HEADER HYDROLASE/DNA 16-FEB-11 3QQY TITLE CRYSTAL STRUCTURE OF A NOVEL LAGLIDADG HOMING ENDONUCLEASE, I-ONUI TITLE 2 (FROM OPHIOSTOMA NOVO-ULMI SUBSP. AMERICANA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN 3/HOMING ENDONUCLEASE-LIKE PROTEIN COMPND 3 FUSION; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 413-715; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (26-MER); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: TARGET DNA SEQUENCE (TOP STRAND); COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (26-MER); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: TARGET DNA SEQUENCE (BOTTOM STRAND) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OPHIOSTOMA NOVO-ULMI SUBSP. AMERICANA; SOURCE 3 ORGANISM_TAXID: 170178; SOURCE 4 GENE: RPS3/HEG FUSION; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: TARGET SEQUENCE FOR THE CO-CRYSTALLIZED PROTEIN; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: TARGET SEQUENCE FOR THE CO-CRYSTALLIZED PROTEIN KEYWDS PROTEIN-DNA COMLEX, LAGLIDADG FAMILY, HYDROLASE, DNA BINDING, KEYWDS 2 MITOCHONDRION, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.TAKEUCHI,B.L.STODDARD REVDAT 4 13-SEP-23 3QQY 1 REMARK SEQADV LINK REVDAT 3 24-AUG-11 3QQY 1 JRNL REVDAT 2 10-AUG-11 3QQY 1 JRNL REVDAT 1 20-JUL-11 3QQY 0 JRNL AUTH R.TAKEUCHI,A.R.LAMBERT,A.N.MAK,K.JACOBY,R.J.DICKSON, JRNL AUTH 2 G.B.GLOOR,A.M.SCHARENBERG,D.R.EDGELL,B.L.STODDARD JRNL TITL TAPPING NATURAL RESERVOIRS OF HOMING ENDONUCLEASES FOR JRNL TITL 2 TARGETED GENE MODIFICATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 13077 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21784983 JRNL DOI 10.1073/PNAS.1107719108 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 44.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 17525 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 955 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) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1172 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2419 REMARK 3 NUCLEIC ACID ATOMS : 1060 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.88000 REMARK 3 B22 (A**2) : -3.29000 REMARK 3 B33 (A**2) : 2.42000 REMARK 3 B12 (A**2) : 0.00000 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): 0.484 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.267 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.343 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3652 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5140 ; 2.217 ; 2.329 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 297 ; 6.311 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;39.068 ;25.370 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 490 ;17.964 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;18.518 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 578 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2324 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1481 ; 0.867 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2399 ; 1.625 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2171 ; 2.511 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2741 ; 3.585 ; 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 : 2 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 2 A 303 REMARK 3 ORIGIN FOR THE GROUP (A): -7.3148 3.0369 36.0521 REMARK 3 T TENSOR REMARK 3 T11: 0.0716 T22: 0.0076 REMARK 3 T33: 0.2168 T12: -0.0049 REMARK 3 T13: 0.0382 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 0.6583 L22: 0.9853 REMARK 3 L33: 3.0347 L12: -0.3184 REMARK 3 L13: -0.5125 L23: 0.8940 REMARK 3 S TENSOR REMARK 3 S11: 0.0481 S12: 0.0488 S13: 0.0688 REMARK 3 S21: -0.0536 S22: -0.0277 S23: 0.0002 REMARK 3 S31: -0.0433 S32: -0.0630 S33: -0.0204 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 26 REMARK 3 RESIDUE RANGE : C 1 C 26 REMARK 3 ORIGIN FOR THE GROUP (A): -12.0311 -5.6309 34.6087 REMARK 3 T TENSOR REMARK 3 T11: 0.1523 T22: 0.0699 REMARK 3 T33: 0.2148 T12: 0.0096 REMARK 3 T13: 0.0374 T23: 0.0154 REMARK 3 L TENSOR REMARK 3 L11: 0.4819 L22: 0.6363 REMARK 3 L33: 5.7243 L12: -0.0368 REMARK 3 L13: 0.6332 L23: 0.7353 REMARK 3 S TENSOR REMARK 3 S11: 0.1482 S12: 0.0302 S13: -0.0122 REMARK 3 S21: 0.0083 S22: 0.0880 S23: 0.0164 REMARK 3 S31: 0.3732 S32: -0.2260 S33: -0.2362 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3QQY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18568 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 (%) : 96.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 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 (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.14000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.620 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 1P8K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE, 100 MM AMMONIUM REMARK 280 SULFATE, 25% PEG 300, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 18.97400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.46500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.96650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 83.46500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.97400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.96650 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: 8660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 -3 REMARK 465 PRO A -2 REMARK 465 LEU A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 LYS A 156 REMARK 465 GLU A 157 REMARK 465 ARG A 158 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 B 7 O3' DA B 7 C3' -0.061 REMARK 500 DA B 7 C5 DA B 7 N7 -0.045 REMARK 500 DT B 13 O3' DT B 13 C3' -0.041 REMARK 500 DA B 16 O3' DA B 16 C3' -0.047 REMARK 500 DC B 18 O3' DC B 18 C3' -0.042 REMARK 500 DG C 18 O3' DG C 18 C3' -0.036 REMARK 500 DT C 19 O3' DT C 19 C3' -0.052 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 LEU A 99 CA - CB - CG ANGL. DEV. = 19.2 DEGREES REMARK 500 DC B 1 N1 - C1' - C2' ANGL. DEV. = 9.7 DEGREES REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = -15.5 DEGREES REMARK 500 DT B 2 N3 - C4 - O4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT B 2 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT B 2 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 DC B 5 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 7 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC B 8 P - O5' - C5' ANGL. DEV. = -11.1 DEGREES REMARK 500 DC B 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT B 9 OP1 - P - OP2 ANGL. DEV. = 12.6 DEGREES REMARK 500 DT B 9 O5' - P - OP2 ANGL. DEV. = -8.8 DEGREES REMARK 500 DT B 9 N3 - C4 - O4 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT B 9 C5 - C4 - O4 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 10 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT B 10 C2 - N3 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT B 10 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 11 O4' - C1' - N9 ANGL. DEV. = -7.1 DEGREES REMARK 500 DT B 13 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA B 15 N1 - C2 - N3 ANGL. DEV. = -4.0 DEGREES REMARK 500 DA B 16 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 18 P - O5' - C5' ANGL. DEV. = -12.5 DEGREES REMARK 500 DC B 18 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 18 C5' - C4' - C3' ANGL. DEV. = -14.1 DEGREES REMARK 500 DC B 18 O4' - C1' - C2' ANGL. DEV. = 3.9 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 7.3 DEGREES REMARK 500 DT B 19 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT B 20 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 20 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DT B 22 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 23 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 DA B 23 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 DC B 24 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 24 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 DC B 25 N3 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 26 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG C 1 C2 - N3 - C4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG C 1 N3 - C4 - C5 ANGL. DEV. = 6.7 DEGREES REMARK 500 DG C 1 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG C 1 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG C 1 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 DG C 1 N9 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG C 1 N3 - C4 - N9 ANGL. DEV. = -9.8 DEGREES REMARK 500 DG C 1 C8 - N9 - C1' ANGL. DEV. = 14.5 DEGREES REMARK 500 DG C 1 C4 - N9 - C1' ANGL. DEV. = -11.6 DEGREES REMARK 500 DG C 2 C5' - C4' - C3' ANGL. DEV. = -13.8 DEGREES REMARK 500 DG C 2 O4' - C1' - N9 ANGL. DEV. = 9.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 81 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 SER A 5 59.83 -141.30 REMARK 500 ASN A 33 -39.90 -37.66 REMARK 500 TYR A 97 76.46 -119.38 REMARK 500 ASN A 139 -111.00 46.31 REMARK 500 GLU A 152 152.94 -46.77 REMARK 500 ASN A 167 -179.30 -176.17 REMARK 500 SER A 230 -106.01 51.25 REMARK 500 ASN A 298 -117.97 54.51 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 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 21 O REMARK 620 2 GLU A 22 OE1 68.1 REMARK 620 3 DC B 14 OP1 124.3 152.1 REMARK 620 4 DA C 16 OP1 72.7 74.9 85.0 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 MG A 304 DBREF 3QQY A 1 303 UNP Q4VWW5 Q4VWW5_OPHNO 413 715 DBREF 3QQY B 1 26 PDB 3QQY 3QQY 1 26 DBREF 3QQY C 1 26 PDB 3QQY 3QQY 1 26 SEQADV 3QQY GLY A -3 UNP Q4VWW5 EXPRESSION TAG SEQADV 3QQY PRO A -2 UNP Q4VWW5 EXPRESSION TAG SEQADV 3QQY LEU A -1 UNP Q4VWW5 EXPRESSION TAG SEQADV 3QQY GLY A 0 UNP Q4VWW5 EXPRESSION TAG SEQRES 1 A 307 GLY PRO LEU GLY SER ALA TYR MET SER ARG ARG GLU SER SEQRES 2 A 307 ILE ASN PRO TRP ILE LEU THR GLY PHE ALA ASP ALA GLU SEQRES 3 A 307 GLY SER PHE LEU LEU ARG ILE ARG ASN ASN ASN LYS SER SEQRES 4 A 307 SER VAL GLY TYR SER THR GLU LEU GLY PHE GLN ILE THR SEQRES 5 A 307 LEU HIS ASN LYS ASP LYS SER ILE LEU GLU ASN ILE GLN SEQRES 6 A 307 SER THR TRP LYS VAL GLY VAL ILE ALA ASN SER GLY ASP SEQRES 7 A 307 ASN ALA VAL SER LEU LYS VAL THR ARG PHE GLU ASP LEU SEQRES 8 A 307 LYS VAL ILE ILE ASP HIS PHE GLU LYS TYR PRO LEU ILE SEQRES 9 A 307 THR GLN LYS LEU GLY ASP TYR MET LEU PHE LYS GLN ALA SEQRES 10 A 307 PHE CYS VAL MET GLU ASN LYS GLU HIS LEU LYS ILE ASN SEQRES 11 A 307 GLY ILE LYS GLU LEU VAL ARG ILE LYS ALA LYS LEU ASN SEQRES 12 A 307 TRP GLY LEU THR ASP GLU LEU LYS LYS ALA PHE PRO GLU SEQRES 13 A 307 ILE ILE SER LYS GLU ARG SER LEU ILE ASN LYS ASN ILE SEQRES 14 A 307 PRO ASN PHE LYS TRP LEU ALA GLY PHE THR SER GLY GLU SEQRES 15 A 307 GLY CYS PHE PHE VAL ASN LEU ILE LYS SER LYS SER LYS SEQRES 16 A 307 LEU GLY VAL GLN VAL GLN LEU VAL PHE SER ILE THR GLN SEQRES 17 A 307 HIS ILE LYS ASP LYS ASN LEU MET ASN SER LEU ILE THR SEQRES 18 A 307 TYR LEU GLY CYS GLY TYR ILE LYS GLU LYS ASN LYS SER SEQRES 19 A 307 GLU PHE SER TRP LEU ASP PHE VAL VAL THR LYS PHE SER SEQRES 20 A 307 ASP ILE ASN ASP LYS ILE ILE PRO VAL PHE GLN GLU ASN SEQRES 21 A 307 THR LEU ILE GLY VAL LYS LEU GLU ASP PHE GLU ASP TRP SEQRES 22 A 307 CYS LYS VAL ALA LYS LEU ILE GLU GLU LYS LYS HIS LEU SEQRES 23 A 307 THR GLU SER GLY LEU ASP GLU ILE LYS LYS ILE LYS LEU SEQRES 24 A 307 ASN MET ASN LYS GLY ARG VAL PHE SEQRES 1 B 26 DC DT DT DT DC DC DA DC DT DT DA DT DT SEQRES 2 B 26 DC DA DA DC DC DT DT DT DT DA DC DC DC SEQRES 1 C 26 DG DG DT DA DA DA DA DG DG DT DT DG DA SEQRES 2 C 26 DA DT DA DA DG DT DG DG DA DA DA DG DG HET MG A 304 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG MG 2+ FORMUL 5 HOH *73(H2 O) HELIX 1 1 ASN A 11 GLU A 22 1 12 HELIX 2 2 ASP A 53 LYS A 65 1 13 HELIX 3 3 ARG A 83 GLU A 85 5 3 HELIX 4 4 ASP A 86 TYR A 97 1 12 HELIX 5 5 GLN A 102 ASN A 119 1 18 HELIX 6 6 LYS A 120 LEU A 123 5 4 HELIX 7 7 LYS A 124 ALA A 136 1 13 HELIX 8 8 THR A 143 PHE A 150 1 8 HELIX 9 9 ASN A 167 GLU A 178 1 12 HELIX 10 10 HIS A 205 LYS A 207 5 3 HELIX 11 11 ASP A 208 GLY A 220 1 13 HELIX 12 12 LYS A 241 LYS A 248 1 8 HELIX 13 13 LYS A 248 ASN A 256 1 9 HELIX 14 14 VAL A 261 GLU A 278 1 18 HELIX 15 15 LYS A 279 LEU A 282 5 4 HELIX 16 16 THR A 283 ASN A 296 1 14 HELIX 17 17 MET A 297 ARG A 301 5 5 SHEET 1 A 4 SER A 24 ASN A 31 0 SHEET 2 A 4 TYR A 39 HIS A 50 -1 O SER A 40 N ARG A 30 SHEET 3 A 4 ALA A 76 VAL A 81 -1 O VAL A 77 N LEU A 49 SHEET 4 A 4 VAL A 68 ASN A 71 -1 N ALA A 70 O SER A 78 SHEET 1 B 4 GLY A 179 LYS A 187 0 SHEET 2 B 4 VAL A 194 GLN A 204 -1 O GLN A 195 N ILE A 186 SHEET 3 B 4 PHE A 232 VAL A 239 -1 O LEU A 235 N GLN A 204 SHEET 4 B 4 TYR A 223 LYS A 229 -1 N LYS A 229 O PHE A 232 LINK O ALA A 21 MG MG A 304 1555 1555 2.76 LINK OE1 GLU A 22 MG MG A 304 1555 1555 2.97 LINK MG MG A 304 OP1 DC B 14 1555 1555 2.99 LINK MG MG A 304 OP1 DA C 16 1555 1555 2.77 SITE 1 AC1 7 ALA A 21 GLU A 22 GLU A 178 DC B 14 SITE 2 AC1 7 DA B 15 DT C 15 DA C 16 CRYST1 37.948 73.933 166.930 90.00 90.00 90.00 P 21 21 21 4 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 0.026352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005991 0.00000