HEADER PROTEIN BINDING 07-FEB-12 4DME TITLE GCN4 LEUCINE ZIPPER DOMAIN IN A TRIMERIC OLIGOMERIZATION STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GCN4-P1 LEUCINE ZIPPER DOMAIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.M.OSHABEN,R.SALARI,L.T.CHONG,W.S.HORNE REVDAT 3 13-SEP-23 4DME 1 REMARK LINK REVDAT 2 12-DEC-12 4DME 1 JRNL REVDAT 1 14-NOV-12 4DME 0 JRNL AUTH K.M.OSHABEN,R.SALARI,D.R.MCCASLIN,L.T.CHONG,W.S.HORNE JRNL TITL THE NATIVE GCN4 LEUCINE-ZIPPER DOMAIN DOES NOT UNIQUELY JRNL TITL 2 SPECIFY A DIMERIC OLIGOMERIZATION STATE. JRNL REF BIOCHEMISTRY V. 51 9581 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 23116373 JRNL DOI 10.1021/BI301132K REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 5198 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 244 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 376 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 828 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.70000 REMARK 3 B22 (A**2) : 0.93000 REMARK 3 B33 (A**2) : -1.93000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.78000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.381 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.268 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 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 857 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 612 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1145 ; 1.387 ; 2.015 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1491 ; 4.042 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 103 ; 4.211 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 45 ;38.965 ;24.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 188 ;14.310 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;18.803 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 128 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 926 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 155 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4DME COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070511. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : NULL 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 : 5443 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.710 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 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 1IJ2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M MES REMARK 280 BUFFER, 30% (W/V) PEG MME 5000, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 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 30.58950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.18950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.58950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.18950 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: 4810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 LYS A 3 NZ REMARK 470 LYS A 8 NZ REMARK 470 LYS A 27 NZ REMARK 470 GLU A 32 CG CD OE1 OE2 REMARK 470 LYS B 3 CE NZ REMARK 470 LYS B 15 CG CD CE NZ REMARK 470 LYS B 27 NZ REMARK 470 GLU B 32 CG CD OE1 OE2 REMARK 470 LYS C 3 NZ REMARK 470 LYS C 8 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 OG SER B 14 O HOH B 211 2.10 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 SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DMD RELATED DB: PDB REMARK 900 RELATED ID: 2ZTA RELATED DB: PDB DBREF 4DME A 0 34 PDB 4DME 4DME 0 34 DBREF 4DME B 0 34 PDB 4DME 4DME 0 34 DBREF 4DME C 0 34 PDB 4DME 4DME 0 34 SEQRES 1 A 35 ACE ARG MET LYS GLN LEU GLU ASP LYS VAL 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 VAL 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 SEQRES 1 C 35 ACE ARG MET LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU SEQRES 2 C 35 LEU SER LYS ASN TYR HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 3 C 35 LEU LYS LYS LEU VAL GLY GLU ARG NH2 HET ACE A 0 3 HET NH2 A 34 2 HET ACE B 0 3 HET NH2 B 34 2 HET ACE C 0 3 HET NH2 C 34 2 HET SO4 A 101 5 HET SO4 B 101 5 HET SO4 C 101 5 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION FORMUL 1 ACE 3(C2 H4 O) FORMUL 1 NH2 3(H2 N) FORMUL 4 SO4 3(O4 S 2-) FORMUL 7 HOH *48(H2 O) HELIX 1 1 ARG A 1 GLY A 31 1 31 HELIX 2 2 ARG B 1 GLY B 31 1 31 HELIX 3 3 ARG C 1 ARG C 33 1 33 LINK C ACE A 0 N ARG A 1 1555 1555 1.32 LINK C ARG A 33 N NH2 A 34 1555 1555 1.34 LINK C ACE B 0 N ARG B 1 1555 1555 1.33 LINK C ARG B 33 N NH2 B 34 1555 1555 1.33 LINK C ACE C 0 N ARG C 1 1555 1555 1.33 LINK C ARG C 33 N NH2 C 34 1555 1555 1.33 SITE 1 AC1 5 ACE A 0 ARG A 1 MET A 2 HOH A 206 SITE 2 AC1 5 LYS C 28 SITE 1 AC2 6 ARG A 1 ACE B 0 MET B 2 LYS B 3 SITE 2 AC2 6 NH2 C 34 HOH C 213 SITE 1 AC3 11 MET A 2 ARG A 25 LYS A 28 HOH A 215 SITE 2 AC3 11 ARG B 33 NH2 B 34 ACE C 0 ARG C 1 SITE 3 AC3 11 MET C 2 ARG C 33 HOH C 206 CRYST1 61.179 34.379 78.117 90.00 139.68 90.00 C 1 2 1 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 0.016346 0.000000 0.019263 0.00000 SCALE2 0.000000 0.029087 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019785 0.00000 HETATM 1 C ACE A 0 7.933 -22.947 -41.885 1.00 24.66 C HETATM 2 O ACE A 0 7.746 -23.170 -40.698 1.00 25.82 O HETATM 3 CH3 ACE A 0 7.318 -23.832 -42.966 1.00 37.41 C