HEADER TRANSCRIPTION/DNA 29-MAR-08 3COQ TITLE STRUCTURAL BASIS FOR DIMERIZATION IN DNA RECOGNITION BY GAL4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*DAP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DAP*DGP*DTP*DCP*DCP*DTP*DC COMPND 4 P*DCP*DGP*DG)-3'); COMPND 5 CHAIN: D; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*DTP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DTP*DGP*DTP*DCP*DCP*DTP*DC COMPND 10 P*DCP*DGP*DG)-3'); COMPND 11 CHAIN: E; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: REGULATORY PROTEIN GAL4; COMPND 15 CHAIN: A, B; COMPND 16 FRAGMENT: DNA BINDING DOMAIN WITH COMPLETE DIMERIZATION DOMAIN; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 11 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 12 ORGANISM_TAXID: 4932; SOURCE 13 GENE: GAL4; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HELIX BUNDLE, PROTEIN-DNA COMPLEX, ZINC BINUCLEAR CLUSTER, ACTIVATOR, KEYWDS 2 CARBOHYDRATE METABOLISM, DNA-BINDING, GALACTOSE METABOLISM, METAL- KEYWDS 3 BINDING, NUCLEUS, PHOSPHOPROTEIN, TRANSCRIPTION, TRANSCRIPTION KEYWDS 4 REGULATION, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.HONG,M.X.FITZGERALD,S.HARPER,C.LUO,D.W.SPEICHER REVDAT 7 21-FEB-24 3COQ 1 REMARK LINK REVDAT 6 24-JUL-19 3COQ 1 SOURCE REMARK REVDAT 5 25-OCT-17 3COQ 1 REMARK REVDAT 4 13-JUL-11 3COQ 1 VERSN REVDAT 3 24-FEB-09 3COQ 1 VERSN REVDAT 2 22-JUL-08 3COQ 1 JRNL REVDAT 1 01-JUL-08 3COQ 0 JRNL AUTH M.HONG,M.X.FITZGERALD,S.HARPER,C.LUO,D.W.SPEICHER, JRNL AUTH 2 R.MARMORSTEIN JRNL TITL STRUCTURAL BASIS FOR DIMERIZATION IN DNA RECOGNITION BY JRNL TITL 2 GAL4. JRNL REF STRUCTURE V. 16 1019 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18611375 JRNL DOI 10.1016/J.STR.2008.03.015 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 14040 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1304 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 889 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.3860 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1454 REMARK 3 NUCLEIC ACID ATOMS : 814 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.19000 REMARK 3 B22 (A**2) : -0.17000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.457 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.312 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.227 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.794 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2391 ; 0.030 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3380 ; 3.337 ; 2.432 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 176 ; 8.318 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 60 ;36.995 ;23.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 330 ;24.666 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;19.743 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 386 ; 0.174 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1440 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1047 ; 0.297 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1527 ; 0.341 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 117 ; 0.195 ; 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): 50 ; 0.276 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.177 ; 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): 933 ; 1.604 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1446 ; 2.632 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1933 ; 3.053 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1934 ; 4.456 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 8 A 96 REMARK 3 ORIGIN FOR THE GROUP (A): 26.5547 11.4820 119.8274 REMARK 3 T TENSOR REMARK 3 T11: 0.0046 T22: -0.4023 REMARK 3 T33: 0.0886 T12: -0.0180 REMARK 3 T13: -0.0243 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 3.9151 L22: 0.8944 REMARK 3 L33: 3.6602 L12: -1.2409 REMARK 3 L13: -1.6391 L23: -0.1813 REMARK 3 S TENSOR REMARK 3 S11: 0.0084 S12: 0.3831 S13: -0.4762 REMARK 3 S21: 0.3413 S22: -0.3943 S23: -0.1464 REMARK 3 S31: 0.2909 S32: -0.2695 S33: 0.3859 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 8 B 96 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4315 29.8245 119.8894 REMARK 3 T TENSOR REMARK 3 T11: 0.0099 T22: -0.2720 REMARK 3 T33: 0.0252 T12: 0.0420 REMARK 3 T13: 0.0188 T23: -0.0388 REMARK 3 L TENSOR REMARK 3 L11: 2.6633 L22: 1.8362 REMARK 3 L33: 4.1381 L12: -1.1300 REMARK 3 L13: 1.5699 L23: -1.1633 REMARK 3 S TENSOR REMARK 3 S11: 0.0139 S12: 0.2503 S13: 0.4275 REMARK 3 S21: 0.3904 S22: -0.4559 S23: 0.0800 REMARK 3 S31: -0.3453 S32: -0.0135 S33: 0.4420 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 20 REMARK 3 ORIGIN FOR THE GROUP (A): 19.8690 21.5164 100.9090 REMARK 3 T TENSOR REMARK 3 T11: -0.1607 T22: 0.2817 REMARK 3 T33: -0.2349 T12: 0.2189 REMARK 3 T13: -0.0140 T23: 0.1032 REMARK 3 L TENSOR REMARK 3 L11: 8.3470 L22: 2.9700 REMARK 3 L33: 0.9413 L12: -2.9739 REMARK 3 L13: -0.1201 L23: 0.1623 REMARK 3 S TENSOR REMARK 3 S11: 0.2689 S12: 1.2570 S13: 0.1994 REMARK 3 S21: -0.0638 S22: -0.4235 S23: -0.1165 REMARK 3 S31: 0.0590 S32: 0.1143 S33: 0.1545 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 21 E 40 REMARK 3 ORIGIN FOR THE GROUP (A): 16.1531 22.3954 100.8826 REMARK 3 T TENSOR REMARK 3 T11: -0.1676 T22: 0.2945 REMARK 3 T33: -0.2529 T12: 0.1864 REMARK 3 T13: 0.0311 T23: 0.0468 REMARK 3 L TENSOR REMARK 3 L11: 6.9143 L22: 3.3132 REMARK 3 L33: 0.8488 L12: -3.2903 REMARK 3 L13: 0.8884 L23: 0.1924 REMARK 3 S TENSOR REMARK 3 S11: 0.2675 S12: 1.1153 S13: 0.1416 REMARK 3 S21: -0.1083 S22: -0.3682 S23: 0.0524 REMARK 3 S31: 0.0235 S32: 0.0211 S33: 0.1008 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3COQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 298; NULL REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; CHESS REMARK 200 BEAMLINE : X25; F1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2823,1.2830,1.2448; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL; NULL REMARK 200 DETECTOR MANUFACTURER : NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18311 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE, CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40MM MG(OAC)2, 25MM SODIUM PHOSPHATE, REMARK 280 5% PEG400, 5% MPD, PH 5.5, VAPOR DIFFUSION, 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 63.24750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.41450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.24750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.41450 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, 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 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 O2 DC D 14 O HOH D 106 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 62 O LEU B 69 4558 2.04 REMARK 500 REMARK 500 REMARK: NULL 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 DA D 1 N9 DA D 1 C4 -0.041 REMARK 500 DG D 7 C6 DG D 7 O6 0.099 REMARK 500 DG D 8 C5 DG D 8 N7 0.043 REMARK 500 DC D 10 O3' DC D 10 C3' -0.064 REMARK 500 DA D 11 C6 DA D 11 N1 0.060 REMARK 500 DA D 11 O3' DG D 12 P -0.082 REMARK 500 DG D 12 C2 DG D 12 N2 0.063 REMARK 500 DG D 12 C6 DG D 12 O6 0.069 REMARK 500 DT D 13 C1' DT D 13 N1 0.117 REMARK 500 DC D 14 C5' DC D 14 C4' 0.048 REMARK 500 DC D 14 O4' DC D 14 C4' 0.071 REMARK 500 DT D 16 C4 DT D 16 C5 0.063 REMARK 500 DC D 17 N3 DC D 17 C4 0.052 REMARK 500 DC E 23 O3' DC E 23 C3' -0.050 REMARK 500 DG E 25 O3' DG E 25 C3' -0.068 REMARK 500 DG E 27 O3' DG E 27 C3' -0.040 REMARK 500 DG E 28 O3' DG E 28 C3' -0.073 REMARK 500 DA E 29 N3 DA E 29 C4 -0.053 REMARK 500 DC E 30 O3' DC E 30 C3' -0.042 REMARK 500 DT E 31 O3' DT E 31 C3' -0.048 REMARK 500 DT E 31 C2 DT E 31 O2 -0.059 REMARK 500 DT E 31 C5 DT E 31 C7 0.048 REMARK 500 DG E 32 C6 DG E 32 O6 0.070 REMARK 500 DC E 34 O4' DC E 34 C1' -0.092 REMARK 500 DG E 39 O3' DG E 39 C3' 0.116 REMARK 500 CYS A 31 CB CYS A 31 SG 0.176 REMARK 500 GLU A 56 CD GLU A 56 OE1 0.073 REMARK 500 GLU A 58 CG GLU A 58 CD 0.098 REMARK 500 GLU A 62 CG GLU A 62 CD 0.119 REMARK 500 CYS B 31 CB CYS B 31 SG 0.229 REMARK 500 ARG B 46 CG ARG B 46 CD 0.163 REMARK 500 GLU B 56 CG GLU B 56 CD 0.093 REMARK 500 SER B 59 CB SER B 59 OG -0.093 REMARK 500 PHE B 68 CE1 PHE B 68 CZ 0.116 REMARK 500 PHE B 72 CB PHE B 72 CG -0.116 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 DA D 1 O4' - C1' - N9 ANGL. DEV. = -8.8 DEGREES REMARK 500 DA D 1 C2 - N3 - C4 ANGL. DEV. = -6.4 DEGREES REMARK 500 DA D 1 C5 - C6 - N1 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC D 2 O5' - P - OP1 ANGL. DEV. = -5.7 DEGREES REMARK 500 DC D 2 O5' - C5' - C4' ANGL. DEV. = -8.2 DEGREES REMARK 500 DC D 2 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 DC D 3 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC D 3 C6 - N1 - C2 ANGL. DEV. = -3.3 DEGREES REMARK 500 DC D 3 N3 - C4 - N4 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG D 4 N1 - C2 - N3 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG D 4 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES REMARK 500 DG D 5 O3' - P - O5' ANGL. DEV. = 13.7 DEGREES REMARK 500 DG D 5 C3' - C2' - C1' ANGL. DEV. = -7.3 DEGREES REMARK 500 DG D 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG D 5 C4 - C5 - N7 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA D 6 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG D 7 O5' - P - OP2 ANGL. DEV. = -7.8 DEGREES REMARK 500 DG D 7 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG D 7 C5 - C6 - N1 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG D 7 C6 - C5 - N7 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG D 7 N1 - C6 - O6 ANGL. DEV. = 6.8 DEGREES REMARK 500 DG D 8 O5' - C5' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 DG D 8 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA D 9 O5' - P - OP1 ANGL. DEV. = -7.8 DEGREES REMARK 500 DA D 9 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC D 10 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA D 11 OP1 - P - OP2 ANGL. DEV. = 11.7 DEGREES REMARK 500 DA D 11 O5' - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 DA D 11 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA D 11 C6 - N1 - C2 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA D 11 C5 - N7 - C8 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA D 11 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA D 11 C5 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG D 12 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 DG D 12 N1 - C2 - N2 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG D 12 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 DT D 13 O3' - P - OP2 ANGL. DEV. = 6.7 DEGREES REMARK 500 DT D 13 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DT D 13 O4' - C1' - N1 ANGL. DEV. = -12.3 DEGREES REMARK 500 DT D 13 C2 - N3 - C4 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT D 13 N3 - C4 - C5 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT D 13 N3 - C4 - O4 ANGL. DEV. = 6.2 DEGREES REMARK 500 DC D 14 C5' - C4' - O4' ANGL. DEV. = 6.7 DEGREES REMARK 500 DC D 14 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DC D 14 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC D 14 N3 - C4 - C5 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC D 14 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC D 15 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT D 16 O3' - P - OP2 ANGL. DEV. = 6.8 DEGREES REMARK 500 DT D 16 O5' - C5' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 157 ANGLE DEVIATIONS. 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 LYS A 23 -5.18 81.11 REMARK 500 ALA A 29 -104.08 -3.37 REMARK 500 LYS A 33 -81.11 -50.14 REMARK 500 ASN A 34 16.54 -64.01 REMARK 500 TYR A 40 76.13 -100.18 REMARK 500 LYS A 43 106.14 -57.71 REMARK 500 GLU A 75 177.29 42.22 REMARK 500 ASP A 76 57.79 -4.87 REMARK 500 LYS B 18 33.95 73.09 REMARK 500 GLU B 24 -173.43 -64.09 REMARK 500 LYS B 27 -159.21 -66.38 REMARK 500 LYS B 33 -81.60 -44.82 REMARK 500 ASN B 35 74.45 70.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 74 GLU A 75 147.38 REMARK 500 GLU A 75 ASP A 76 -138.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 11 SG REMARK 620 2 CYS A 14 SG 89.0 REMARK 620 3 CYS A 28 SG 97.0 123.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 11 SG REMARK 620 2 CYS A 28 SG 99.9 REMARK 620 3 CYS A 31 SG 93.0 121.3 REMARK 620 4 CYS A 38 SG 134.1 101.5 109.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 11 SG REMARK 620 2 CYS B 14 SG 88.2 REMARK 620 3 CYS B 21 SG 129.3 104.3 REMARK 620 4 CYS B 28 SG 104.4 128.7 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 11 SG REMARK 620 2 CYS B 28 SG 98.3 REMARK 620 3 CYS B 31 SG 102.1 137.6 REMARK 620 4 CYS B 38 SG 112.6 82.3 121.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD D 100 DBREF 3COQ A 8 96 UNP P04386 GAL4_YEAST 8 96 DBREF 3COQ B 8 96 UNP P04386 GAL4_YEAST 8 96 DBREF 3COQ D 1 20 PDB 3COQ 3COQ 1 20 DBREF 3COQ E 21 40 PDB 3COQ 3COQ 21 40 SEQRES 1 D 20 DA DC DC DG DG DA DG DG DA DC DA DG DT SEQRES 2 D 20 DC DC DT DC DC DG DG SEQRES 1 E 20 DT DC DC DG DG DA DG DG DA DC DT DG DT SEQRES 2 E 20 DC DC DT DC DC DG DG SEQRES 1 A 89 GLU GLN ALA CYS ASP ILE CYS ARG LEU LYS LYS LEU LYS SEQRES 2 A 89 CYS SER LYS GLU LYS PRO LYS CYS ALA LYS CYS LEU LYS SEQRES 3 A 89 ASN ASN TRP GLU CYS ARG TYR SER PRO LYS THR LYS ARG SEQRES 4 A 89 SER PRO LEU THR ARG ALA HIS LEU THR GLU VAL GLU SER SEQRES 5 A 89 ARG LEU GLU ARG LEU GLU GLN LEU PHE LEU LEU ILE PHE SEQRES 6 A 89 PRO ARG GLU ASP LEU ASP MET ILE LEU LYS MET ASP SER SEQRES 7 A 89 LEU GLN ASP ILE LYS ALA LEU LEU THR GLY LEU SEQRES 1 B 89 GLU GLN ALA CYS ASP ILE CYS ARG LEU LYS LYS LEU LYS SEQRES 2 B 89 CYS SER LYS GLU LYS PRO LYS CYS ALA LYS CYS LEU LYS SEQRES 3 B 89 ASN ASN TRP GLU CYS ARG TYR SER PRO LYS THR LYS ARG SEQRES 4 B 89 SER PRO LEU THR ARG ALA HIS LEU THR GLU VAL GLU SER SEQRES 5 B 89 ARG LEU GLU ARG LEU GLU GLN LEU PHE LEU LEU ILE PHE SEQRES 6 B 89 PRO ARG GLU ASP LEU ASP MET ILE LEU LYS MET ASP SER SEQRES 7 B 89 LEU GLN ASP ILE LYS ALA LEU LEU THR GLY LEU HET MPD D 100 8 HET ZN A1001 1 HET ZN A1002 1 HET ZN B 1 1 HET ZN B 2 1 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM ZN ZINC ION FORMUL 5 MPD C6 H14 O2 FORMUL 6 ZN 4(ZN 2+) FORMUL 10 HOH *33(H2 O) HELIX 1 1 CYS A 11 LYS A 18 1 8 HELIX 2 2 CYS A 28 ASN A 34 1 7 HELIX 3 3 THR A 50 PHE A 72 1 23 HELIX 4 4 ASP A 76 MET A 83 1 8 HELIX 5 5 SER A 85 THR A 94 1 10 HELIX 6 6 CYS B 11 LYS B 18 1 8 HELIX 7 7 CYS B 28 ASN B 35 1 8 HELIX 8 8 THR B 50 PHE B 72 1 23 HELIX 9 9 PRO B 73 LYS B 82 1 10 HELIX 10 10 SER B 85 GLY B 95 1 11 LINK SG CYS A 11 ZN ZN A1001 1555 1555 2.49 LINK SG CYS A 11 ZN ZN A1002 1555 1555 2.58 LINK SG CYS A 14 ZN ZN A1001 1555 1555 2.32 LINK SG CYS A 28 ZN ZN A1001 1555 1555 2.53 LINK SG CYS A 28 ZN ZN A1002 1555 1555 2.32 LINK SG CYS A 31 ZN ZN A1002 1555 1555 2.28 LINK SG CYS A 38 ZN ZN A1002 1555 1555 2.34 LINK ZN ZN B 1 SG CYS B 11 1555 1555 2.23 LINK ZN ZN B 1 SG CYS B 14 1555 1555 2.22 LINK ZN ZN B 1 SG CYS B 21 1555 1555 2.23 LINK ZN ZN B 1 SG CYS B 28 1555 1555 2.69 LINK ZN ZN B 2 SG CYS B 11 1555 1555 2.58 LINK ZN ZN B 2 SG CYS B 28 1555 1555 2.58 LINK ZN ZN B 2 SG CYS B 31 1555 1555 1.96 LINK ZN ZN B 2 SG CYS B 38 1555 1555 2.02 CISPEP 1 LYS A 25 PRO A 26 0 5.06 CISPEP 2 LYS B 25 PRO B 26 0 14.31 SITE 1 AC1 4 CYS A 11 CYS A 14 CYS A 21 CYS A 28 SITE 1 AC2 4 CYS A 11 CYS A 28 CYS A 31 CYS A 38 SITE 1 AC3 4 CYS B 11 CYS B 14 CYS B 21 CYS B 28 SITE 1 AC4 4 CYS B 11 CYS B 28 CYS B 31 CYS B 38 SITE 1 AC5 7 LEU A 49 DA D 11 DG D 12 DT D 13 SITE 2 AC5 7 DT E 31 DG E 32 DT E 33 CRYST1 126.495 40.829 90.418 90.00 95.88 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 0.007905 0.000000 0.000814 0.00000 SCALE2 0.000000 0.024492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011118 0.00000