HEADER DNA BINDING PROTEIN/DNA 28-JUL-23 8K86 TITLE CRYSTAL STRUCTURE OF NFIL3 IN COMPLEX WITH TTATGTAA DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR FACTOR INTERLEUKIN-3-REGULATED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: E4 PROMOTER-BINDING PROTEIN 4,INTERLEUKIN-3 PROMOTER COMPND 5 TRANSCRIPTIONAL ACTIVATOR,INTERLEUKIN-3-BINDING PROTEIN 1, COMPND 6 TRANSCRIPTIONAL ACTIVATOR NF-IL3A; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*TP*AP*AP*CP*G)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*GP*TP*TP*AP*CP*AP*TP*AP*AP*TP*G)-3'); COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NFIL3, E4BP4, IL3BP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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 NFIL3, BZIP, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.MIN,S.Z.CHEN,K.LIU REVDAT 2 27-MAR-24 8K86 1 JRNL REVDAT 1 06-MAR-24 8K86 0 JRNL AUTH S.CHEN,M.LEI,K.LIU,J.MIN JRNL TITL STRUCTURAL BASIS FOR SPECIFIC DNA SEQUENCE RECOGNITION BY JRNL TITL 2 THE TRANSCRIPTION FACTOR NFIL3. JRNL REF J.BIOL.CHEM. V. 300 05776 2024 JRNL REFN ESSN 1083-351X JRNL PMID 38382670 JRNL DOI 10.1016/J.JBC.2024.105776 REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17941 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1794 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.9100 - 4.8300 1.00 1354 149 0.1955 0.2108 REMARK 3 2 4.8300 - 3.8500 1.00 1282 142 0.1891 0.2184 REMARK 3 3 3.8400 - 3.3600 1.00 1250 139 0.2102 0.2416 REMARK 3 4 3.3600 - 3.0500 1.00 1255 140 0.2272 0.2813 REMARK 3 5 3.0500 - 2.8400 1.00 1235 138 0.2629 0.3075 REMARK 3 6 2.8400 - 2.6700 1.00 1244 139 0.2555 0.3015 REMARK 3 7 2.6700 - 2.5400 1.00 1229 135 0.2391 0.2647 REMARK 3 8 2.5400 - 2.4300 1.00 1213 134 0.2403 0.2838 REMARK 3 9 2.4300 - 2.3300 1.00 1234 138 0.2314 0.2772 REMARK 3 10 2.3300 - 2.2500 0.99 1221 135 0.2564 0.2982 REMARK 3 11 2.2500 - 2.1800 0.99 1208 135 0.2751 0.3462 REMARK 3 12 2.1800 - 2.1200 1.00 1228 137 0.2757 0.3140 REMARK 3 13 2.1200 - 2.0600 1.00 1194 133 0.2775 0.3840 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1550 REMARK 3 ANGLE : 0.875 2170 REMARK 3 CHIRALITY : 0.042 241 REMARK 3 PLANARITY : 0.007 192 REMARK 3 DIHEDRAL : 26.592 365 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8K86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300039755. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18067 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 58.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE PH REMARK 280 5.6, 8% W/V POLYETHYLENE GLYCOL 4000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K 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 37.04200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.76000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.04200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.76000 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: 5380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 218 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 228 LIES ON A SPECIAL POSITION. 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 GLY A 64 REMARK 465 GLU A 65 REMARK 465 PHE A 66 REMARK 465 SER A 130 REMARK 465 SER A 131 REMARK 465 THR A 132 REMARK 465 ALA A 133 REMARK 465 TYR A 134 REMARK 465 ALA A 135 REMARK 465 GLN A 136 REMARK 465 GLY B 64 REMARK 465 GLU B 65 REMARK 465 PHE B 66 REMARK 465 MET B 67 REMARK 465 PRO B 68 REMARK 465 ASP B 69 REMARK 465 GLU B 70 REMARK 465 LYS B 71 REMARK 465 SER B 130 REMARK 465 SER B 131 REMARK 465 THR B 132 REMARK 465 ALA B 133 REMARK 465 TYR B 134 REMARK 465 ALA B 135 REMARK 465 GLN B 136 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 DT D 11 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES 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 A 269 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH C 115 DISTANCE = 8.15 ANGSTROMS DBREF 8K86 A 68 136 UNP Q16649 NFIL3_HUMAN 68 136 DBREF 8K86 B 68 136 UNP Q16649 NFIL3_HUMAN 68 136 DBREF 8K86 C 1 12 PDB 8K86 8K86 1 12 DBREF 8K86 D 1 12 PDB 8K86 8K86 1 12 SEQADV 8K86 GLY A 64 UNP Q16649 EXPRESSION TAG SEQADV 8K86 GLU A 65 UNP Q16649 EXPRESSION TAG SEQADV 8K86 PHE A 66 UNP Q16649 EXPRESSION TAG SEQADV 8K86 MET A 67 UNP Q16649 EXPRESSION TAG SEQADV 8K86 GLY B 64 UNP Q16649 EXPRESSION TAG SEQADV 8K86 GLU B 65 UNP Q16649 EXPRESSION TAG SEQADV 8K86 PHE B 66 UNP Q16649 EXPRESSION TAG SEQADV 8K86 MET B 67 UNP Q16649 EXPRESSION TAG SEQRES 1 A 73 GLY GLU PHE MET PRO ASP GLU LYS LYS ASP ALA MET TYR SEQRES 2 A 73 TRP GLU LYS ARG ARG LYS ASN ASN GLU ALA ALA LYS ARG SEQRES 3 A 73 SER ARG GLU LYS ARG ARG LEU ASN ASP LEU VAL LEU GLU SEQRES 4 A 73 ASN LYS LEU ILE ALA LEU GLY GLU GLU ASN ALA THR LEU SEQRES 5 A 73 LYS ALA GLU LEU LEU SER LEU LYS LEU LYS PHE GLY LEU SEQRES 6 A 73 ILE SER SER THR ALA TYR ALA GLN SEQRES 1 B 73 GLY GLU PHE MET PRO ASP GLU LYS LYS ASP ALA MET TYR SEQRES 2 B 73 TRP GLU LYS ARG ARG LYS ASN ASN GLU ALA ALA LYS ARG SEQRES 3 B 73 SER ARG GLU LYS ARG ARG LEU ASN ASP LEU VAL LEU GLU SEQRES 4 B 73 ASN LYS LEU ILE ALA LEU GLY GLU GLU ASN ALA THR LEU SEQRES 5 B 73 LYS ALA GLU LEU LEU SER LEU LYS LEU LYS PHE GLY LEU SEQRES 6 B 73 ILE SER SER THR ALA TYR ALA GLN SEQRES 1 C 12 DC DA DT DT DA DT DG DT DA DA DC DG SEQRES 1 D 12 DC DG DT DT DA DC DA DT DA DA DT DG FORMUL 5 HOH *138(H2 O) HELIX 1 AA1 PRO A 68 LYS A 72 5 5 HELIX 2 AA2 ASP A 73 PHE A 126 1 54 HELIX 3 AA3 ASP B 73 PHE B 126 1 54 CRYST1 74.084 97.520 39.007 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 0.013498 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010254 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025636 0.00000