HEADER DNA BINDING PROTEIN 29-JUL-23 8K89 TITLE CRYSTAL STRUCTURE OF NFIL3 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 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 KEYWDS NFIL3, BZIP, C/EBP-RELATED PROTEIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.R.MIN,S.Z.CHEN,K.LIU REVDAT 2 27-MAR-24 8K89 1 JRNL REVDAT 1 06-MAR-24 8K89 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 12493 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 609 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 19.5200 - 3.3300 0.99 3362 186 0.2058 0.2708 REMARK 3 2 3.3200 - 2.7200 1.00 2707 122 0.2895 0.3146 REMARK 3 3 2.6000 - 2.3100 0.99 2856 157 0.2855 0.3037 REMARK 3 4 2.3100 - 2.1000 0.92 2959 144 0.2944 0.3923 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.160 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 : 0.008 1230 REMARK 3 ANGLE : 0.955 1637 REMARK 3 CHIRALITY : 0.048 182 REMARK 3 PLANARITY : 0.009 206 REMARK 3 DIHEDRAL : 4.563 165 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 16.8452 45.1132 48.7933 REMARK 3 T TENSOR REMARK 3 T11: 0.3561 T22: 0.3592 REMARK 3 T33: 0.3650 T12: 0.0105 REMARK 3 T13: 0.0046 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 0.9733 L22: 0.8741 REMARK 3 L33: 1.2526 L12: 0.0216 REMARK 3 L13: -0.2003 L23: -0.6918 REMARK 3 S TENSOR REMARK 3 S11: 0.0252 S12: 0.2652 S13: 0.0627 REMARK 3 S21: -0.0568 S22: 0.0287 S23: 0.0798 REMARK 3 S31: 0.0008 S32: 0.0150 S33: 0.0064 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 8K89 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_1300039754. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12570 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 35.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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: MAD 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 (%): 50.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE TRIHYDRATE PH REMARK 280 6.5, 1.4 M SODIUM ACETATE TRIHYDRATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.05800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.61000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.84200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.61000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.05800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.84200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 64 REMARK 465 GLU A 65 REMARK 465 PHE A 66 REMARK 465 MSE A 67 REMARK 465 PRO A 68 REMARK 465 ASP A 69 REMARK 465 GLU A 70 REMARK 465 LYS A 71 REMARK 465 GLN A 150 REMARK 465 ASP A 151 REMARK 465 TYR A 152 REMARK 465 GLN A 153 REMARK 465 THR A 154 REMARK 465 SER A 155 REMARK 465 LYS A 156 REMARK 465 SER A 157 REMARK 465 ASN A 158 REMARK 465 VAL A 159 REMARK 465 SER A 160 REMARK 465 SER A 161 REMARK 465 GLY B 64 REMARK 465 GLU B 65 REMARK 465 PHE B 66 REMARK 465 MSE 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 144 REMARK 465 THR B 145 REMARK 465 ALA B 146 REMARK 465 VAL B 147 REMARK 465 TYR B 148 REMARK 465 PHE B 149 REMARK 465 GLN B 150 REMARK 465 ASP B 151 REMARK 465 TYR B 152 REMARK 465 GLN B 153 REMARK 465 THR B 154 REMARK 465 SER B 155 REMARK 465 LYS B 156 REMARK 465 SER B 157 REMARK 465 ASN B 158 REMARK 465 VAL B 159 REMARK 465 SER B 160 REMARK 465 SER B 161 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 TYR A 148 -68.33 -96.13 REMARK 500 ASP B 73 -159.92 -96.76 REMARK 500 REMARK 500 REMARK: NULL DBREF 8K89 A 68 161 UNP Q16649 NFIL3_HUMAN 68 161 DBREF 8K89 B 68 161 UNP Q16649 NFIL3_HUMAN 68 161 SEQADV 8K89 GLY A 64 UNP Q16649 EXPRESSION TAG SEQADV 8K89 GLU A 65 UNP Q16649 EXPRESSION TAG SEQADV 8K89 PHE A 66 UNP Q16649 EXPRESSION TAG SEQADV 8K89 MSE A 67 UNP Q16649 EXPRESSION TAG SEQADV 8K89 MSE A 138 UNP Q16649 ILE 138 CONFLICT SEQADV 8K89 GLY B 64 UNP Q16649 EXPRESSION TAG SEQADV 8K89 GLU B 65 UNP Q16649 EXPRESSION TAG SEQADV 8K89 PHE B 66 UNP Q16649 EXPRESSION TAG SEQADV 8K89 MSE B 67 UNP Q16649 EXPRESSION TAG SEQADV 8K89 MSE B 138 UNP Q16649 ILE 138 CONFLICT SEQRES 1 A 98 GLY GLU PHE MSE PRO ASP GLU LYS LYS ASP ALA MSE TYR SEQRES 2 A 98 TRP GLU LYS ARG ARG LYS ASN ASN GLU ALA ALA LYS ARG SEQRES 3 A 98 SER ARG GLU LYS ARG ARG LEU ASN ASP LEU VAL LEU GLU SEQRES 4 A 98 ASN LYS LEU ILE ALA LEU GLY GLU GLU ASN ALA THR LEU SEQRES 5 A 98 LYS ALA GLU LEU LEU SER LEU LYS LEU LYS PHE GLY LEU SEQRES 6 A 98 ILE SER SER THR ALA TYR ALA GLN GLU MSE GLN LYS LEU SEQRES 7 A 98 SER ASN SER THR ALA VAL TYR PHE GLN ASP TYR GLN THR SEQRES 8 A 98 SER LYS SER ASN VAL SER SER SEQRES 1 B 98 GLY GLU PHE MSE PRO ASP GLU LYS LYS ASP ALA MSE TYR SEQRES 2 B 98 TRP GLU LYS ARG ARG LYS ASN ASN GLU ALA ALA LYS ARG SEQRES 3 B 98 SER ARG GLU LYS ARG ARG LEU ASN ASP LEU VAL LEU GLU SEQRES 4 B 98 ASN LYS LEU ILE ALA LEU GLY GLU GLU ASN ALA THR LEU SEQRES 5 B 98 LYS ALA GLU LEU LEU SER LEU LYS LEU LYS PHE GLY LEU SEQRES 6 B 98 ILE SER SER THR ALA TYR ALA GLN GLU MSE GLN LYS LEU SEQRES 7 B 98 SER ASN SER THR ALA VAL TYR PHE GLN ASP TYR GLN THR SEQRES 8 B 98 SER LYS SER ASN VAL SER SER MODRES 8K89 MSE A 75 MET MODIFIED RESIDUE MODRES 8K89 MSE B 75 MET MODIFIED RESIDUE HET MSE A 75 8 HET MSE A 138 8 HET MSE B 75 8 HET MSE B 138 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 HOH *17(H2 O) HELIX 1 AA1 ASP A 73 PHE A 126 1 54 HELIX 2 AA2 SER A 130 VAL A 147 1 18 HELIX 3 AA3 ASP B 73 PHE B 126 1 54 HELIX 4 AA4 SER B 130 LYS B 140 1 11 LINK C ALA A 74 N MSE A 75 1555 1555 1.32 LINK C MSE A 75 N TYR A 76 1555 1555 1.34 LINK C GLU A 137 N MSE A 138 1555 1555 1.33 LINK C MSE A 138 N GLN A 139 1555 1555 1.34 LINK C ALA B 74 N MSE B 75 1555 1555 1.33 LINK C MSE B 75 N TYR B 76 1555 1555 1.34 LINK C GLU B 137 N MSE B 138 1555 1555 1.33 LINK C MSE B 138 N GLN B 139 1555 1555 1.34 CRYST1 40.116 65.684 85.220 90.00 90.00 90.00 P 21 21 21 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 0.024928 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015224 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011734 0.00000