HEADER TRANSCRIPTION 08-NOV-13 4NIZ TITLE GCN4-P1 SINGLE VAL9 TO AMINOBUTYRIC ACID MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENERAL CONTROL PROTEIN GCN4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 249-281; COMPND 5 SYNONYM: AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 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: 559292; SOURCE 6 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.M.OSHABEN,W.S.HORNE REVDAT 3 06-DEC-23 4NIZ 1 REMARK REVDAT 2 20-SEP-23 4NIZ 1 REMARK SEQADV LINK REVDAT 1 20-AUG-14 4NIZ 0 JRNL AUTH K.M.OSHABEN,W.S.HORNE JRNL TITL TUNING ASSEMBLY SIZE IN PEPTIDE-BASED SUPRAMOLECULAR JRNL TITL 2 POLYMERS BY MODULATION OF SUBUNIT ASSOCIATION AFFINITY. JRNL REF BIOMACROMOLECULES V. 15 1436 2014 JRNL REFN ISSN 1525-7797 JRNL PMID 24598042 JRNL DOI 10.1021/BM5000423 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.220 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 4572 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.620 REMARK 3 FREE R VALUE TEST SET COUNT : 211 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.550 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 : 0.005 535 REMARK 3 ANGLE : 0.623 713 REMARK 3 CHIRALITY : 0.044 79 REMARK 3 PLANARITY : 0.002 93 REMARK 3 DIHEDRAL : 13.071 218 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 4NIZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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 FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : RIGAKU VARIMAX OPTICS REMARK 200 OPTICS : RIGAKU VARIMAX OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4580 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.380 REMARK 200 R MERGE (I) : 0.03400 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: PDB ENTRY 4DMD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M SODIUM ACETATE, 0.1 M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, 20% W/V PEG 4000, PH 5.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 41.13150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.13150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.07000 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: 2130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 GLY A 31 REMARK 465 GLU A 32 REMARK 465 ARG A 33 REMARK 465 NH2 A 34 REMARK 465 ARG B 33 REMARK 465 NH2 B 34 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 MET A 2 CE REMARK 470 LYS A 3 CD CE NZ REMARK 470 GLN A 4 CG CD OE1 NE2 REMARK 470 LYS A 28 CD CE NZ REMARK 470 LYS B 28 CD CE NZ 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 B 204 O HOH B 221 2.11 REMARK 500 O HOH A 107 O HOH A 115 2.13 REMARK 500 NH1 ARG B 25 O HOH B 221 2.16 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 GOL B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DMD RELATED DB: PDB REMARK 900 RELATED ID: 2ZTA RELATED DB: PDB REMARK 900 RELATED ID: 4NJ0 RELATED DB: PDB REMARK 900 RELATED ID: 4NJ1 RELATED DB: PDB REMARK 900 RELATED ID: 4NJ2 RELATED DB: PDB DBREF 4NIZ A 1 33 UNP P03069 GCN4_YEAST 249 281 DBREF 4NIZ B 1 33 UNP P03069 GCN4_YEAST 249 281 SEQADV 4NIZ ACE A 0 UNP P03069 ACETYLATION SEQADV 4NIZ ABA A 9 UNP P03069 VAL 257 ENGINEERED MUTATION SEQADV 4NIZ NH2 A 34 UNP P03069 AMIDATION SEQADV 4NIZ ACE B 0 UNP P03069 ACETYLATION SEQADV 4NIZ ABA B 9 UNP P03069 VAL 257 ENGINEERED MUTATION SEQADV 4NIZ NH2 B 34 UNP P03069 AMIDATION SEQRES 1 A 35 ACE ARG MET LYS GLN LEU GLU ASP LYS ABA GLU GLU LEU SEQRES 2 A 35 LEU SER LYS ASN TYR HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 3 A 35 LEU LYS LYS LEU VAL GLY GLU ARG NH2 SEQRES 1 B 35 ACE ARG MET LYS GLN LEU GLU ASP LYS ABA GLU GLU LEU SEQRES 2 B 35 LEU SER LYS ASN TYR HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 3 B 35 LEU LYS LYS LEU VAL GLY GLU ARG NH2 MODRES 4NIZ ABA A 9 ALA ALPHA-AMINOBUTYRIC ACID MODRES 4NIZ ABA B 9 ALA ALPHA-AMINOBUTYRIC ACID HET ACE A 0 3 HET ABA A 9 6 HET ACE B 0 3 HET ABA B 9 6 HET GOL B 101 6 HETNAM ACE ACETYL GROUP HETNAM ABA ALPHA-AMINOBUTYRIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 ABA 2(C4 H9 N O2) FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *53(H2 O) HELIX 1 1 ARG A 1 VAL A 30 1 30 HELIX 2 2 ARG B 1 GLY B 31 1 31 LINK C ACE A 0 N ARG A 1 1555 1555 1.33 LINK C LYS A 8 N ABA A 9 1555 1555 1.33 LINK C ABA A 9 N GLU A 10 1555 1555 1.33 LINK C ACE B 0 N ARG B 1 1555 1555 1.33 LINK C LYS B 8 N ABA B 9 1555 1555 1.33 LINK C ABA B 9 N GLU B 10 1555 1555 1.33 SITE 1 AC1 7 LYS A 15 ARG A 25 HOH A 115 HOH A 116 SITE 2 AC1 7 LYS B 8 HOH B 220 HOH B 230 CRYST1 82.263 30.140 27.845 90.00 101.32 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 0.012156 0.000000 0.002434 0.00000 SCALE2 0.000000 0.033178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036626 0.00000 HETATM 1 C ACE A 0 36.112 -2.073 -3.465 1.00 46.30 C HETATM 2 O ACE A 0 35.404 -2.281 -2.478 1.00 35.92 O HETATM 3 CH3 ACE A 0 37.567 -2.501 -3.479 1.00 43.44 C