PDB Short entry for 1RB4 HEADER DNA BINDING PROTEIN 01-NOV-03 1RB4 TITLE ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TITLE 2 TETRAGONAL AUTOMATIC SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENERAL CONTROL PROTEIN GCN4; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: LEUCINE-ZIPPER (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 OTHER_DETAILS: THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN SOURCE 4 SACCHAROMYCES CEREVISIAE. THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS COILED COIL, LEUCINE ZIPPER, AUTOMATION, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.HOLTON,T.ALBER REVDAT 6 14-FEB-24 1RB4 1 REMARK REVDAT 5 27-OCT-21 1RB4 1 SEQADV REVDAT 4 11-OCT-17 1RB4 1 REMARK REVDAT 3 24-FEB-09 1RB4 1 VERSN REVDAT 2 17-FEB-04 1RB4 1 JRNL REVDAT 1 13-JAN-04 1RB4 0 JRNL AUTH J.HOLTON,T.ALBER JRNL TITL AUTOMATED PROTEIN CRYSTAL STRUCTURE DETERMINATION USING JRNL TITL 2 ELVES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 1537 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 14752198 JRNL DOI 10.1073/PNAS.0306241101 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.GONZALEZ JR.,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 DOI 10.1038/371080A0 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 COILED REMARK 1 TITL 2 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 TWO-STRANDED, REMARK 1 TITL 2 PARALLEL COILED COIL. REMARK 1 REF SCIENCE V. 254 539 1991 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 26/11/99 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13638 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 809 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 762 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.00 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): NULL 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 1RB4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-NOV-03. REMARK 100 THE DEPOSITION ID IS D_1000020632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 90.0 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL1-5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15956 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.8 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: ELVES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MM PHOSPHATE PH 7.3 400 MM NACL 15% REMARK 280 PEG8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 39.00600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.47350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.47350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.50900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.47350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.47350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.50300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.47350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.47350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.50900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.47350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.47350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.50300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 39.00600 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: 3820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6170 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 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 ARG B 33 REMARK 465 VAL C 30 REMARK 465 GLY C 31 REMARK 465 GLU C 32 REMARK 465 ARG C 33 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 ARG A 1 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 25 CD - NE - CZ ANGL. DEV. = 11.1 DEGREES REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 1 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 MET B 2 CG - SD - CE ANGL. DEV. = -14.3 DEGREES REMARK 500 GLU B 10 OE1 - CD - OE2 ANGL. DEV. = 9.1 DEGREES REMARK 500 GLU C 22 OE1 - CD - OE2 ANGL. DEV. = -12.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RB1 RELATED DB: PDB REMARK 900 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A REMARK 900 TRIGONAL AUTOMATIC SOLUTION REMARK 900 RELATED ID: 1RB5 RELATED DB: PDB REMARK 900 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A REMARK 900 TRIGONAL FORM REMARK 900 RELATED ID: 1RB6 RELATED DB: PDB REMARK 900 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A REMARK 900 TETRAGONAL FORM DBREF 1RB4 A 1 33 UNP P03069 GCN4_YEAST 249 281 DBREF 1RB4 B 1 33 UNP P03069 GCN4_YEAST 249 281 DBREF 1RB4 C 1 33 UNP P03069 GCN4_YEAST 249 281 SEQADV 1RB4 ALA A 16 UNP P03069 ASN 264 ENGINEERED MUTATION SEQADV 1RB4 ALA B 16 UNP P03069 ASN 264 ENGINEERED MUTATION SEQADV 1RB4 ALA C 16 UNP P03069 ASN 264 ENGINEERED MUTATION SEQRES 1 A 33 ARG MET LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU LEU SEQRES 2 A 33 SER LYS ALA TYR HIS LEU GLU ASN GLU VAL ALA ARG LEU SEQRES 3 A 33 LYS LYS LEU VAL GLY GLU ARG SEQRES 1 B 33 ARG MET LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU LEU SEQRES 2 B 33 SER LYS ALA TYR HIS LEU GLU ASN GLU VAL ALA ARG LEU SEQRES 3 B 33 LYS LYS LEU VAL GLY GLU ARG SEQRES 1 C 33 ARG MET LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU LEU SEQRES 2 C 33 SER LYS ALA TYR HIS LEU GLU ASN GLU VAL ALA ARG LEU SEQRES 3 C 33 LYS LYS LEU VAL GLY GLU ARG FORMUL 4 HOH *157(H2 O) HELIX 1 1 ARG A 1 VAL A 30 1 30 HELIX 2 2 ARG B 1 GLU B 32 1 32 HELIX 3 3 ARG C 1 LEU C 29 1 29 CRYST1 64.947 64.947 78.012 90.00 90.00 90.00 P 43 21 2 24 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 0.015397 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015397 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012819 0.00000