HEADER TRANSCRIPTION/DNA 21-APR-03 1P47 TITLE CRYSTAL STRUCTURE OF TANDEM ZIF268 MOLECULES COMPLEXED TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*TP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*GP*CP*GP*TP*GP*GP COMPND 3 *GP*CP*GP*T)-3'; COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*AP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*GP*CP*CP*CP*AP*CP COMPND 8 *GP*CP*CP*A)-3'; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: EARLY GROWTH RESPONSE PROTEIN 1; COMPND 13 CHAIN: A, B; COMPND 14 FRAGMENT: RESIDUES 333-419; COMPND 15 SYNONYM: EGR-1, KROX-24 PROTEIN, ZIF268, NERVE GROWTH FACTOR-INDUCED COMPND 16 PROTEIN A, NGFI-A; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED DNA OLIGO; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHESIZED DNA OLIGO; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 9 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 GENE: EGR1 OR EGR-1 OR KROX-24; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PZIF89 KEYWDS ZINC FINGER, DNA-BINDING PROTEIN, COMPLEX (ZINC FINGER-DNA), KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.PEISACH,C.O.PABO REVDAT 3 16-AUG-23 1P47 1 REMARK LINK REVDAT 2 24-FEB-09 1P47 1 VERSN REVDAT 1 24-JUN-03 1P47 0 JRNL AUTH E.PEISACH,C.O.PABO JRNL TITL CONSTRAINTS FOR ZINC FINGER LINKER DESIGN AS INFERRED FROM JRNL TITL 2 X-RAY CRYSTAL STRUCTURE OF TANDEM ZIF268-DNA COMPLEXES JRNL REF J.MOL.BIOL. V. 330 1 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12818197 JRNL DOI 10.1016/S0022-2836(03)00572-2 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.ELROD-ERICKSON,M.A.ROULD,L.NEKLUDOVA,C.O.PABO REMARK 1 TITL ZIF268 PROTEIN-DNA COMPLEX REFINED AT 1.6A: IMPLICATIONS FOR REMARK 1 TITL 2 UNDERSTANDING ZINC FINGER DNA RECOGNITION REMARK 1 REF STRUCTURE V. 6 451 1996 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(98)00047-1 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.S.KIM,C.O.PABO REMARK 1 TITL GETTING A HANDHOLD ON DNA: DESIGN OF POLY-ZINC FINGER REMARK 1 TITL 2 PROTEINS WITH FEMTOMOLAR DISSOCIATION CONSTANTS. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 95 2812 1998 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.95.6.2812 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.22 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 22393 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2429 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) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 626 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3760 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.4600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1431 REMARK 3 NUCLEIC ACID ATOMS : 896 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.08000 REMARK 3 B12 (A**2) : -0.03000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.223 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.157 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.785 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2493 ; 0.045 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1723 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3514 ; 4.433 ; 2.396 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4076 ; 1.616 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 169 ; 9.907 ; 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): 331 ; 0.215 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2080 ; 0.021 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 367 ; 0.013 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 518 ; 0.244 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2119 ; 0.296 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1077 ; 0.118 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 150 ; 0.241 ; 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): 11 ; 0.160 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 35 ; 0.245 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.105 ; 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): 857 ; 1.883 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1392 ; 3.239 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1636 ; 5.245 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2122 ; 7.140 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1P47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018985. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : BENT GE(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24823 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 REMARK 200 FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.12 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.40500 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1AAY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS PROPANE-HCL, SODIUM CHLORIDE, REMARK 280 ZINC CLORIDE, AMMONIUM ACETATE, PEG 400, PH 8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.20267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 66.40533 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 APPLY THE FOLLOWING TO CHAINS: C, D, 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 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 GLU B 102 REMARK 465 ARG B 187 REMARK 465 GLN B 188 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 NH2 ARG B 118 OD2 ASP B 120 2.10 REMARK 500 OP2 DG C 9 O HOH C 46 2.12 REMARK 500 OP2 DC D 59 O HOH D 67 2.15 REMARK 500 O6 DG C 17 N4 DC D 48 2.17 REMARK 500 O HOH C 29 O HOH C 35 2.18 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 DG C 1 C5' DG C 1 C4' 0.045 REMARK 500 DG C 1 O3' DG C 1 C3' 0.140 REMARK 500 DG C 1 N1 DG C 1 C2 0.073 REMARK 500 DG C 1 C6 DG C 1 N1 -0.048 REMARK 500 DG C 1 C5 DG C 1 N7 0.113 REMARK 500 DG C 1 C8 DG C 1 N9 0.063 REMARK 500 DG C 1 C6 DG C 1 O6 0.122 REMARK 500 DG C 1 O3' DT C 2 P 0.100 REMARK 500 DT C 2 C2' DT C 2 C1' 0.077 REMARK 500 DT C 2 O4' DT C 2 C1' -0.087 REMARK 500 DT C 2 C5 DT C 2 C6 -0.057 REMARK 500 DT C 2 C2 DT C 2 O2 0.105 REMARK 500 DG C 3 P DG C 3 O5' 0.072 REMARK 500 DG C 3 C5' DG C 3 C4' 0.045 REMARK 500 DG C 3 O3' DG C 3 C3' -0.097 REMARK 500 DG C 3 C2 DG C 3 N3 0.051 REMARK 500 DG C 3 C4 DG C 3 C5 -0.072 REMARK 500 DG C 3 N7 DG C 3 C8 0.064 REMARK 500 DG C 3 C8 DG C 3 N9 -0.046 REMARK 500 DG C 3 N9 DG C 3 C4 0.065 REMARK 500 DG C 4 N3 DG C 4 C4 0.080 REMARK 500 DG C 4 C4 DG C 4 C5 0.044 REMARK 500 DG C 4 C5 DG C 4 C6 -0.060 REMARK 500 DG C 4 C6 DG C 4 N1 0.080 REMARK 500 DG C 4 C5 DG C 4 N7 -0.049 REMARK 500 DC C 5 P DC C 5 OP1 -0.104 REMARK 500 DC C 5 C4' DC C 5 C3' 0.112 REMARK 500 DC C 5 N1 DC C 5 C6 -0.046 REMARK 500 DC C 5 C4 DC C 5 C5 -0.084 REMARK 500 DG C 6 C2' DG C 6 C1' 0.102 REMARK 500 DG C 6 O3' DG C 6 C3' 0.090 REMARK 500 DG C 6 N1 DG C 6 C2 0.077 REMARK 500 DG C 6 C4 DG C 6 C5 -0.053 REMARK 500 DG C 6 C6 DG C 6 N1 -0.067 REMARK 500 DG C 6 N7 DG C 6 C8 -0.046 REMARK 500 DT C 7 O4' DT C 7 C4' 0.057 REMARK 500 DT C 7 C1' DT C 7 N1 0.080 REMARK 500 DT C 7 N1 DT C 7 C2 -0.048 REMARK 500 DT C 7 N3 DT C 7 C4 -0.065 REMARK 500 DT C 7 C5 DT C 7 C6 -0.054 REMARK 500 DT C 7 C4 DT C 7 O4 0.066 REMARK 500 DG C 8 C5' DG C 8 C4' 0.064 REMARK 500 DG C 8 C4 DG C 8 C5 -0.044 REMARK 500 DG C 8 C5 DG C 8 N7 0.119 REMARK 500 DG C 8 N7 DG C 8 C8 0.043 REMARK 500 DG C 9 N7 DG C 9 C8 0.047 REMARK 500 DG C 9 C8 DG C 9 N9 0.043 REMARK 500 DG C 10 O3' DG C 10 C3' -0.055 REMARK 500 DG C 10 N1 DG C 10 C2 0.090 REMARK 500 DG C 10 C2 DG C 10 N3 -0.053 REMARK 500 REMARK 500 THIS ENTRY HAS 207 BOND DEVIATIONS. 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 DG C 1 C4' - C3' - C2' ANGL. DEV. = -7.8 DEGREES REMARK 500 DG C 1 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG C 1 C6 - N1 - C2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG C 1 N3 - C2 - N2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG C 1 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DT C 2 OP1 - P - OP2 ANGL. DEV. = 10.8 DEGREES REMARK 500 DT C 2 O5' - P - OP1 ANGL. DEV. = -15.9 DEGREES REMARK 500 DT C 2 O4' - C4' - C3' ANGL. DEV. = 9.4 DEGREES REMARK 500 DT C 2 C5' - C4' - O4' ANGL. DEV. = -17.5 DEGREES REMARK 500 DT C 2 C4' - C3' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 DT C 2 N1 - C1' - C2' ANGL. DEV. = 9.5 DEGREES REMARK 500 DT C 2 C5 - C4 - O4 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT C 2 C3' - O3' - P ANGL. DEV. = -12.6 DEGREES REMARK 500 DG C 3 O4' - C4' - C3' ANGL. DEV. = 4.8 DEGREES REMARK 500 DG C 3 C1' - O4' - C4' ANGL. DEV. = -8.0 DEGREES REMARK 500 DG C 3 O4' - C1' - C2' ANGL. DEV. = 7.2 DEGREES REMARK 500 DG C 3 N1 - C2 - N3 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG C 3 C2 - N3 - C4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG C 3 C5 - C6 - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 DG C 3 N3 - C2 - N2 ANGL. DEV. = 4.9 DEGREES REMARK 500 DG C 3 C5 - C6 - O6 ANGL. DEV. = -7.1 DEGREES REMARK 500 DG C 4 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DG C 4 C4 - C5 - N7 ANGL. DEV. = -6.7 DEGREES REMARK 500 DG C 4 C5 - N7 - C8 ANGL. DEV. = 12.8 DEGREES REMARK 500 DG C 4 N7 - C8 - N9 ANGL. DEV. = -9.6 DEGREES REMARK 500 DG C 4 C8 - N9 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG C 4 C6 - C5 - N7 ANGL. DEV. = 6.4 DEGREES REMARK 500 DG C 4 N1 - C6 - O6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG C 4 C5 - C6 - O6 ANGL. DEV. = 7.0 DEGREES REMARK 500 DC C 5 O3' - P - O5' ANGL. DEV. = -12.8 DEGREES REMARK 500 DC C 5 O3' - P - OP2 ANGL. DEV. = 7.2 DEGREES REMARK 500 DC C 5 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC C 5 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = 7.3 DEGREES REMARK 500 DC C 5 C2 - N3 - C4 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC C 5 C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC C 5 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DC C 5 N3 - C4 - N4 ANGL. DEV. = -8.9 DEGREES REMARK 500 DC C 5 C5 - C4 - N4 ANGL. DEV. = 8.3 DEGREES REMARK 500 DG C 6 O3' - P - OP1 ANGL. DEV. = 7.6 DEGREES REMARK 500 DG C 6 O5' - P - OP1 ANGL. DEV. = 10.7 DEGREES REMARK 500 DG C 6 O5' - P - OP2 ANGL. DEV. = -7.1 DEGREES REMARK 500 DG C 6 O4' - C1' - C2' ANGL. DEV. = -8.2 DEGREES REMARK 500 DG C 6 C6 - N1 - C2 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG C 6 N1 - C2 - N3 ANGL. DEV. = 8.6 DEGREES REMARK 500 DG C 6 C2 - N3 - C4 ANGL. DEV. = -8.3 DEGREES REMARK 500 DG C 6 C4 - C5 - C6 ANGL. DEV. = 5.6 DEGREES REMARK 500 DG C 6 C6 - C5 - N7 ANGL. DEV. = -9.1 DEGREES REMARK 500 DG C 6 N3 - C2 - N2 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG C 6 C8 - N9 - C1' ANGL. DEV. = -8.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 433 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 ARG A 103 89.34 79.01 REMARK 500 GLU A 110 -79.80 -51.35 REMARK 500 LYS A 133 78.16 -159.79 REMARK 500 MET A 141 2.45 47.20 REMARK 500 ARG A 187 -99.81 -124.63 REMARK 500 GLU B 110 -56.79 -1.60 REMARK 500 ARG B 114 133.77 -36.97 REMARK 500 ARG B 127 -8.33 -56.73 REMARK 500 LYS B 161 72.94 -158.97 REMARK 500 PRO B 162 -146.50 -51.81 REMARK 500 PHE B 163 112.22 58.34 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 187 GLN A 188 -147.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC C 14 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALA A 164 10.36 REMARK 500 ARG A 174 -10.04 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 A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 107 SG REMARK 620 2 CYS A 112 SG 105.9 REMARK 620 3 HIS A 125 NE2 106.4 86.3 REMARK 620 4 HIS A 129 NE2 125.5 108.4 116.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 137 SG REMARK 620 2 CYS A 140 SG 115.9 REMARK 620 3 HIS A 153 NE2 117.1 98.6 REMARK 620 4 HIS A 157 NE2 101.5 122.7 100.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 165 SG REMARK 620 2 CYS A 168 SG 113.8 REMARK 620 3 HIS A 181 NE2 113.9 95.6 REMARK 620 4 HIS A 185 NE2 107.4 113.8 112.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 107 SG REMARK 620 2 CYS B 112 SG 94.2 REMARK 620 3 HIS B 125 NE2 103.1 111.7 REMARK 620 4 HIS B 129 NE2 106.1 120.3 116.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 205 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 137 SG REMARK 620 2 CYS B 140 SG 105.0 REMARK 620 3 HIS B 153 NE2 98.2 107.7 REMARK 620 4 HIS B 157 NE2 109.3 138.3 90.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 206 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 165 SG REMARK 620 2 CYS B 168 SG 120.6 REMARK 620 3 HIS B 181 NE2 83.7 95.1 REMARK 620 4 HIS B 185 NE2 78.7 150.6 109.8 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 206 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AAY RELATED DB: PDB REMARK 900 MODEL USED FOR MOLECULAR REPLACEMENT DBREF 1P47 A 102 188 UNP P08046 EGR1_MOUSE 333 419 DBREF 1P47 B 102 188 UNP P08046 EGR1_MOUSE 333 419 DBREF 1P47 C 1 22 PDB 1P47 1P47 1 22 DBREF 1P47 D 42 63 PDB 1P47 1P47 42 63 SEQRES 1 C 22 DG DT DG DG DC DG DT DG DG DG DC DG DG SEQRES 2 C 22 DC DG DT DG DG DG DC DG DT SEQRES 1 D 22 DC DA DC DG DC DC DC DA DC DG DC DC DG SEQRES 2 D 22 DC DC DC DA DC DG DC DC DA SEQRES 1 A 87 GLU ARG PRO TYR ALA CYS PRO VAL GLU SER CYS ASP ARG SEQRES 2 A 87 ARG PHE SER ARG SER ASP GLU LEU THR ARG HIS ILE ARG SEQRES 3 A 87 ILE HIS THR GLY GLN LYS PRO PHE GLN CYS ARG ILE CYS SEQRES 4 A 87 MET ARG ASN PHE SER ARG SER ASP HIS LEU THR THR HIS SEQRES 5 A 87 ILE ARG THR HIS THR GLY GLU LYS PRO PHE ALA CYS ASP SEQRES 6 A 87 ILE CYS GLY ARG LYS PHE ALA ARG SER ASP GLU ARG LYS SEQRES 7 A 87 ARG HIS THR LYS ILE HIS LEU ARG GLN SEQRES 1 B 87 GLU ARG PRO TYR ALA CYS PRO VAL GLU SER CYS ASP ARG SEQRES 2 B 87 ARG PHE SER ARG SER ASP GLU LEU THR ARG HIS ILE ARG SEQRES 3 B 87 ILE HIS THR GLY GLN LYS PRO PHE GLN CYS ARG ILE CYS SEQRES 4 B 87 MET ARG ASN PHE SER ARG SER ASP HIS LEU THR THR HIS SEQRES 5 B 87 ILE ARG THR HIS THR GLY GLU LYS PRO PHE ALA CYS ASP SEQRES 6 B 87 ILE CYS GLY ARG LYS PHE ALA ARG SER ASP GLU ARG LYS SEQRES 7 B 87 ARG HIS THR LYS ILE HIS LEU ARG GLN HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET ZN B 204 1 HET ZN B 205 1 HET ZN B 206 1 HETNAM ZN ZINC ION FORMUL 5 ZN 6(ZN 2+) FORMUL 11 HOH *100(H2 O) HELIX 1 1 ARG A 118 ARG A 127 1 10 HELIX 2 2 ARG A 146 GLY A 159 1 14 HELIX 3 3 ARG A 174 LYS A 183 1 10 HELIX 4 4 ILE A 184 ARG A 187 5 4 HELIX 5 5 ARG B 118 GLY B 131 1 14 HELIX 6 6 ARG B 146 GLY B 159 1 14 HELIX 7 7 ARG B 174 LYS B 183 1 10 SHEET 1 A 2 TYR A 105 ALA A 106 0 SHEET 2 A 2 ARG A 115 PHE A 116 -1 O PHE A 116 N TYR A 105 SHEET 1 B 2 PHE A 135 GLN A 136 0 SHEET 2 B 2 ASN A 143 PHE A 144 -1 O PHE A 144 N PHE A 135 SHEET 1 C 2 PHE A 163 ALA A 164 0 SHEET 2 C 2 LYS A 171 PHE A 172 -1 O PHE A 172 N PHE A 163 SHEET 1 D 2 TYR B 105 ALA B 106 0 SHEET 2 D 2 ARG B 115 PHE B 116 -1 O PHE B 116 N TYR B 105 SHEET 1 E 2 PHE B 135 GLN B 136 0 SHEET 2 E 2 ASN B 143 PHE B 144 -1 O PHE B 144 N PHE B 135 LINK SG CYS A 107 ZN ZN A 201 1555 1555 2.29 LINK SG CYS A 112 ZN ZN A 201 1555 1555 2.31 LINK NE2 HIS A 125 ZN ZN A 201 1555 1555 2.18 LINK NE2 HIS A 129 ZN ZN A 201 1555 1555 2.00 LINK SG CYS A 137 ZN ZN A 202 1555 1555 2.22 LINK SG CYS A 140 ZN ZN A 202 1555 1555 2.32 LINK NE2 HIS A 153 ZN ZN A 202 1555 1555 2.09 LINK NE2 HIS A 157 ZN ZN A 202 1555 1555 1.97 LINK SG CYS A 165 ZN ZN A 203 1555 1555 2.24 LINK SG CYS A 168 ZN ZN A 203 1555 1555 2.09 LINK NE2 HIS A 181 ZN ZN A 203 1555 1555 2.25 LINK NE2 HIS A 185 ZN ZN A 203 1555 1555 2.12 LINK SG CYS B 107 ZN ZN B 204 1555 1555 2.27 LINK SG CYS B 112 ZN ZN B 204 1555 1555 2.37 LINK NE2 HIS B 125 ZN ZN B 204 1555 1555 2.02 LINK NE2 HIS B 129 ZN ZN B 204 1555 1555 2.17 LINK SG CYS B 137 ZN ZN B 205 1555 1555 2.37 LINK SG CYS B 140 ZN ZN B 205 1555 1555 2.28 LINK NE2 HIS B 153 ZN ZN B 205 1555 1555 2.17 LINK NE2 HIS B 157 ZN ZN B 205 1555 1555 2.10 LINK SG CYS B 165 ZN ZN B 206 1555 1555 2.28 LINK SG CYS B 168 ZN ZN B 206 1555 1555 2.36 LINK NE2 HIS B 181 ZN ZN B 206 1555 1555 2.38 LINK NE2 HIS B 185 ZN ZN B 206 1555 1555 2.07 SITE 1 AC1 4 CYS A 107 CYS A 112 HIS A 125 HIS A 129 SITE 1 AC2 4 CYS A 137 CYS A 140 HIS A 153 HIS A 157 SITE 1 AC3 4 CYS A 165 CYS A 168 HIS A 181 HIS A 185 SITE 1 AC4 4 CYS B 107 CYS B 112 HIS B 125 HIS B 129 SITE 1 AC5 4 CYS B 137 CYS B 140 HIS B 153 HIS B 157 SITE 1 AC6 4 CYS B 165 CYS B 168 HIS B 181 HIS B 185 CRYST1 70.629 70.629 99.608 90.00 90.00 120.00 P 31 6 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 0.014158 0.008174 0.000000 0.00000 SCALE2 0.000000 0.016349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010039 0.00000