HEADER TRANSCRIPTION 06-MAY-22 7XQ5 TITLE CRYSTAL STRUCTURE OF SCINO2P-SCINO4P BOUND PROMOTER DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN INO4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN INO2; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*CP*CP*TP*GP*CP*AP*TP*GP*TP*GP*AP*AP*AP*AP*T)- COMPND 11 3'); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA (5'-D(*GP*AP*TP*TP*TP*TP*CP*AP*CP*AP*TP*GP*CP*AP*G)- COMPND 16 3'); COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 STRAIN: S288C; SOURCE 6 GENE: INO4; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 4932; SOURCE 14 STRAIN: S288C; SOURCE 15 GENE: INO2; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 22 ORGANISM_TAXID: 4932; SOURCE 23 MOL_ID: 4; SOURCE 24 SYNTHETIC: YES; SOURCE 25 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 26 ORGANISM_TAXID: 4932 KEYWDS TRANSCRIPTIONAL REGULATORS, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.H.KHAN,X.LU REVDAT 3 29-NOV-23 7XQ5 1 REMARK REVDAT 2 10-AUG-22 7XQ5 1 JRNL REVDAT 1 20-JUL-22 7XQ5 0 JRNL AUTH M.H.KHAN,L.XUE,J.YUE,H.J.SCHULLER,Z.ZHU,L.NIU JRNL TITL STRUCTURAL ANALYSIS OF INO2P/INO4P MUTUAL INTERACTIONS AND JRNL TITL 2 THEIR BINDING INTERFACE WITH PROMOTER DNA. JRNL REF INT J MOL SCI V. 23 2022 JRNL REFN ESSN 1422-0067 JRNL PMID 35886947 JRNL DOI 10.3390/IJMS23147600 REMARK 2 REMARK 2 RESOLUTION. 2.25 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 23856 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1205 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 48.9500 - 4.6800 1.00 2667 142 0.1776 0.1853 REMARK 3 2 4.6800 - 3.7100 1.00 2549 148 0.1748 0.1924 REMARK 3 3 3.7100 - 3.2400 1.00 2488 154 0.2049 0.2284 REMARK 3 4 3.2400 - 2.9500 1.00 2513 138 0.2356 0.2773 REMARK 3 5 2.9500 - 2.7400 1.00 2520 124 0.2815 0.3127 REMARK 3 6 2.7400 - 2.5800 0.99 2495 137 0.2931 0.3196 REMARK 3 7 2.5800 - 2.4500 1.00 2508 107 0.2821 0.2974 REMARK 3 8 2.4500 - 2.3400 0.99 2476 123 0.2746 0.3319 REMARK 3 9 2.3400 - 2.2500 0.98 2435 132 0.3194 0.3434 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) : 0.283 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.021 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.14 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 1959 REMARK 3 ANGLE : 1.045 2749 REMARK 3 CHIRALITY : 0.046 308 REMARK 3 PLANARITY : 0.007 242 REMARK 3 DIHEDRAL : 23.591 818 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 7XQ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029362. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-21 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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97847 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23995 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 48.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 19.40 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.59200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5GNJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M COBALT (II) CHLORIDE REMARK 280 HEXAHYDRATE, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 5.0, 1.2 M 1, 6- REMARK 280 HEXANDIOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.92667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.85333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.85333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.92667 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: 8030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 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 DT C 3 O2 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 GLU A 64 CD 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 OG SER A 44 OP1 DC C 5 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT C 3 O3' DT C 3 C3' -0.037 REMARK 500 DG C 4 O3' DG C 4 C3' -0.044 REMARK 500 DC D 13 O3' DC D 13 C3' -0.037 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 ASP B 3 82.97 53.63 REMARK 500 LYS B 39 93.75 -63.05 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XQ5 A 2 75 UNP P13902 INO4_YEAST 40 113 DBREF 7XQ5 B 2 74 UNP P26798 INO2_YEAST 231 303 DBREF 7XQ5 C 1 15 PDB 7XQ5 7XQ5 1 15 DBREF 7XQ5 D 1 15 PDB 7XQ5 7XQ5 1 15 SEQADV 7XQ5 MET A 1 UNP P13902 INITIATING METHIONINE SEQRES 1 A 75 MET LYS LEU THR ASP GLY GLN ILE ARG ILE ASN HIS VAL SEQRES 2 A 75 SER SER GLU LYS LYS ARG ARG GLU LEU GLU ARG ALA ILE SEQRES 3 A 75 PHE ASP GLU LEU VAL ALA VAL VAL PRO ASP LEU GLN PRO SEQRES 4 A 75 GLN GLU SER ARG SER GLU LEU ILE ILE TYR LEU LYS SER SEQRES 5 A 75 LEU SER TYR LEU SER TRP LEU TYR GLU ARG ASN GLU LYS SEQRES 6 A 75 LEU ARG LYS GLN ILE ILE ALA LYS HIS GLU SEQRES 1 B 73 ASP ASP PRO VAL LYS VAL ARG LYS TRP LYS HIS VAL GLN SEQRES 2 B 73 MET GLU LYS ILE ARG ARG ILE ASN THR LYS GLU ALA PHE SEQRES 3 B 73 GLU ARG LEU ILE LYS SER VAL ARG THR PRO PRO LYS GLU SEQRES 4 B 73 ASN GLY LYS ARG ILE PRO LYS HIS ILE LEU LEU THR CYS SEQRES 5 B 73 VAL MET ASN ASP ILE LYS SER ILE ARG SER ALA ASN GLU SEQRES 6 B 73 ALA LEU GLN HIS ILE LEU ASP ASP SEQRES 1 C 15 DC DC DT DG DC DA DT DG DT DG DA DA DA SEQRES 2 C 15 DA DT SEQRES 1 D 15 DG DA DT DT DT DT DC DA DC DA DT DG DC SEQRES 2 D 15 DA DG HET HEZ A 101 8 HET HEZ C 101 8 HET HEZ D 101 8 HETNAM HEZ HEXANE-1,6-DIOL FORMUL 5 HEZ 3(C6 H14 O2) FORMUL 8 HOH *77(H2 O) HELIX 1 AA1 THR A 4 VAL A 34 1 31 HELIX 2 AA2 GLN A 38 SER A 42 5 5 HELIX 3 AA3 SER A 44 HIS A 74 1 31 HELIX 4 AA4 ASP B 3 SER B 33 1 31 HELIX 5 AA5 LYS B 39 LYS B 43 5 5 HELIX 6 AA6 PRO B 46 ASP B 73 1 28 CRYST1 97.893 97.893 89.780 90.00 90.00 120.00 P 31 2 1 6 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 0.010215 0.005898 0.000000 0.00000 SCALE2 0.000000 0.011796 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011138 0.00000