HEADER DNA BINDING PROTEIN 18-OCT-02 1N1J TITLE CRYSTAL STRUCTURE OF THE NF-YB/NF-YC HISTONE PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: NF-YB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NF-YB3; COMPND 5 SYNONYM: NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NF-YC; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: NF-YC2; COMPND 11 SYNONYM: NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PACYC11B; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HISTONE-LIKE PAIR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.ROMIER,F.COCCHIARELLA,R.MANTOVANI,D.MORAS REVDAT 5 13-MAR-24 1N1J 1 REMARK SEQADV REVDAT 4 11-OCT-17 1N1J 1 REMARK REVDAT 3 16-APR-14 1N1J 1 REMARK VERSN REVDAT 2 24-FEB-09 1N1J 1 VERSN REVDAT 1 18-FEB-03 1N1J 0 JRNL AUTH C.ROMIER,F.COCCHIARELLA,R.MANTOVANI,D.MORAS JRNL TITL THE NF-YB/NF-YC STRUCTURE GIVES INSIGHT INTO DNA BINDING AND JRNL TITL 2 TRANSCRIPTION REGULATION BY CCAAT FACTOR NF-Y JRNL REF J.BIOL.CHEM. V. 278 1336 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12401788 JRNL DOI 10.1074/JBC.M209635200 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1171267.130 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 22463 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 SET) : 0.181 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1095 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.67 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3498 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE : 0.2300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 178 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1337 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 299 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.69000 REMARK 3 B22 (A**2) : 1.67000 REMARK 3 B33 (A**2) : -0.98000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.01 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.05 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.080 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.510 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.200 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.180 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 73.83 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1N1J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000017402. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.920023 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PRODC REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22726 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02600 REMARK 200 FOR THE DATA SET : 43.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.05300 REMARK 200 FOR SHELL : 17.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MAGNESIUM ACETATE, SODIUM REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 25.81200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.82250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.17250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.82250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.81200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.17250 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: 4470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 SER A 49 REMARK 465 PHE A 50 REMARK 465 ARG A 51 REMARK 465 GLU A 52 REMARK 465 GLN A 53 REMARK 465 ASP A 54 REMARK 465 GLY B 24 REMARK 465 SER B 25 REMARK 465 HIS B 26 REMARK 465 MET B 27 REMARK 465 GLU B 28 REMARK 465 GLU B 29 REMARK 465 ILE B 30 REMARK 465 ARG B 31 REMARK 465 ASN B 32 REMARK 465 LEU B 33 REMARK 465 THR B 34 REMARK 465 VAL B 35 REMARK 465 LYS B 36 REMARK 465 ASP B 37 REMARK 465 PHE B 38 REMARK 465 ARG B 39 REMARK 465 VAL B 40 REMARK 465 GLN B 41 REMARK 465 GLU B 42 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 64 NE CZ NH1 NH2 REMARK 480 LYS A 67 CD CE NZ REMARK 480 GLU A 114 CD OE1 OE2 REMARK 480 LEU A 134 CG CD1 CD2 REMARK 480 GLN A 137 CD OE1 NE2 REMARK 480 LYS A 138 CD CE NZ REMARK 480 LYS B 50 CE NZ REMARK 480 GLU B 56 CB CG CD OE1 OE2 REMARK 480 ASP B 57 CG OD1 OD2 REMARK 480 LYS B 59 CD CE NZ DBREF 1N1J A 49 141 UNP P25208 NFYB_HUMAN 51 143 DBREF 1N1J B 27 120 UNP Q13952 NFYC_HUMAN 27 120 SEQADV 1N1J GLY B 24 UNP Q13952 CLONING ARTIFACT SEQADV 1N1J SER B 25 UNP Q13952 CLONING ARTIFACT SEQADV 1N1J HIS B 26 UNP Q13952 CLONING ARTIFACT SEQRES 1 A 93 SER PHE ARG GLU GLN ASP ILE TYR LEU PRO ILE ALA ASN SEQRES 2 A 93 VAL ALA ARG ILE MET LYS ASN ALA ILE PRO GLN THR GLY SEQRES 3 A 93 LYS ILE ALA LYS ASP ALA LYS GLU CYS VAL GLN GLU CYS SEQRES 4 A 93 VAL SER GLU PHE ILE SER PHE ILE THR SER GLU ALA SER SEQRES 5 A 93 GLU ARG CYS HIS GLN GLU LYS ARG LYS THR ILE ASN GLY SEQRES 6 A 93 GLU ASP ILE LEU PHE ALA MET SER THR LEU GLY PHE ASP SEQRES 7 A 93 SER TYR VAL GLU PRO LEU LYS LEU TYR LEU GLN LYS PHE SEQRES 8 A 93 ARG GLU SEQRES 1 B 97 GLY SER HIS MET GLU GLU ILE ARG ASN LEU THR VAL LYS SEQRES 2 B 97 ASP PHE ARG VAL GLN GLU LEU PRO LEU ALA ARG ILE LYS SEQRES 3 B 97 LYS ILE MET LYS LEU ASP GLU ASP VAL LYS MET ILE SER SEQRES 4 B 97 ALA GLU ALA PRO VAL LEU PHE ALA LYS ALA ALA GLN ILE SEQRES 5 B 97 PHE ILE THR GLU LEU THR LEU ARG ALA TRP ILE HIS THR SEQRES 6 B 97 GLU ASP ASN LYS ARG ARG THR LEU GLN ARG ASN ASP ILE SEQRES 7 B 97 ALA MET ALA ILE THR LYS PHE ASP GLN PHE ASP PHE LEU SEQRES 8 B 97 ILE ASP ILE VAL PRO ARG FORMUL 3 HOH *299(H2 O) HELIX 1 1 PRO A 58 ALA A 69 1 12 HELIX 2 2 ALA A 77 GLU A 106 1 30 HELIX 3 3 ASN A 112 LEU A 123 1 12 HELIX 4 4 PHE A 125 SER A 127 5 3 HELIX 5 5 TYR A 128 GLU A 141 1 14 HELIX 6 6 PRO B 44 LYS B 53 1 10 HELIX 7 7 ALA B 63 ASN B 91 1 29 HELIX 8 8 GLN B 97 THR B 106 1 10 HELIX 9 9 LYS B 107 ILE B 115 5 9 SHEET 1 A 2 LYS A 75 ILE A 76 0 SHEET 2 A 2 THR B 95 LEU B 96 1 O LEU B 96 N LYS A 75 CRYST1 51.624 60.345 61.645 90.00 90.00 90.00 P 21 21 21 4 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 0.019371 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016222 0.00000