HEADER TRANSCRIPTION 17-JUL-21 7FDO TITLE CRYSTAL STRUCTURE OF TRANSCRIPTION FACTOR CPC IN COMPLEX WITH EGL3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR EGL1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BASIC HELIX-LOOP-HELIX PROTEIN 2,ATMYC146,ATBHLH2,BHLH 2, COMPND 5 PROTEIN ENHANCER OF GLABRA 3,TRANSCRIPTION FACTOR EN 30,BHLH COMPND 6 TRANSCRIPTION FACTOR BHLH002; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TRANSCRIPTION FACTOR CPC; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: PROTEIN CAPRICE; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: BHLH2, EGL1, EGL3, EN30, MYC146, AT1G63650, F24D7.16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 10 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 11 ORGANISM_TAXID: 3702; SOURCE 12 GENE: CPC, AT2G46410, F11C10.10; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRANSCRIPTION FACTOR COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR B.WANG,Q.LUO REVDAT 4 29-NOV-23 7FDO 1 REMARK REVDAT 3 05-OCT-22 7FDO 1 JRNL REVDAT 2 28-SEP-22 7FDO 1 JRNL REVDAT 1 20-JUL-22 7FDO 0 JRNL AUTH B.WANG,Q.LUO,Y.LI,K.DU,Z.WU,T.LI,W.H.SHEN,C.H.HUANG,J.GAN, JRNL AUTH 2 A.DONG JRNL TITL STRUCTURAL INSIGHTS INTO PARTNER SELECTION FOR MYB AND BHLH JRNL TITL 2 TRANSCRIPTION FACTOR COMPLEXES. JRNL REF NAT.PLANTS V. 8 1108 2021 JRNL REFN ESSN 2055-0278 JRNL PMID 35995835 JRNL DOI 10.1038/S41477-022-01223-W REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 7.0.076 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 32622 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1679 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1695 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.04 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.180 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7FDO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-18 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 : BL17U1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34121 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.02400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.31300 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: REFMAC REMARK 200 STARTING MODEL: 4RRU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 6.5, 20% PEG3350, REMARK 280 0.2 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 43.02700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.17900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.02700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.17900 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: 1570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 THR A 8 REMARK 465 THR A 55 REMARK 465 ARG A 56 REMARK 465 LYS A 57 REMARK 465 THR A 58 REMARK 465 ILE A 59 REMARK 465 GLN A 60 REMARK 465 ALA A 61 REMARK 465 ALA A 62 REMARK 465 GLU A 63 REMARK 465 ALA A 87 REMARK 465 GLU A 88 REMARK 465 SER A 89 REMARK 465 SER A 90 REMARK 465 ALA A 91 REMARK 465 SER A 92 REMARK 465 GLY A 93 REMARK 465 SER A 94 REMARK 465 SER A 95 REMARK 465 GLN A 96 REMARK 465 VAL A 97 REMARK 465 THR A 98 REMARK 465 ARG A 99 REMARK 465 ARG A 100 REMARK 465 ALA A 101 REMARK 465 SER A 102 REMARK 465 ALA A 103 REMARK 465 ALA A 104 REMARK 465 ALA A 205 REMARK 465 GLY B 81 REMARK 465 VAL B 82 REMARK 465 VAL B 83 REMARK 465 PHE B 84 REMARK 465 ALA B 85 REMARK 465 ASN B 86 REMARK 465 ARG B 87 REMARK 465 ARG B 88 REMARK 465 ARG B 89 REMARK 465 ASP B 90 REMARK 465 PHE B 91 REMARK 465 PHE B 92 REMARK 465 ARG B 93 REMARK 465 LYS B 94 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 9 CG1 CG2 REMARK 470 ASP A 11 CG OD1 OD2 REMARK 470 VAL A 64 CG1 CG2 REMARK 470 GLU A 204 CG CD OE1 OE2 REMARK 470 VAL B 36 CG1 CG2 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 O HOH A 412 O HOH A 517 2.18 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 SER A 85 33.13 -83.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 7FDO A 8 205 UNP Q9CAD0 EGL1_ARATH 8 205 DBREF 7FDO B 36 94 UNP O22059 CPC_ARATH 36 94 SEQRES 1 A 198 THR VAL PRO ASP ASN LEU LYS LYS GLN LEU ALA VAL SER SEQRES 2 A 198 VAL ARG ASN ILE GLN TRP SER TYR GLY ILE PHE TRP SER SEQRES 3 A 198 VAL SER ALA SER GLN PRO GLY VAL LEU GLU TRP GLY ASP SEQRES 4 A 198 GLY TYR TYR ASN GLY ASP ILE LYS THR ARG LYS THR ILE SEQRES 5 A 198 GLN ALA ALA GLU VAL LYS ILE ASP GLN LEU GLY LEU GLU SEQRES 6 A 198 ARG SER GLU GLN LEU ARG GLU LEU TYR GLU SER LEU SER SEQRES 7 A 198 LEU ALA GLU SER SER ALA SER GLY SER SER GLN VAL THR SEQRES 8 A 198 ARG ARG ALA SER ALA ALA ALA LEU SER PRO GLU ASP LEU SEQRES 9 A 198 THR ASP THR GLU TRP TYR TYR LEU VAL CYS MET SER PHE SEQRES 10 A 198 VAL PHE ASN ILE GLY GLU GLY ILE PRO GLY GLY ALA LEU SEQRES 11 A 198 SER ASN GLY GLU PRO ILE TRP LEU CYS ASN ALA GLU THR SEQRES 12 A 198 ALA ASP SER LYS VAL PHE THR ARG SER LEU LEU ALA LYS SEQRES 13 A 198 SER ALA SER LEU GLN THR VAL VAL CYS PHE PRO PHE LEU SEQRES 14 A 198 GLY GLY VAL LEU GLU ILE GLY THR THR GLU HIS ILE LYS SEQRES 15 A 198 GLU ASP MET ASN VAL ILE GLN SER VAL LYS THR LEU PHE SEQRES 16 A 198 LEU GLU ALA SEQRES 1 B 59 VAL LYS MET SER GLU GLU GLU GLU ASP LEU ILE SER ARG SEQRES 2 B 59 MET TYR LYS LEU VAL GLY ASP ARG TRP GLU LEU ILE ALA SEQRES 3 B 59 GLY ARG ILE PRO GLY ARG THR PRO GLU GLU ILE GLU ARG SEQRES 4 B 59 TYR TRP LEU MET LYS HIS GLY VAL VAL PHE ALA ASN ARG SEQRES 5 B 59 ARG ARG ASP PHE PHE ARG LYS HET CL A 301 1 HET SO4 B 101 5 HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 3 CL CL 1- FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *139(H2 O) HELIX 1 AA1 ASN A 12 GLN A 25 1 14 HELIX 2 AA2 LEU A 71 SER A 85 1 15 HELIX 3 AA3 SER A 107 LEU A 111 5 5 HELIX 4 AA4 THR A 112 MET A 122 1 11 HELIX 5 AA5 GLU A 130 GLY A 140 1 11 HELIX 6 AA6 ASN A 147 ALA A 151 5 5 HELIX 7 AA7 ARG A 158 ALA A 165 1 8 HELIX 8 AA8 ASP A 191 LEU A 203 1 13 HELIX 9 AA9 SER B 39 GLY B 54 1 16 HELIX 10 AB1 ARG B 56 GLY B 62 1 7 HELIX 11 AB2 THR B 68 HIS B 80 1 13 SHEET 1 AA1 6 VAL A 125 PHE A 126 0 SHEET 2 AA1 6 LEU A 42 TYR A 49 -1 N LEU A 42 O PHE A 126 SHEET 3 AA1 6 TYR A 28 VAL A 34 -1 N PHE A 31 O ASP A 46 SHEET 4 AA1 6 GLY A 178 THR A 184 -1 O VAL A 179 N TRP A 32 SHEET 5 AA1 6 THR A 169 PHE A 175 -1 N VAL A 171 O ILE A 182 SHEET 6 AA1 6 ILE A 143 LEU A 145 -1 N LEU A 145 O VAL A 170 SSBOND 1 CYS A 146 CYS A 146 1555 2555 2.04 CRYST1 86.054 50.358 81.657 90.00 97.23 90.00 C 1 2 1 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 0.011621 0.000000 0.001475 0.00000 SCALE2 0.000000 0.019858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012345 0.00000