HEADER TRANSCRIPTION 02-JUL-20 6XNF TITLE GCN4-P1 PEPTIDE TRIMER WITH TETRAFLUOROIODOPHENYLALANINE RESIDUE AT TITLE 2 POSITION 16 (TFI-F16) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GCN4-P1 PEPTIDE WITH TFI-F16; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GCN4-P1 PEPTIDE WITH A16; COMPND 9 CHAIN: B, C; COMPND 10 SYNONYM: AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 4932; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 9 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 10 ORGANISM_TAXID: 4932 KEYWDS COIL-COIL, TETRAFLUOROIODO-MODIFIED PHENYLALANINE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR R.K.ROWE HARTJE,R.S.CZARNY,A.HO REVDAT 3 15-NOV-23 6XNF 1 LINK REVDAT 2 18-OCT-23 6XNF 1 REMARK REVDAT 1 07-JUL-21 6XNF 0 JRNL AUTH R.K.ROWE HARTJE,M.FERRERO,G.CAVALLO,P.METRANGOLO,A.HO, JRNL AUTH 2 R.CZARNY,P.S.HO JRNL TITL ENGINEERING SPECIFIC PROTEIN-PROTEIN INTERACTIONS THROUGH JRNL TITL 2 HALOGEN AND HYDROGEN BONDS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 12124 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 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 46.2100 - 3.1700 0.96 2888 154 0.1704 0.2205 REMARK 3 2 3.1700 - 2.5200 0.99 2996 159 0.2141 0.2901 REMARK 3 3 2.5200 - 2.2000 0.97 2952 156 0.2232 0.2710 REMARK 3 4 2.2000 - 2.0000 0.89 2679 140 0.2514 0.3183 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.204 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.45 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 : 0.008 829 REMARK 3 ANGLE : 1.070 1111 REMARK 3 CHIRALITY : 0.058 128 REMARK 3 PLANARITY : 0.005 133 REMARK 3 DIHEDRAL : 2.909 884 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.3960 5.9381 18.8870 REMARK 3 T TENSOR REMARK 3 T11: 0.1649 T22: 0.1917 REMARK 3 T33: 0.2010 T12: -0.0146 REMARK 3 T13: -0.0165 T23: 0.0098 REMARK 3 L TENSOR REMARK 3 L11: 0.9613 L22: 3.0933 REMARK 3 L33: 4.0829 L12: 0.8920 REMARK 3 L13: -1.0365 L23: -3.5634 REMARK 3 S TENSOR REMARK 3 S11: 0.1964 S12: -0.1382 S13: -0.0833 REMARK 3 S21: -0.1771 S22: -0.1554 S23: 0.0458 REMARK 3 S31: 0.5152 S32: 0.1142 S33: -0.0525 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0043 5.4584 18.7749 REMARK 3 T TENSOR REMARK 3 T11: 0.1805 T22: 0.2159 REMARK 3 T33: 0.2224 T12: 0.0203 REMARK 3 T13: 0.0072 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 0.5760 L22: 1.9886 REMARK 3 L33: 3.1420 L12: 0.3308 REMARK 3 L13: -0.7459 L23: 1.5450 REMARK 3 S TENSOR REMARK 3 S11: 0.0039 S12: -0.0106 S13: -0.1060 REMARK 3 S21: 0.0921 S22: -0.1092 S23: -0.0010 REMARK 3 S31: 0.5949 S32: -0.6735 S33: 0.1185 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7137 13.8608 20.6637 REMARK 3 T TENSOR REMARK 3 T11: 0.2009 T22: 0.2133 REMARK 3 T33: 0.2291 T12: 0.0034 REMARK 3 T13: -0.0152 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 2.5940 L22: 2.7141 REMARK 3 L33: 4.0033 L12: 0.3555 REMARK 3 L13: 2.4887 L23: -1.7538 REMARK 3 S TENSOR REMARK 3 S11: -0.0106 S12: -0.0879 S13: -0.2343 REMARK 3 S21: 0.2679 S22: -0.0390 S23: -0.1457 REMARK 3 S31: -0.8370 S32: -0.1618 S33: 0.0700 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 6XNF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-003 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43081 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.09809 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.75780 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.690 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.16_3549 REMARK 200 STARTING MODEL: 1SWI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION DROPS WERE PREPARED BY REMARK 280 MIXING 2 UL OF STOCK PEPTIDE SOLUTION WITH 2 UL OF MOTHER LIQUOR REMARK 280 AND ALLOWED TO EQUILIBRATE AT 298 K OVER A WELL CONTAINING 500 REMARK 280 UL OF MOTHER LIQUOR. THE STOCK PEPTIDE SOLUTION (TOTAL REMARK 280 CONCENTRATION 1.5 MM) WAS PREPARED BY MIXING 2:1 RATIOS OF THE REMARK 280 A16 PEPTIDE WITH TFI-F16 IN 10 MM POTASSIUM PHOSPHATE, 100 MM REMARK 280 POTASSIUM CHLORIDE PH 7.0., VAPOR DIFFUSION, HANGING DROP 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 29.82500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.59500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.82500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.59500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 LEU A 12 F14 V61 A 16 1.97 REMARK 500 OD1 ASP C 7 O HOH C 201 2.17 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 B 14 33.39 -79.53 REMARK 500 LYS B 15 -34.42 -138.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 101 DBREF 6XNF A 1 30 UNP P03069 GCN4_YEAST 249 278 DBREF 6XNF B 1 30 UNP P03069 GCN4_YEAST 249 278 DBREF 6XNF C 1 30 UNP P03069 GCN4_YEAST 249 278 SEQADV 6XNF V61 A 16 UNP P03069 ASN 264 ENGINEERED MUTATION SEQADV 6XNF ALA B 16 UNP P03069 ASN 264 ENGINEERED MUTATION SEQADV 6XNF ALA C 16 UNP P03069 ASN 264 ENGINEERED MUTATION SEQRES 1 A 30 ARG MET LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU LEU SEQRES 2 A 30 SER LYS V61 TYR HIS LEU GLU ASN GLU VAL ALA ARG LEU SEQRES 3 A 30 LYS LYS LEU VAL SEQRES 1 B 30 ARG MET LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU LEU SEQRES 2 B 30 SER LYS ALA TYR HIS LEU GLU ASN GLU VAL ALA ARG LEU SEQRES 3 B 30 LYS LYS LEU VAL SEQRES 1 C 30 ARG MET LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU LEU SEQRES 2 C 30 SER LYS ALA TYR HIS LEU GLU ASN GLU VAL ALA ARG LEU SEQRES 3 C 30 LYS LYS LEU VAL HET V61 A 16 29 HET NA A 101 1 HET NA B 101 1 HET NA B 102 1 HET NA C 101 1 HETNAM V61 2,3,5,6-TETRAFLUORO-4-IODO-L-PHENYLALANINE HETNAM NA SODIUM ION FORMUL 1 V61 C9 H6 F4 I N O2 FORMUL 4 NA 4(NA 1+) FORMUL 8 HOH *70(H2 O) HELIX 1 AA1 ARG A 1 VAL A 30 1 30 HELIX 2 AA2 MET B 2 LYS B 28 1 27 HELIX 3 AA3 MET C 2 VAL C 30 1 29 LINK C LYS A 15 N V61 A 16 1555 1555 1.33 LINK C V61 A 16 N TYR A 17 1555 1555 1.32 LINK NA NA B 101 O HOH B 218 1555 1555 2.79 LINK O HOH B 206 NA NA C 101 4555 1555 2.64 SITE 1 AC1 2 HIS A 18 GLU A 22 SITE 1 AC2 3 ALA B 24 LYS B 27 HOH B 218 SITE 1 AC3 4 LYS A 27 LYS B 3 HOH B 206 GLU C 22 CRYST1 59.650 35.190 47.020 90.00 100.65 90.00 C 1 2 1 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 0.016764 0.000000 0.003152 0.00000 SCALE2 0.000000 0.028417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021640 0.00000