PDB Short entry for 1ZIJ HEADER LEUCINE ZIPPER 30-OCT-96 1ZIJ TITLE GCN4-LEUCINE ZIPPER CORE MUTANT ASN16ABA IN THE TRIMERIC TITLE 2 STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENERAL CONTROL PROTEIN GCN4; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: GCN4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: THIS STRUCTURE IS IN THE TRIMERIC STATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS LEUCINE ZIPPER, AMINO-ACID BIOSYNTHESIS, TRANSCRIPTION KEYWDS 2 REGULATION, ACTIVATOR, DNA-BINDING, NUCLEAR PROTEIN, COILED KEYWDS 3 COIL EXPDTA X-RAY DIFFRACTION AUTHOR L.GONZALEZ JUNIOR,R.A.BROWN,D.RICHARDSON,T.ALBER REVDAT 3 24-FEB-09 1ZIJ 1 VERSN REVDAT 2 01-APR-03 1ZIJ 1 JRNL REVDAT 1 07-JUL-97 1ZIJ 0 JRNL AUTH L.GONZALEZ JUNIOR,R.A.BROWN,D.RICHARDSON,T.ALBER JRNL TITL CRYSTAL STRUCTURES OF A SINGLE COILED-COIL PEPTIDE JRNL TITL 2 IN TWO OLIGOMERIC STATES REVEAL THE BASIS FOR JRNL TITL 3 STRUCTURAL POLYMORPHISM JRNL REF NAT.STRUCT.BIOL. V. 3 1002 1996 JRNL REFN ISSN 1072-8368 JRNL PMID 8946853 JRNL DOI 10.1038/NSB1296-1002 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.GONZALEZ JUNIOR,J.J.PLECS,T.ALBER REMARK 1 TITL AN ENGINEERED ALLOSTERIC SWITCH IN LEUCINE-ZIPPER REMARK 1 TITL 2 OLIGOMERIZATION REMARK 1 REF NAT.STRUCT.BIOL. V. 3 510 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.B.HARBURY,P.S.KIM,T.ALBER REMARK 1 TITL CRYSTAL STRUCTURE OF AN ISOLEUCINE-ZIPPER TRIMER REMARK 1 REF NATURE V. 371 80 1994 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 3 REMARK 1 AUTH P.B.HARBURY,T.ZHANG,P.S.KIM,T.ALBER REMARK 1 TITL A SWITCH BETWEEN TWO-, THREE-, AND FOUR-STRANDED REMARK 1 TITL 2 COILED COILS IN GCN4 LEUCINE ZIPPER MUTANTS REMARK 1 REF SCIENCE V. 262 1401 1993 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 4 REMARK 1 AUTH E.K.O'SHEA,J.D.KLEMM,P.S.KIM,T.ALBER REMARK 1 TITL X-RAY STRUCTURE OF THE GCN4 LEUCINE ZIPPER, A REMARK 1 TITL 2 TWO-STRANDED, PARALLEL COILED COIL REMARK 1 REF SCIENCE V. 254 539 1991 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 5954 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 835 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.010 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.900 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZIJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-94 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5954 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 18.59500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.76500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.76500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.59500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.29500 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 300 REMARK: REMARK 300 THERE ARE THREE PEPTIDE CHAINS DENOTED *A*, *B* AND *C* REMARK 300 IN THE ASYMMETRIC UNIT. 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: 4540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 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 GLU C 32 CB CG CD OE1 OE2 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 GLU A 6 CD GLU A 6 OE2 0.073 REMARK 500 GLU B 11 CD GLU B 11 OE1 0.066 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP A 7 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 7 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP B 7 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 7 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 33 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP C 7 CB - CG - OD1 ANGL. DEV. = -6.1 DEGREES 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 LEU B 29 25.51 -67.46 REMARK 500 VAL B 30 -107.58 -141.07 REMARK 500 GLU B 32 100.86 -38.48 REMARK 500 GLN C 4 -73.63 -69.94 REMARK 500 VAL C 30 -83.60 -49.94 REMARK 500 GLU C 32 -136.79 169.88 REMARK 500 REMARK 500 REMARK: NULL DBREF 1ZIJ A 1 33 UNP P03069 GCN4_YEAST 249 281 DBREF 1ZIJ B 1 33 UNP P03069 GCN4_YEAST 249 281 DBREF 1ZIJ C 1 33 UNP P03069 GCN4_YEAST 249 281 SEQADV 1ZIJ ABA A 16 UNP P03069 ASN 264 MODIFIED RESIDUE SEQADV 1ZIJ ABA B 16 UNP P03069 ASN 264 MODIFIED RESIDUE SEQADV 1ZIJ ABA C 16 UNP P03069 ASN 264 MODIFIED RESIDUE SEQRES 1 A 34 ACE ARG MET LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU SEQRES 2 A 34 LEU SER LYS ABA TYR HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 3 A 34 LEU LYS LYS LEU VAL GLY GLU ARG SEQRES 1 B 34 ACE ARG MET LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU SEQRES 2 B 34 LEU SER LYS ABA TYR HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 3 B 34 LEU LYS LYS LEU VAL GLY GLU ARG SEQRES 1 C 34 ACE ARG MET LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU SEQRES 2 C 34 LEU SER LYS ABA TYR HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 3 C 34 LEU LYS LYS LEU VAL GLY GLU ARG MODRES 1ZIJ ABA A 16 ALA ALPHA-AMINOBUTYRIC ACID MODRES 1ZIJ ABA B 16 ALA ALPHA-AMINOBUTYRIC ACID MODRES 1ZIJ ABA C 16 ALA ALPHA-AMINOBUTYRIC ACID HET ACE A 0 3 HET ABA A 16 6 HET ACE B 0 3 HET ABA B 16 6 HET ACE C 0 3 HET ABA C 16 6 HETNAM ACE ACETYL GROUP HETNAM ABA ALPHA-AMINOBUTYRIC ACID FORMUL 1 ACE 3(C2 H4 O) FORMUL 1 ABA 3(C4 H9 N O2) FORMUL 4 HOH *34(H2 O) HELIX 1 1 ARG A 1 VAL A 30 1 30 HELIX 2 2 ARG B 1 VAL B 30 1 30 HELIX 3 3 ARG C 1 VAL C 30 1 30 LINK C ACE A 0 N ARG A 1 1555 1555 1.33 LINK N ABA A 16 C LYS A 15 1555 1555 1.33 LINK C ABA A 16 N TYR A 17 1555 1555 1.36 LINK C ACE B 0 N ARG B 1 1555 1555 1.34 LINK N ABA B 16 C LYS B 15 1555 1555 1.33 LINK C ABA B 16 N TYR B 17 1555 1555 1.33 LINK C ACE C 0 N ARG C 1 1555 1555 1.33 LINK N ABA C 16 C LYS C 15 1555 1555 1.33 LINK C ABA C 16 N TYR C 17 1555 1555 1.33 CRYST1 37.190 46.590 51.530 90.00 90.00 90.00 P 21 21 21 12 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 0.026889 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019406 0.00000 HETATM 1 C ACE A 0 -15.615 -28.016 38.261 1.00 38.17 C HETATM 2 O ACE A 0 -15.863 -26.839 38.508 1.00 63.01 O HETATM 3 CH3 ACE A 0 -16.757 -29.020 38.340 1.00 38.47 C