HEADER DNA BINDING PROTEIN/DNA 29-JUL-23 8K8C TITLE CRYSTAL STRUCTURE OF C/EBPALPHA BZIP DOMAIN BOUND TO A HIGH AFFINITY TITLE 2 DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CCAAT/ENHANCER-BINDING PROTEIN ALPHA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*A)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*T)-3'); COMPND 11 CHAIN: D; COMPND 12 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: CEBPA; 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 C/EBPALPHA, DNA BINDING, BZIP, DNA BINDING PROTEIN, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.MIN,S.Z.CHEN,K.LIU REVDAT 2 27-MAR-24 8K8C 1 JRNL REVDAT 1 06-MAR-24 8K8C 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) : 19.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 20673 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.610 REMARK 3 FREE R VALUE TEST SET COUNT : 1986 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 19.9600 - 4.9300 1.00 1448 154 0.1887 0.2727 REMARK 3 2 4.9300 - 3.9200 1.00 1375 146 0.1780 0.2138 REMARK 3 3 3.9200 - 3.4300 0.99 1355 145 0.1878 0.2835 REMARK 3 4 3.4300 - 3.1200 0.99 1334 142 0.2045 0.2352 REMARK 3 5 3.1200 - 2.8900 1.00 1334 140 0.2368 0.2741 REMARK 3 6 2.8900 - 2.7200 1.00 1335 142 0.2435 0.3066 REMARK 3 7 2.7200 - 2.5900 1.00 1322 141 0.2452 0.2974 REMARK 3 8 2.5900 - 2.4800 1.00 1291 138 0.2402 0.2672 REMARK 3 9 2.4800 - 2.3800 1.00 1358 144 0.2556 0.3287 REMARK 3 10 2.3800 - 2.3000 1.00 1298 138 0.3103 0.3555 REMARK 3 11 2.3000 - 2.2300 0.99 1314 141 0.3314 0.3716 REMARK 3 12 2.2300 - 2.1600 0.99 1307 136 0.4008 0.4274 REMARK 3 13 2.1600 - 2.1100 0.99 1305 140 0.4436 0.4734 REMARK 3 14 2.1100 - 2.0600 1.00 1311 139 0.4970 0.5043 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.150 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 1604 REMARK 3 ANGLE : 1.073 2250 REMARK 3 CHIRALITY : 0.049 248 REMARK 3 PLANARITY : 0.011 207 REMARK 3 DIHEDRAL : 25.259 398 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 281:402) REMARK 3 ORIGIN FOR THE GROUP (A): 6.0150 5.6201 33.7934 REMARK 3 T TENSOR REMARK 3 T11: 0.4444 T22: 0.3295 REMARK 3 T33: 0.3704 T12: 0.0609 REMARK 3 T13: 0.0336 T23: 0.0387 REMARK 3 L TENSOR REMARK 3 L11: 0.1942 L22: 0.1833 REMARK 3 L33: 1.0803 L12: 0.0122 REMARK 3 L13: 0.5608 L23: -0.5033 REMARK 3 S TENSOR REMARK 3 S11: -0.1909 S12: 0.0847 S13: -0.1852 REMARK 3 S21: 0.0317 S22: -0.0084 S23: -0.1551 REMARK 3 S31: 0.0353 S32: -0.1833 S33: -0.0010 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESSEQ 283:340) REMARK 3 ORIGIN FOR THE GROUP (A): -0.0919 13.5955 37.6300 REMARK 3 T TENSOR REMARK 3 T11: 0.4695 T22: 0.3656 REMARK 3 T33: 0.3990 T12: 0.0259 REMARK 3 T13: -0.0241 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.1556 L22: 0.6074 REMARK 3 L33: 0.9392 L12: 0.0629 REMARK 3 L13: -0.3784 L23: -0.9032 REMARK 3 S TENSOR REMARK 3 S11: -0.1131 S12: 0.1572 S13: 0.1764 REMARK 3 S21: 0.1844 S22: -0.1662 S23: -0.1538 REMARK 3 S31: -0.2746 S32: 0.1210 S33: -0.0006 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN C AND RESSEQ 1:13) REMARK 3 ORIGIN FOR THE GROUP (A): 0.1106 14.6901 13.6178 REMARK 3 T TENSOR REMARK 3 T11: 0.3912 T22: 0.4292 REMARK 3 T33: 0.4206 T12: 0.0059 REMARK 3 T13: 0.0587 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.5465 L22: 1.8167 REMARK 3 L33: 2.0134 L12: -0.2782 REMARK 3 L13: 0.0355 L23: 0.3001 REMARK 3 S TENSOR REMARK 3 S11: -0.2884 S12: -0.0524 S13: 0.2255 REMARK 3 S21: 0.0335 S22: -0.0346 S23: 0.1942 REMARK 3 S31: 0.0850 S32: -0.2185 S33: -0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN D AND RESSEQ 1:13) REMARK 3 ORIGIN FOR THE GROUP (A): 4.6994 16.9808 14.6827 REMARK 3 T TENSOR REMARK 3 T11: 0.3916 T22: 0.4678 REMARK 3 T33: 0.3893 T12: 0.0056 REMARK 3 T13: 0.0038 T23: -0.0264 REMARK 3 L TENSOR REMARK 3 L11: 1.1921 L22: 0.9404 REMARK 3 L33: 1.7618 L12: -0.9712 REMARK 3 L13: -0.4042 L23: -0.1973 REMARK 3 S TENSOR REMARK 3 S11: -0.0924 S12: -0.3242 S13: -0.1801 REMARK 3 S21: 0.1185 S22: -0.0416 S23: 0.0576 REMARK 3 S31: 0.0333 S32: 0.1633 S33: -0.0004 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 8K8C 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_1300039783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20836 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 64.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 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) : 2.17 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 (%): 65.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.015 M CALCIUM CHLORIDE DIHYDRATE,0.1 REMARK 280 M SODIUM ACETATE TRIHYDRATE PH 4.6, 30% V/V 2-METHYL-2,4- REMARK 280 PENTANEDIOL, VAPOR DIFFUSION, SITTING 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 19.69100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.27300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.68300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.27300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.69100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.68300 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: 6010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 GLY A 280 REMARK 465 GLY B 280 REMARK 465 ASN B 281 REMARK 465 SER B 282 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 DG C 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT D 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 8K8C A 281 340 UNP P49715 CEBPA_HUMAN 281 340 DBREF 8K8C B 281 340 UNP P49715 CEBPA_HUMAN 281 340 DBREF 8K8C C 1 13 PDB 8K8C 8K8C 1 13 DBREF 8K8C D 1 13 PDB 8K8C 8K8C 1 13 SEQADV 8K8C GLY A 280 UNP P49715 EXPRESSION TAG SEQADV 8K8C GLY B 280 UNP P49715 EXPRESSION TAG SEQRES 1 A 61 GLY ASN SER ASN GLU TYR ARG VAL ARG ARG GLU ARG ASN SEQRES 2 A 61 ASN ILE ALA VAL ARG LYS SER ARG ASP LYS ALA LYS GLN SEQRES 3 A 61 ARG ASN VAL GLU THR GLN GLN LYS VAL LEU GLU LEU THR SEQRES 4 A 61 SER ASP ASN ASP ARG LEU ARG LYS ARG VAL GLU GLN LEU SEQRES 5 A 61 SER ARG GLU LEU ASP THR LEU ARG GLY SEQRES 1 B 61 GLY ASN SER ASN GLU TYR ARG VAL ARG ARG GLU ARG ASN SEQRES 2 B 61 ASN ILE ALA VAL ARG LYS SER ARG ASP LYS ALA LYS GLN SEQRES 3 B 61 ARG ASN VAL GLU THR GLN GLN LYS VAL LEU GLU LEU THR SEQRES 4 B 61 SER ASP ASN ASP ARG LEU ARG LYS ARG VAL GLU GLN LEU SEQRES 5 B 61 SER ARG GLU LEU ASP THR LEU ARG GLY SEQRES 1 C 13 DC DA DT DT DA DC DG DT DA DA DT DG DA SEQRES 1 D 13 DC DA DT DT DA DC DG DT DA DA DT DG DT HET GOL A 401 6 HET GOL A 402 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *55(H2 O) HELIX 1 AA1 ASN A 283 ARG A 339 1 57 HELIX 2 AA2 GLU B 284 LEU B 338 1 55 CRYST1 39.382 63.366 128.546 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 0.025392 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007779 0.00000