HEADER BIOSYNTHETIC PROTEIN 12-OCT-06 2IPZ TITLE A PARALLEL COILED-COIL TETRAMER WITH OFFSET HELICES COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENERAL CONTROL PROTEIN GCN4; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN; COMPND 5 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 GENE: GCN4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PAE4 KEYWDS COILED COILS, PROTEIN DESIGN, PARALLEL TETRAMER, PROTEIN STRUCTURE, KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,M.LU REVDAT 5 30-AUG-23 2IPZ 1 REMARK SEQADV REVDAT 4 18-OCT-17 2IPZ 1 REMARK REVDAT 3 13-JUL-11 2IPZ 1 VERSN REVDAT 2 24-FEB-09 2IPZ 1 VERSN REVDAT 1 16-JAN-07 2IPZ 0 JRNL AUTH J.LIU,Y.DENG,Q.ZHENG,C.S.CHENG,N.R.KALLENBACH,M.LU JRNL TITL A PARALLEL COILED-COIL TETRAMER WITH OFFSET HELICES. JRNL REF BIOCHEMISTRY V. 45 15224 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 17176044 JRNL DOI 10.1021/BI061914M REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 27103 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2729 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1774 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 202 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1116 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.70000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.88000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.43000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.004 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1128 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1500 ; 1.260 ; 2.018 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 132 ; 4.095 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 184 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 768 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 564 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 87 ; 0.127 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 30 ; 0.225 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.101 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 676 ; 0.876 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1092 ; 1.760 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 452 ; 2.733 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 408 ; 4.495 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2IPZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039872. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A 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 : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27103 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 52.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.39500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.900 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 2B22 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% ISO-PROPANOL, 20% PEG 4000, 0.1M REMARK 280 SODIUM BROMIDE, 0.1M SODIUM HEPES, PH 7.8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.93900 REMARK 290 SMTRY3 2 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: THE BIOLOGICAL ASSEMBLY IS A TETRAMER. 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: 6180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA D 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZTA RELATED DB: PDB REMARK 900 RELATED ID: 2B1F RELATED DB: PDB REMARK 900 MUTANT OF 2ZTA REMARK 900 RELATED ID: 2B22 RELATED DB: PDB REMARK 900 MUTANT OF 2ZTA REMARK 900 RELATED ID: 2HY6 RELATED DB: PDB REMARK 900 MUTANT OF 2ZTA DBREF 2IPZ A 1 34 UNP P03069 GCN4_YEAST 250 281 DBREF 2IPZ B 1 34 UNP P03069 GCN4_YEAST 250 281 DBREF 2IPZ C 1 34 UNP P03069 GCN4_YEAST 250 281 DBREF 2IPZ D 1 34 UNP P03069 GCN4_YEAST 250 281 SEQADV 2IPZ LYS A 2 UNP P03069 CLONING ARTIFACT SEQADV 2IPZ VAL A 3 UNP P03069 CLONING ARTIFACT SEQADV 2IPZ VAL A 7 UNP P03069 GLU 254 CONFLICT SEQADV 2IPZ VAL A 21 UNP P03069 GLU 268 CONFLICT SEQADV 2IPZ VAL A 28 UNP P03069 LYS 275 CONFLICT SEQADV 2IPZ LYS B 2 UNP P03069 CLONING ARTIFACT SEQADV 2IPZ VAL B 3 UNP P03069 CLONING ARTIFACT SEQADV 2IPZ VAL B 7 UNP P03069 GLU 254 CONFLICT SEQADV 2IPZ VAL B 21 UNP P03069 GLU 268 CONFLICT SEQADV 2IPZ VAL B 28 UNP P03069 LYS 275 CONFLICT SEQADV 2IPZ LYS C 2 UNP P03069 CLONING ARTIFACT SEQADV 2IPZ VAL C 3 UNP P03069 CLONING ARTIFACT SEQADV 2IPZ VAL C 7 UNP P03069 GLU 254 CONFLICT SEQADV 2IPZ VAL C 21 UNP P03069 GLU 268 CONFLICT SEQADV 2IPZ VAL C 28 UNP P03069 LYS 275 CONFLICT SEQADV 2IPZ LYS D 2 UNP P03069 CLONING ARTIFACT SEQADV 2IPZ VAL D 3 UNP P03069 CLONING ARTIFACT SEQADV 2IPZ VAL D 7 UNP P03069 GLU 254 CONFLICT SEQADV 2IPZ VAL D 21 UNP P03069 GLU 268 CONFLICT SEQADV 2IPZ VAL D 28 UNP P03069 LYS 275 CONFLICT SEQRES 1 A 34 MET LYS VAL LYS GLN LEU VAL ASP LYS VAL GLU GLU LEU SEQRES 2 A 34 LEU SER LYS ASN TYR HIS LEU VAL ASN GLU VAL ALA ARG SEQRES 3 A 34 LEU VAL LYS LEU VAL GLY GLU ARG SEQRES 1 B 34 MET LYS VAL LYS GLN LEU VAL ASP LYS VAL GLU GLU LEU SEQRES 2 B 34 LEU SER LYS ASN TYR HIS LEU VAL ASN GLU VAL ALA ARG SEQRES 3 B 34 LEU VAL LYS LEU VAL GLY GLU ARG SEQRES 1 C 34 MET LYS VAL LYS GLN LEU VAL ASP LYS VAL GLU GLU LEU SEQRES 2 C 34 LEU SER LYS ASN TYR HIS LEU VAL ASN GLU VAL ALA ARG SEQRES 3 C 34 LEU VAL LYS LEU VAL GLY GLU ARG SEQRES 1 D 34 MET LYS VAL LYS GLN LEU VAL ASP LYS VAL GLU GLU LEU SEQRES 2 D 34 LEU SER LYS ASN TYR HIS LEU VAL ASN GLU VAL ALA ARG SEQRES 3 D 34 LEU VAL LYS LEU VAL GLY GLU ARG HET GOL B 201 6 HET IPA D 301 4 HETNAM GOL GLYCEROL HETNAM IPA ISOPROPYL ALCOHOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN IPA 2-PROPANOL FORMUL 5 GOL C3 H8 O3 FORMUL 6 IPA C3 H8 O FORMUL 7 HOH *164(H2 O) HELIX 1 1 MET A 1 ARG A 34 1 34 HELIX 2 2 LYS B 2 GLU B 33 1 32 HELIX 3 3 MET C 1 ARG C 34 1 34 HELIX 4 4 MET D 1 GLU D 33 1 33 SITE 1 AC1 1 TYR B 18 SITE 1 AC2 2 GLU D 23 HOH D 315 CRYST1 23.783 53.878 52.016 90.00 95.77 90.00 P 1 21 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 0.042047 0.000000 0.004249 0.00000 SCALE2 0.000000 0.018560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019323 0.00000