 A 287 PHE GLN VAL THR VAL ARG ASP PRO ALA GLY ARG PRO LEU SEQRES 13 A 287 LEU LEU THR PRO VAL LEU SER HIS PRO ILE PHE ASP ASN SEQRES 14 A 287 ARG ALA PRO ASN THR ALA GLU LEU LYS ILE CYS ARG VAL SEQRES 15 A 287 ASN ARG ASN SER GLY SER CYS LEU GLY GLY ASP GLU ILE SEQRES 16 A 287 PHE LEU LEU CYS ASP LYS VAL GLN LYS GLU ASP ILE GLU SEQRES 17 A 287 VAL TYR PHE THR GLY PRO GLY TRP GLU ALA ARG GLY SER SEQRES 18 A 287 PHE SER GLN ALA ASP VAL HIS ARG GLN VAL ALA ILE VAL SEQRES 19 A 287 PHE ARG THR PRO PRO TYR ALA ASP PRO SER LEU GLN ALA SEQRES 20 A 287 PRO VAL ARG VAL SER MET GLN LEU ARG ARG PRO SER ASP SEQRES 21 A 287 ARG GLU LEU SER GLU PRO MET GLU PHE GLN TYR LEU PRO SEQRES 22 A 287 ASP THR ASP ASP ARG HIS ARG ILE GLU GLU LYS ARG LYS SEQRES 23 A 287 ARG SEQRES 1 B 287 MET PRO TYR VAL GLU ILE ILE GLU GLN PRO LYS GLN ARG SEQRES 2 B 287 GLY MET ARG PHE ARG TYR LYS CYS GLU GLY ARG SER ALA SEQRES 3 B 287 GLY SER ILE PRO GLY GLU ARG SER THR ASP THR THR LYS SEQRES 4 B 287 THR HIS PRO THR ILE LYS ILE ASN GLY TYR THR GLY PRO SEQRES 5 B 287 GLY THR VAL ARG ILE SER LEU VAL THR LYS ASP PRO PRO SEQRES 6 B 287 HIS ARG PRO HIS PRO HIS GLU LEU VAL GLY LYS ASP CYS SEQRES 7 B 287 ARG ASP GLY TYR TYR GLU ALA ASP LEU CYS PRO ASP ARG SEQRES 8 B 287 SER ILE HIS SER PHE GLN ASN LEU GLY ILE GLN CYS VAL SEQRES 9 B 287 LYS LYS ARG ASP LEU GLU GLN ALA ILE SER GLN ARG ILE SEQRES 10 B 287 GLN THR ASN ASN ASN PRO PHE HIS VAL PRO ILE GLU GLU SEQRES 11 B 287 GLN ARG GLY ASP TYR ASP LEU ASN ALA VAL ARG LEU CYS SEQRES 12 B 287 PHE GLN VAL THR VAL ARG ASP PRO ALA GLY ARG PRO LEU SEQRES 13 B 287 LEU LEU THR PRO VAL LEU SER HIS PRO ILE PHE ASP ASN SEQRES 14 B 287 ARG ALA PRO ASN THR ALA GLU LEU LYS ILE CYS ARG VAL SEQRES 15 B 287 ASN ARG ASN SER GLY SER CYS LEU GLY GLY ASP GLU ILE SEQRES 16 B 287 PHE LEU LEU CYS ASP LYS VAL GLN LYS GLU ASP ILE GLU SEQRES 17 B 287 VAL TYR PHE THR GLY PRO GLY TRP GLU ALA ARG GLY SER SEQRES 18 B 287 PHE SER GLN ALA ASP VAL HIS ARG GLN VAL ALA ILE VAL SEQRES 19 B 287 PHE ARG THR PRO PRO TYR ALA ASP PRO SER LEU GLN ALA SEQRES 20 B 287 PRO VAL ARG VAL SER MET GLN LEU ARG ARG PRO SER ASP SEQRES 21 B 287 ARG GLU LEU SER GLU PRO MET GLU PHE GLN TYR LEU PRO SEQRES 22 B 287 ASP THR ASP ASP ARG HIS ARG ILE GLU GLU LYS ARG LYS SEQRES 23 B 287 ARG SEQRES 1 C 19 DA DC DT DG DG DG DA DA DG DT DT DC DC SEQRES 2 C 19 DA DG DT DG DA DT SEQRES 1 D 19 DA DT DC DA DC DT DG DG DA DA DC DT DT SEQRES 2 D 19 DC DC DC DA DG DT HET SO4 A 400 5 HET SO4 B 401 5 HET SO4 B 402 5 HET SO4 B 403 5 HET SO4 B 404 5 HET BOG C 900 20 HETNAM SO4 SULFATE ION HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE FORMUL 5 SO4 5(O4 S 2-) FORMUL 10 BOG C14 H28 O6 FORMUL 11 HOH *564(H2 O) HELIX 1 AA1 CYS A 38 GLY A 40 5 3 HELIX 2 AA2 LYS A 122 ARG A 124 5 3 HELIX 3 AA3 ASP A 125 THR A 136 1 12 HELIX 4 AA4 PRO A 144 GLY A 150 5 7 HELIX 5 AA5 ALA A 188 ALA A 192 5 5 HELIX 6 AA6 SER A 240 ALA A 242 5 3 HELIX 7 AA7 CYS B 38 GLY B 40 5 3 HELIX 8 AA8 LYS B 122 ARG B 124 5 3 HELIX 9 AA9 ASP B 125 THR B 136 1 12 HELIX 10 AB1 PRO B 144 GLN B 148 5 5 HELIX 11 AB2 SER B 240 ALA B 242 5 3 SHEET 1 AA1 3 TYR A 20 GLU A 25 0 SHEET 2 AA1 3 THR A 60 ASN A 64 -1 O ASN A 64 N TYR A 20 SHEET 3 AA1 3 ILE A 110 SER A 112 -1 O HIS A 111 N ILE A 61 SHEET 1 AA2 3 ARG A 35 TYR A 36 0 SHEET 2 AA2 3 GLY A 117 CYS A 120 1 O CYS A 120 N ARG A 35 SHEET 3 AA2 3 GLU A 89 VAL A 91 -1 N GLU A 89 O GLN A 119 SHEET 1 AA3 5 CYS A 95 ARG A 96 0 SHEET 2 AA3 5 TYR A 99 ASP A 103 -1 O TYR A 99 N ARG A 96 SHEET 3 AA3 5 THR A 71 VAL A 77 -1 N VAL A 72 O ALA A 102 SHEET 4 AA3 5 ALA A 156 ARG A 166 -1 O GLN A 162 N ARG A 73 SHEET 5 AA3 5 PRO A 172 LEU A 174 -1 O LEU A 173 N VAL A 165 SHEET 1 AA4 5 CYS A 95 ARG A 96 0 SHEET 2 AA4 5 TYR A 99 ASP A 103 -1 O TYR A 99 N ARG A 96 SHEET 3 AA4 5 THR A 71 VAL A 77 -1 N VAL A 72 O ALA A 102 SHEET 4 AA4 5 ALA A 156 ARG A 166 -1 O GLN A 162 N ARG A 73 SHEET 5 AA4 5 VAL A 178 PHE A 184 -1 O VAL A 178 N PHE A 161 SHEET 1 AA5 4 ILE A 196 VAL A 199 0 SHEET 2 AA5 4 GLU A 211 CYS A 216 -1 O LEU A 215 N ARG A 198 SHEET 3 AA5 4 ALA A 249 ARG A 253 -1 O PHE A 252 N ILE A 212 SHEET 4 AA5 4 VAL A 244 HIS A 245 -1 N HIS A 245 O ALA A 249 SHEET 1 AA6 5 SER A 203 SER A 205 0 SHEET 2 AA6 5 MET A 284 LEU A 289 1 O LEU A 289 N GLY A 204 SHEET 3 AA6 5 VAL A 266 ARG A 274 -1 N VAL A 268 O PHE A 286 SHEET 4 AA6 5 GLU A 225 GLY A 230 -1 N TYR A 227 O GLN A 271 SHEET 5 AA6 5 TRP A 233 ARG A 236 -1 O ALA A 235 N PHE A 228 SHEET 1 AA7 4 SER A 203 SER A 205 0 SHEET 2 AA7 4 MET A 284 LEU A 289 1 O LEU A 289 N GLY A 204 SHEET 3 AA7 4 VAL A 266 ARG A 274 -1 N VAL A 268 O PHE A 286 SHEET 4 AA7 4 GLU A 279 LEU A 280 -1 O GLU A 279 N ARG A 274 SHEET 1 AA8 3 TYR B 20 GLU B 25 0 SHEET 2 AA8 3 THR B 60 ASN B 64 -1 O LYS B 62 N GLU B 22 SHEET 3 AA8 3 ILE B 110 SER B 112 -1 O HIS B 111 N ILE B 61 SHEET 1 AA9 3 ARG B 35 TYR B 36 0 SHEET 2 AA9 3 GLY B 117 CYS B 120 1 O ILE B 118 N ARG B 35 SHEET 3 AA9 3 GLU B 89 VAL B 91 -1 N GLU B 89 O GLN B 119 SHEET 1 AB1 5 CYS B 95 ARG B 96 0 SHEET 2 AB1 5 TYR B 99 ASP B 103 -1 O TYR B 99 N ARG B 96 SHEET 3 AB1 5 THR B 71 VAL B 77 -1 N ILE B 74 O TYR B 100 SHEET 4 AB1 5 ALA B 156 ARG B 166 -1 O THR B 164 N THR B 71 SHEET 5 AB1 5 VAL B 178 LEU B 179 -1 O VAL B 178 N PHE B 161 SHEET 1 AB2 3 PRO B 172 LEU B 174 0 SHEET 2 AB2 3 ALA B 156 ARG B 166 -1 N VAL B 165 O LEU B 173 SHEET 3 AB2 3 ILE B 183 PHE B 184 -1 O ILE B 183 N VAL B 157 SHEET 1 AB3 4 ILE B 196 VAL B 199 0 SHEET 2 AB3 4 GLU B 211 CYS B 216 -1 O LEU B 215 N ARG B 198 SHEET 3 AB3 4 ALA B 249 ARG B 253 -1 O PHE B 252 N ILE B 212 SHEET 4 AB3 4 VAL B 244 HIS B 245 -1 N HIS B 245 O ALA B 249 SHEET 1 AB4 5 SER B 203 SER B 205 0 SHEET 2 AB4 5 MET B 284 LEU B 289 1 O LEU B 289 N GLY B 204 SHEET 3 AB4 5 VAL B 266 ARG B 273 -1 N VAL B 268 O PHE B 286 SHEET 4 AB4 5 GLU B 225 GLY B 230 -1 N TYR B 227 O GLN B 271 SHEET 5 AB4 5 TRP B 233 ARG B 236 -1 O TRP B 233 N GLY B 230 CISPEP 1 PRO A 81 PRO A 82 0 -3.46 CISPEP 2 PRO B 81 PRO B 82 0 -7.92 CRYST1 119.263 133.084 45.670 90.00 90.00 90.00 P 21 21 2 8 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 0.008385 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021896 0.00000