HEADER DNA BINDING PROTEIN/DNA 12-APR-24 9BDU TITLE NF-KAPPAB RELA HOMO-DIMER BOUND TO AT-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*AP*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*TP*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: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS RELA, KAPPAB DNA, PROMOTER, TRANSCRIPTION, DNA BINDING PROTEIN, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.BISWAS,D.HUANG,G.GHOSH REVDAT 1 24-APR-24 9BDU 0 JRNL AUTH T.BISWAS,S.SHANDY,O.V.TSODIKOV,D.HUANG,T.LI,V.WANG,Y.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. 2.03 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 75.3 REMARK 3 NUMBER OF REFLECTIONS : 33225 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1739 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) : 2.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 489 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 15.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4384 REMARK 3 NUCLEIC ACID ATOMS : 781 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 397 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.02000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.254 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.363 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5376 ; 0.006 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4427 ; 0.026 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7457 ; 1.204 ; 1.694 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10414 ; 0.845 ; 1.561 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 548 ; 7.314 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 50 ; 4.656 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 754 ;15.022 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 805 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5672 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 995 ; 0.004 ; 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): 2198 ; 0.410 ; 3.576 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2198 ; 0.410 ; 3.576 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2744 ; 0.497 ; 5.350 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2745 ; 0.497 ; 5.352 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3178 ; 0.428 ; 4.234 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3167 ; 0.424 ; 4.224 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4696 ; 0.512 ; 6.284 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6198 ; 1.167 ;55.606 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6124 ; 1.121 ;54.458 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 9767 ; 2.627 ; 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 9BDU 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_1000282431. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 5-6.5 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 : 46270 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.99400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 2.32000 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 (%): 45.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, MES, BETA-OCTYLGLUCOSIDE, REMARK 280 SPERMINE, 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 57.75800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.78400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.75800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.78400 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: 7390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 18 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 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 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 N7 DA C 109 O HOH C 201 2.10 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 -0.074 REMARK 500 DA D 201 P DA D 201 OP3 -0.081 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 PRO B 81 N - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 DA C 107 O4' - C1' - N9 ANGL. DEV. = 2.7 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 ARG A 41 -2.53 -154.53 REMARK 500 SER A 42 145.90 60.23 REMARK 500 ASN A 138 78.27 -110.61 REMARK 500 ASN A 139 76.11 -152.09 REMARK 500 HIS A 142 51.89 39.98 REMARK 500 ASP A 223 61.42 -151.48 REMARK 500 GLN A 247 -1.46 68.05 REMARK 500 SER A 261 67.73 -119.73 REMARK 500 THR A 292 57.66 -103.75 REMARK 500 SER B 42 135.72 71.46 REMARK 500 PRO B 81 -44.45 -25.15 REMARK 500 ASN B 138 77.77 -101.84 REMARK 500 ASN B 139 74.39 -150.52 REMARK 500 ARG B 149 -25.92 -173.10 REMARK 500 VAL B 165 -169.91 -104.97 REMARK 500 ASN B 190 -33.86 106.99 REMARK 500 ASP B 223 52.55 -141.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 80 PRO A 81 -148.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 9BDU A 19 304 UNP Q04207 TF65_MOUSE 19 304 DBREF 9BDU B 19 304 UNP Q04207 TF65_MOUSE 19 304 DBREF 9BDU C 101 119 PDB 9BDU 9BDU 101 119 DBREF 9BDU D 201 219 PDB 9BDU 9BDU 201 219 SEQADV 9BDU MET A 18 UNP Q04207 INITIATING METHIONINE SEQADV 9BDU 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 DA 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 DT DT DT SEQRES 2 D 19 DC DC DC DA DG DT HET SO4 A 401 5 HET SO4 B 401 5 HET SO4 B 402 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 3(O4 S 2-) FORMUL 8 HOH *397(H2 O) HELIX 1 AA1 LYS A 122 ARG A 124 5 3 HELIX 2 AA2 ASP A 125 THR A 136 1 12 HELIX 3 AA3 GLU A 146 GLY A 150 5 5 HELIX 4 AA4 ALA A 188 ALA A 192 5 5 HELIX 5 AA5 SER A 240 ALA A 242 5 3 HELIX 6 AA6 TYR B 36 GLY B 40 5 5 HELIX 7 AA7 LYS B 122 ARG B 124 5 3 HELIX 8 AA8 ASP B 125 THR B 136 1 12 HELIX 9 AA9 PRO B 144 GLN B 148 5 5 HELIX 10 AB1 SER B 240 VAL B 244 5 5 SHEET 1 AA1 3 TYR A 20 GLU A 25 0 SHEET 2 AA1 3 THR A 60 ASN A 64 -1 O LYS A 62 N GLU A 22 SHEET 3 AA1 3 ILE A 110 SER A 112 -1 O HIS A 111 N ILE A 61 SHEET 1 AA2 5 CYS A 95 ARG A 96 0 SHEET 2 AA2 5 TYR A 99 ASP A 103 -1 O TYR A 99 N ARG A 96 SHEET 3 AA2 5 THR A 71 VAL A 77 -1 N ILE A 74 O TYR A 100 SHEET 4 AA2 5 ALA A 156 ARG A 166 -1 O THR A 164 N THR A 71 SHEET 5 AA2 5 PRO A 172 LEU A 174 -1 O LEU A 173 N VAL A 165 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 ILE A 74 O TYR A 100 SHEET 4 AA3 5 ALA A 156 ARG A 166 -1 O THR A 164 N THR A 71 SHEET 5 AA3 5 VAL A 178 PHE A 184 -1 O ILE A 183 N VAL A 157 SHEET 1 AA4 2 GLU A 89 VAL A 91 0 SHEET 2 AA4 2 GLY A 117 GLN A 119 -1 O GLN A 119 N GLU A 89 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 5 CYS B 95 ARG B 96 0 SHEET 2 AA9 5 TYR B 99 ASP B 103 -1 O TYR B 99 N ARG B 96 SHEET 3 AA9 5 THR B 71 VAL B 77 -1 N ILE B 74 O TYR B 100 SHEET 4 AA9 5 ALA B 156 ARG B 166 -1 O GLN B 162 N ARG B 73 SHEET 5 AA9 5 PRO B 172 LEU B 174 -1 O LEU B 173 N VAL B 165 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 GLN B 162 N ARG B 73 SHEET 5 AB1 5 VAL B 178 PHE B 184 -1 O ILE B 183 N VAL B 157 SHEET 1 AB2 2 GLU B 89 VAL B 91 0 SHEET 2 AB2 2 GLY B 117 GLN B 119 -1 O GLN B 119 N GLU B 89 SHEET 1 AB3 3 ILE B 196 VAL B 199 0 SHEET 2 AB3 3 GLU B 211 CYS B 216 -1 O LEU B 215 N ARG B 198 SHEET 3 AB3 3 ALA B 249 ARG B 253 -1 O PHE B 252 N ILE B 212 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 ALA B 235 N PHE B 228 CRYST1 115.516 133.568 45.443 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 0.008657 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007487 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022006 0.00000