PDB Short entry for 3R7P HEADER HYDROLASE/DNA 22-MAR-11 3R7P TITLE THE CRYSTAL STRUCTURE OF I-LTRI COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN 3/HOMING ENDONUCLEASE-LIKE FUSION COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: I-LTRI (UNP RESIDUES 398-712); COMPND 6 EC: 3.1.21.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)- COMPND 10 3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(P*AP*GP*GP*AP*GP*CP*AP*TP*TP*TP*G)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA (5'-D(*CP*AP*AP*AP*TP*GP*CP*TP*CP*CP*TP*AP*TP*AP*C)- COMPND 19 3'); COMPND 20 CHAIN: D; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 5; COMPND 23 MOLECULE: DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*AP*GP*AP*CP*C)-3'); COMPND 24 CHAIN: E; COMPND 25 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEPTOGRAPHIUM TRUNCATUM; SOURCE 3 ORGANISM_TAXID: 330483; SOURCE 4 GENE: RPS3/HEG FUSION; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: RIL (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-200-D-TOPO; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: SYNTHETIC; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 OTHER_DETAILS: SYNTHETIC; SOURCE 19 MOL_ID: 5; SOURCE 20 SYNTHETIC: YES; SOURCE 21 OTHER_DETAILS: SYNTHETIC KEYWDS HOMING ENDONUCLEASE, GENE THERAPY, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.N.S.MAK,R.TAKEUCHI,D.R.EDGELL,B.L.STODDARD REVDAT 6 13-SEP-23 3R7P 1 REMARK LINK REVDAT 5 21-JAN-15 3R7P 1 DBREF REVDAT 4 03-APR-13 3R7P 1 TITLE REVDAT 3 24-AUG-11 3R7P 1 JRNL REVDAT 2 10-AUG-11 3R7P 1 JRNL REVDAT 1 20-JUL-11 3R7P 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. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 12060 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 679 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 802 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2356 REMARK 3 NUCLEIC ACID ATOMS : 1103 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.57000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : -0.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.402 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.302 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.274 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3629 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5127 ; 1.337 ; 2.347 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 290 ; 5.846 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;37.890 ;24.364 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 462 ;19.828 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.873 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 585 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2316 ; 0.004 ; 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): 1448 ; 0.301 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2353 ; 0.592 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2181 ; 0.819 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2774 ; 1.306 ; 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 15 A 308 REMARK 3 ORIGIN FOR THE GROUP (A): 18.5280 11.7540 28.3070 REMARK 3 T TENSOR REMARK 3 T11: 0.0755 T22: 0.0967 REMARK 3 T33: 0.0962 T12: -0.0104 REMARK 3 T13: -0.0822 T23: 0.0224 REMARK 3 L TENSOR REMARK 3 L11: 3.0212 L22: 0.9968 REMARK 3 L33: 1.7347 L12: -0.5410 REMARK 3 L13: -1.3644 L23: 0.5094 REMARK 3 S TENSOR REMARK 3 S11: -0.0245 S12: 0.0190 S13: 0.0364 REMARK 3 S21: -0.0411 S22: 0.0588 S23: -0.0174 REMARK 3 S31: 0.0149 S32: 0.1204 S33: -0.0343 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 16 REMARK 3 RESIDUE RANGE : C 17 C 27 REMARK 3 RESIDUE RANGE : D 1 D 15 REMARK 3 RESIDUE RANGE : E 16 E 27 REMARK 3 ORIGIN FOR THE GROUP (A): 15.7720 11.6720 19.0430 REMARK 3 T TENSOR REMARK 3 T11: 0.0612 T22: 0.1387 REMARK 3 T33: 0.0648 T12: 0.0101 REMARK 3 T13: -0.0521 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 5.4845 L22: 0.6555 REMARK 3 L33: 2.3616 L12: -0.4733 REMARK 3 L13: -2.9076 L23: 0.3283 REMARK 3 S TENSOR REMARK 3 S11: -0.0322 S12: 0.4207 S13: 0.1941 REMARK 3 S21: -0.0113 S22: 0.0837 S23: -0.0183 REMARK 3 S31: 0.0812 S32: -0.1036 S33: -0.0515 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 3R7P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064593. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12060 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 48.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 356.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : 0.42500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 3QQY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, PH 6.5, 0.2M MGCL2, 20% REMARK 280 PEG 3500, 1MM MNCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 56.54450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.29750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.54450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.29750 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 SER A 1 REMARK 465 TYR A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 LEU A 5 REMARK 465 ALA A 6 REMARK 465 ASN A 7 REMARK 465 PHE A 8 REMARK 465 PRO A 9 REMARK 465 VAL A 10 REMARK 465 GLN A 11 REMARK 465 ALA A 12 REMARK 465 ARG A 13 REMARK 465 ASN A 14 REMARK 465 TYR A 236 REMARK 465 LYS A 237 REMARK 465 GLY A 238 REMARK 465 SER A 239 REMARK 465 GLU A 240 REMARK 465 GLY A 241 REMARK 465 ILE A 242 REMARK 465 HIS A 243 REMARK 465 ASP A 244 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 C 17 P DA C 17 OP3 -0.122 REMARK 500 DG E 16 P DG E 16 OP3 -0.121 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 B 1 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA B 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 13 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = -7.0 DEGREES REMARK 500 DG C 18 C1' - O4' - C4' ANGL. DEV. = -8.0 DEGREES REMARK 500 DG C 18 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG C 19 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DG C 27 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC D 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA D 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA D 3 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC D 9 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 DT D 11 O4' - C1' - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT D 13 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA D 14 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC D 15 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA E 17 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC E 18 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC E 18 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG E 19 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 DG E 24 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG E 24 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES 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 ASN A 58 -35.31 -38.57 REMARK 500 VAL A 61 -39.44 -38.55 REMARK 500 ASP A 79 -106.69 -126.88 REMARK 500 LEU A 128 23.86 -73.54 REMARK 500 LEU A 143 -148.96 -65.95 REMARK 500 ASN A 144 -88.73 -58.31 REMARK 500 MET A 309 -128.84 -85.33 REMARK 500 ASN A 310 -88.47 -48.04 REMARK 500 SER A 314 -156.68 -156.28 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 317 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 28 O REMARK 620 2 GLU A 184 OE2 86.0 REMARK 620 3 HOH A 322 O 68.7 74.8 REMARK 620 4 HOH A 323 O 80.4 151.9 77.3 REMARK 620 5 DA C 17 OP2 83.1 97.0 151.0 105.6 REMARK 620 6 DC D 15 OP1 154.6 81.3 86.7 100.9 120.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 316 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 29 OE2 REMARK 620 2 GLU A 29 OE1 57.5 REMARK 620 3 GLU A 184 OE1 90.4 147.7 REMARK 620 4 DA C 17 OP2 98.0 87.6 94.3 REMARK 620 5 DA C 17 OP3 141.3 87.3 121.9 62.0 REMARK 620 6 DG E 16 OP3 101.1 84.3 107.4 150.8 89.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 17 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 320 O REMARK 620 2 HOH A 336 O 110.5 REMARK 620 3 DT B 16 OP1 71.6 153.3 REMARK 620 4 DG E 16 OP2 149.8 85.6 82.7 REMARK 620 5 HOH E 28 O 84.7 69.9 84.1 76.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG E 2 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 21 O REMARK 620 2 DA C 17 OP3 81.3 REMARK 620 3 DC D 15 O3' 169.4 88.8 REMARK 620 4 HOH D 22 O 79.1 88.3 97.0 REMARK 620 5 DG E 16 OP1 97.4 103.2 88.4 167.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 17 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 317 DBREF 3R7P A 1 315 UNP C7SWF3 C7SWF3_9PEZI 398 712 DBREF 3R7P B 1 16 PDB 3R7P 3R7P 1 16 DBREF 3R7P C 17 27 PDB 3R7P 3R7P 17 27 DBREF 3R7P D 1 15 PDB 3R7P 3R7P 1 15 DBREF 3R7P E 16 27 PDB 3R7P 3R7P 16 27 SEQRES 1 A 315 SER TYR SER THR LEU ALA ASN PHE PRO VAL GLN ALA ARG SEQRES 2 A 315 ASN ASP ASN ILE SER PRO TRP THR ILE THR GLY PHE ALA SEQRES 3 A 315 ASP ALA GLU SER SER PHE MET LEU THR VAL SER LYS ASP SEQRES 4 A 315 SER LYS ARG ASN THR GLY TRP SER VAL ARG PRO ARG PHE SEQRES 5 A 315 ARG ILE GLY LEU HIS ASN LYS ASP VAL THR ILE LEU LYS SEQRES 6 A 315 SER ILE ARG GLU TYR LEU GLY ALA GLY ILE ILE THR SER SEQRES 7 A 315 ASP ILE ASP ALA ARG ILE ARG PHE GLU SER LEU LYS GLU SEQRES 8 A 315 LEU GLU VAL VAL ILE ASN HIS PHE ASP LYS TYR PRO LEU SEQRES 9 A 315 ILE THR GLN LYS ARG ALA ASP TYR LEU LEU PHE LYS LYS SEQRES 10 A 315 ALA PHE TYR LEU ILE LYS ASN LYS GLU HIS LEU THR GLU SEQRES 11 A 315 GLU GLY LEU ASN GLN ILE LEU THR LEU LYS ALA SER LEU SEQRES 12 A 315 ASN LEU GLY LEU SER GLU GLU LEU LYS GLU ALA PHE PRO SEQRES 13 A 315 ASN THR ILE PRO ALA GLU ARG LEU LEU VAL THR GLY GLN SEQRES 14 A 315 GLU ILE PRO ASP SER ASN TRP VAL ALA GLY PHE THR ALA SEQRES 15 A 315 GLY GLU GLY SER PHE TYR ILE ARG ILE ALA LYS ASN SER SEQRES 16 A 315 THR LEU LYS THR GLY TYR GLN VAL GLN SER VAL PHE GLN SEQRES 17 A 315 ILE THR GLN ASP THR ARG ASP ILE GLU LEU MET LYS ASN SEQRES 18 A 315 LEU ILE SER TYR LEU ASN CYS GLY ASN ILE ARG ILE ARG SEQRES 19 A 315 LYS TYR LYS GLY SER GLU GLY ILE HIS ASP THR CYS VAL SEQRES 20 A 315 ASP LEU VAL VAL THR ASN LEU ASN ASP ILE LYS GLU LYS SEQRES 21 A 315 ILE ILE PRO PHE PHE ASN LYS ASN HIS ILE ILE GLY VAL SEQRES 22 A 315 LYS LEU GLN ASP TYR ARG ASP TRP CYS LYS VAL VAL THR SEQRES 23 A 315 LEU ILE ASP ASN LYS GLU HIS LEU THR SER GLU GLY LEU SEQRES 24 A 315 GLU LYS ILE GLN LYS ILE LYS GLU GLY MET ASN ARG GLY SEQRES 25 A 315 ARG SER LEU SEQRES 1 B 16 DG DG DT DC DT DA DA DA DC DG DT DC DG SEQRES 2 B 16 DT DA DT SEQRES 1 C 11 DA DG DG DA DG DC DA DT DT DT DG SEQRES 1 D 15 DC DA DA DA DT DG DC DT DC DC DT DA DT SEQRES 2 D 15 DA DC SEQRES 1 E 12 DG DA DC DG DT DT DT DA DG DA DC DC HET MN A 316 1 HET MG A 317 1 HET MG B 17 1 HET MG D 16 1 HET MG E 2 1 HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION FORMUL 6 MN MN 2+ FORMUL 7 MG 4(MG 2+) FORMUL 11 HOH *43(H2 O) HELIX 1 1 SER A 18 SER A 30 1 13 HELIX 2 2 HIS A 57 LYS A 59 5 3 HELIX 3 3 ASP A 60 GLY A 72 1 13 HELIX 4 4 SER A 88 TYR A 102 1 15 HELIX 5 5 GLN A 107 ASN A 124 1 18 HELIX 6 6 THR A 129 LEU A 143 1 15 HELIX 7 7 SER A 148 PHE A 155 1 8 HELIX 8 8 ASP A 173 GLU A 184 1 12 HELIX 9 9 ASP A 215 ASN A 227 1 13 HELIX 10 10 ASN A 253 LYS A 260 1 8 HELIX 11 11 LYS A 260 ASN A 268 1 9 HELIX 12 12 VAL A 273 ASN A 290 1 18 HELIX 13 13 LYS A 291 LEU A 294 5 4 HELIX 14 14 THR A 295 GLY A 308 1 14 SHEET 1 A 4 SER A 31 LYS A 38 0 SHEET 2 A 4 TRP A 46 LEU A 56 -1 O SER A 47 N SER A 37 SHEET 3 A 4 ALA A 82 PHE A 86 -1 O ALA A 82 N LEU A 56 SHEET 4 A 4 ILE A 75 SER A 78 -1 N ILE A 75 O ARG A 85 SHEET 1 B 4 GLY A 185 LYS A 193 0 SHEET 2 B 4 TYR A 201 ASP A 212 -1 O VAL A 206 N TYR A 188 SHEET 3 B 4 CYS A 246 VAL A 251 -1 O LEU A 249 N ILE A 209 SHEET 4 B 4 ASN A 230 ARG A 234 -1 N ARG A 232 O ASP A 248 LINK O ALA A 28 MG MG A 317 1555 1555 2.35 LINK OE2 GLU A 29 MN MN A 316 1555 1555 2.07 LINK OE1 GLU A 29 MN MN A 316 1555 1555 2.42 LINK OE1 GLU A 184 MN MN A 316 1555 1555 2.13 LINK OE2 GLU A 184 MG MG A 317 1555 1555 2.06 LINK MN MN A 316 OP2 DA C 17 1555 1555 2.01 LINK MN MN A 316 OP3 DA C 17 1555 1555 2.56 LINK MN MN A 316 OP3 DG E 16 1555 1555 2.10 LINK MG MG A 317 O HOH A 322 1555 1555 2.25 LINK MG MG A 317 O HOH A 323 1555 1555 1.81 LINK MG MG A 317 OP2 DA C 17 1555 1555 2.01 LINK MG MG A 317 OP1 DC D 15 1555 1555 1.95 LINK O HOH A 320 MG MG B 17 1555 1555 2.88 LINK O HOH A 336 MG MG B 17 1555 1555 1.78 LINK OP1 DT B 16 MG MG B 17 1555 1555 2.03 LINK MG MG B 17 OP2 DG E 16 1555 1555 2.27 LINK MG MG B 17 O HOH E 28 1555 1555 2.50 LINK O HOH B 21 MG MG E 2 1555 1555 2.41 LINK OP3 DA C 17 MG MG E 2 1555 1555 2.18 LINK O3' DC D 15 MG MG E 2 1555 1555 2.27 LINK O HOH D 22 MG MG E 2 1555 1555 1.86 LINK MG MG E 2 OP1 DG E 16 1555 1555 1.89 SITE 1 AC1 6 GLU A 29 GLU A 184 MG A 317 DA C 17 SITE 2 AC1 6 DC D 15 DG E 16 SITE 1 AC2 6 LYS A 274 HOH A 320 HOH A 336 DT B 16 SITE 2 AC2 6 DG E 16 HOH E 28 SITE 1 AC3 5 HOH B 21 DA C 17 DC D 15 HOH D 22 SITE 2 AC3 5 DG E 16 SITE 1 AC4 7 ALA A 28 GLU A 184 MN A 316 HOH A 322 SITE 2 AC4 7 HOH A 323 DA C 17 DC D 15 CRYST1 113.089 42.595 103.195 90.00 110.63 90.00 C 1 2 1 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 0.008843 0.000000 0.003330 0.00000 SCALE2 0.000000 0.023477 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010355 0.00000