PDB Short entry for 5E63 HEADER HYDROLASE/DNA 09-OCT-15 5E63 TITLE K262A MUTANT OF I-SMAMI COMPND MOL_ID: 1; COMPND 2 MOLECULE: I-SMAMI LAGLIDADG MEGANUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 114-415; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA RIGHT HALF SITE BOTTOM STRAND; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA LEFT HALF SITE BOTTOM STRAND; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA LEFT SITE TOP STRAND; COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3'); COMPND 21 CHAIN: E; COMPND 22 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SORDARIA MACROSPORA (STRAIN ATCC MYA-333 / DSM SOURCE 3 997 / K(L3346) / K-HELL); SOURCE 4 ORGANISM_TAXID: 771870; SOURCE 5 STRAIN: ATCC MYA-333 / DSM 997 / K(L3346) / K-HELL; SOURCE 6 GENE: SMAC_12671; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21D(+); SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630; SOURCE 23 MOL_ID: 5; SOURCE 24 SYNTHETIC: YES; SOURCE 25 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 26 ORGANISM_TAXID: 32630 KEYWDS LAGLIDADG, I-SMAMI, K262A, MUTANT, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.SHEN,B.STODDARD REVDAT 2 10-FEB-16 5E63 1 JRNL REVDAT 1 13-JAN-16 5E63 0 JRNL AUTH B.W.SHEN,A.LAMBERT,B.C.WALKER,B.L.STODDARD,B.K.KAISER JRNL TITL THE STRUCTURAL BASIS OF ASYMMETRY IN DNA BINDING AND JRNL TITL 2 CLEAVAGE AS EXHIBITED BY THE I-SMAMI LAGLIDADG MEGANUCLEASE. JRNL REF J.MOL.BIOL. V. 428 206 2016 JRNL REFN ESSN 1089-8638 JRNL PMID 26705195 JRNL DOI 10.1016/J.JMB.2015.12.005 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0124 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12093 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 618 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 867 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 33 REMARK 3 BIN FREE R VALUE : 0.4450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2334 REMARK 3 NUCLEIC ACID ATOMS : 1021 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.50000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : 0.99000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.392 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.292 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.858 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.880 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3548 ; 0.017 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 2940 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4988 ; 2.040 ; 1.693 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6826 ; 1.305 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 292 ; 7.888 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;35.917 ;24.388 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 445 ;19.860 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;22.333 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 503 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3234 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 789 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1171 ; 0.822 ; 1.435 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1170 ; 0.816 ; 1.433 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1462 ; 1.432 ; 2.147 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1463 ; 1.432 ; 2.150 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2377 ; 0.708 ; 1.567 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2377 ; 0.704 ; 1.567 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3527 ; 1.203 ; 2.327 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4360 ; 2.984 ;13.049 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4360 ; 2.983 ;13.050 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 : 5 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 300 REMARK 3 ORIGIN FOR THE GROUP (A): 6.1207 -0.8933 -0.9327 REMARK 3 T TENSOR REMARK 3 T11: 0.1376 T22: 0.1328 REMARK 3 T33: 0.0114 T12: 0.0223 REMARK 3 T13: -0.0094 T23: 0.0172 REMARK 3 L TENSOR REMARK 3 L11: 0.7939 L22: 2.8712 REMARK 3 L33: 2.1508 L12: 0.3922 REMARK 3 L13: 0.1794 L23: 1.7290 REMARK 3 S TENSOR REMARK 3 S11: -0.0006 S12: -0.0699 S13: 0.0677 REMARK 3 S21: -0.0423 S22: -0.0018 S23: 0.0400 REMARK 3 S31: -0.1580 S32: -0.1197 S33: 0.0025 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 1 B 14 REMARK 3 ORIGIN FOR THE GROUP (A): -5.1600 -10.9485 -16.0072 REMARK 3 T TENSOR REMARK 3 T11: 0.1780 T22: 0.2185 REMARK 3 T33: 0.1999 T12: -0.0139 REMARK 3 T13: -0.0170 T23: -0.0488 REMARK 3 L TENSOR REMARK 3 L11: 1.6473 L22: 5.1320 REMARK 3 L33: 4.5635 L12: -0.6644 REMARK 3 L13: -0.8357 L23: 2.5318 REMARK 3 S TENSOR REMARK 3 S11: 0.0361 S12: -0.1660 S13: 0.4858 REMARK 3 S21: 0.0588 S22: 0.0034 S23: 0.2910 REMARK 3 S31: -0.1865 S32: -0.3336 S33: -0.0395 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 : C 15 C 25 REMARK 3 ORIGIN FOR THE GROUP (A): -2.3359 11.9048 18.0515 REMARK 3 T TENSOR REMARK 3 T11: 0.3187 T22: 0.2042 REMARK 3 T33: 0.3209 T12: -0.0287 REMARK 3 T13: 0.0240 T23: -0.0404 REMARK 3 L TENSOR REMARK 3 L11: 5.3974 L22: 2.6112 REMARK 3 L33: 7.0566 L12: -0.6488 REMARK 3 L13: 0.2724 L23: 1.2896 REMARK 3 S TENSOR REMARK 3 S11: -0.1161 S12: -0.6850 S13: 0.0744 REMARK 3 S21: 0.3223 S22: -0.2685 S23: -0.1132 REMARK 3 S31: -0.1197 S32: -0.7311 S33: 0.3845 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 : D 1 D 15 REMARK 3 ORIGIN FOR THE GROUP (A): -3.0135 10.0522 12.9090 REMARK 3 T TENSOR REMARK 3 T11: 0.2776 T22: 0.2221 REMARK 3 T33: 0.1577 T12: 0.0273 REMARK 3 T13: 0.0105 T23: -0.0264 REMARK 3 L TENSOR REMARK 3 L11: 1.8368 L22: 3.6381 REMARK 3 L33: 4.4082 L12: 0.0629 REMARK 3 L13: 0.0022 L23: 3.0419 REMARK 3 S TENSOR REMARK 3 S11: 0.0196 S12: -0.1676 S13: -0.0159 REMARK 3 S21: 0.0303 S22: -0.1071 S23: 0.3231 REMARK 3 S31: -0.2601 S32: -0.6022 S33: 0.0875 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 16 E 25 REMARK 3 ORIGIN FOR THE GROUP (A): -4.7878 -14.4378 -21.9424 REMARK 3 T TENSOR REMARK 3 T11: 0.3269 T22: 0.1133 REMARK 3 T33: 0.1746 T12: 0.0147 REMARK 3 T13: -0.0847 T23: -0.0229 REMARK 3 L TENSOR REMARK 3 L11: 6.6091 L22: 3.7918 REMARK 3 L33: 8.0198 L12: 0.9888 REMARK 3 L13: 2.3118 L23: 3.7311 REMARK 3 S TENSOR REMARK 3 S11: 0.0048 S12: 0.1046 S13: 0.0962 REMARK 3 S21: -0.0542 S22: -0.2411 S23: 0.2115 REMARK 3 S31: 0.1072 S32: -0.8068 S33: 0.2363 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5E63 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 70 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12826 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.66100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 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: 4LOX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28-32% PEGMME550, HEPES MG++, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 29.91750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.89000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.84700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.89000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.91750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.84700 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: 9450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 LYS A 2 REMARK 465 GLY A 3 REMARK 465 GLU A 4 REMARK 465 ASN A 5 REMARK 465 SER A 6 REMARK 465 LYS A 7 REMARK 465 ARG A 301 REMARK 465 LEU A 302 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 OP1 DA B 14 OP2 DC E 16 2.06 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 DT C 15 P DT C 15 OP3 -0.102 REMARK 500 DC E 16 P DC E 16 OP3 -0.095 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 ASP A 95 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 DC B 5 O5' - P - OP2 ANGL. DEV. = -8.0 DEGREES REMARK 500 DG C 20 O5' - P - OP1 ANGL. DEV. = 7.5 DEGREES REMARK 500 DG C 20 O5' - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 DC D 9 O5' - P - OP2 ANGL. DEV. = -7.4 DEGREES REMARK 500 DT D 15 O5' - P - OP1 ANGL. DEV. = -9.1 DEGREES REMARK 500 DC E 16 O5' - P - OP2 ANGL. DEV. = -7.5 DEGREES REMARK 500 DG E 21 O5' - P - OP2 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC E 24 C1' - O4' - C4' 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 PHE A 62 47.14 -88.19 REMARK 500 SER A 71 -60.39 -103.67 REMARK 500 SER A 74 25.40 -142.04 REMARK 500 ASN A 139 -124.02 47.67 REMARK 500 ASN A 163 79.56 29.33 REMARK 500 ARG A 209 -28.98 -36.25 REMARK 500 LYS A 248 -54.13 -120.25 REMARK 500 SER A 261 -39.90 -39.10 REMARK 500 HIS A 281 -19.28 -48.68 REMARK 500 ASN A 298 58.56 70.57 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 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 19 O REMARK 620 2 ASP A 179 OD2 93.2 REMARK 620 3 DT C 15 OP3 95.1 100.8 REMARK 620 4 DT C 15 OP1 88.1 172.5 71.7 REMARK 620 5 DT D 15 OP1 153.1 98.0 106.5 83.9 REMARK 620 6 HOH D 101 O 78.7 87.3 170.1 100.2 77.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 20 OE1 REMARK 620 2 GLU A 20 OE2 44.7 REMARK 620 3 ASP A 179 OD1 117.2 76.5 REMARK 620 4 DA B 14 O3' 70.0 109.4 172.4 REMARK 620 5 DT C 15 OP3 115.4 140.9 95.1 83.3 REMARK 620 6 DT D 15 O3' 146.0 127.4 82.3 90.2 88.0 REMARK 620 7 DC E 16 OP1 97.9 72.9 80.0 97.0 144.1 56.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 178 O REMARK 620 2 DC E 16 OP2 85.4 REMARK 620 N 1 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MXE A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG0 E 101 DBREF 5E63 A 1 302 UNP F7WD42 F7WD42_SORMK 114 415 DBREF 5E63 B 1 14 PDB 5E63 5E63 1 14 DBREF 5E63 C 15 25 PDB 5E63 5E63 15 25 DBREF 5E63 D 1 15 PDB 5E63 5E63 1 15 DBREF 5E63 E 16 25 PDB 5E63 5E63 16 25 SEQADV 5E63 ASN A 165 UNP F7WD42 LEU 278 CONFLICT SEQADV 5E63 ALA A 262 UNP F7WD42 LYS 375 ENGINEERED MUTATION SEQADV 5E63 GLN A 267 UNP F7WD42 MET 380 CONFLICT SEQRES 1 A 302 SER LYS GLY GLU ASN SER LYS LEU ASN PRO TRP ALA VAL SEQRES 2 A 302 VAL GLY PHE ILE ASP ALA GLU GLY SER PHE MET VAL ARG SEQRES 3 A 302 VAL ARG LYS ASN SER LYS TYR LYS THR GLY TRP LEU VAL SEQRES 4 A 302 VAL ALA ILE PHE SER VAL THR VAL ASP LYS LYS ASP LEU SEQRES 5 A 302 PHE LEU LEU GLU SER LEU LYS THR PHE PHE GLY GLY LEU SEQRES 6 A 302 GLY SER ILE LYS LYS SER GLY ASN SER THR PHE SER TYR SEQRES 7 A 302 ARG ILE GLU SER SER GLU GLN LEU THR LYS ILE ILE LEU SEQRES 8 A 302 PRO PHE PHE ASP LYS TYR SER LEU ILE THR GLU LYS LEU SEQRES 9 A 302 GLY ASP TYR LEU LEU PHE LYS LYS VAL LEU GLU LEU MET SEQRES 10 A 302 GLY THR LYS GLU HIS LEU THR GLN ARG GLY LEU GLU LYS SEQRES 11 A 302 ILE VAL SER LEU LYS ALA SER ILE ASN LYS GLY LEU SER SEQRES 12 A 302 GLU GLU LEU GLN ALA ALA PHE PRO GLN CYS VAL PRO THR SEQRES 13 A 302 PRO ARG PRO GLU ILE ASN ASN LYS ASN ILE PRO ASP PRO SEQRES 14 A 302 PHE TRP LEU ALA GLY PHE VAL SER GLY ASP GLY SER PHE SEQRES 15 A 302 LYS SER ILE LEU LYS LYS SER GLU SER ILE LYS VAL GLY SEQRES 16 A 302 PHE GLN SER ILE LEU VAL PHE GLN ILE THR GLN HIS ALA SEQRES 17 A 302 ARG ASP VAL LYS LEU MET GLU SER LEU ILE SER TYR LEU SEQRES 18 A 302 GLY CYS GLY PHE ILE GLU LYS ASP SER ARG GLY PRO TRP SEQRES 19 A 302 LEU TYR TYR THR VAL THR ASN PHE SER ASP ILE GLN GLY SEQRES 20 A 302 LYS ILE ILE PRO PHE PHE HIS GLN TYR LYS ILE ILE GLY SEQRES 21 A 302 SER ALA TYR GLY ASP TYR GLN ASP TRP CYS LYS ILE ALA SEQRES 22 A 302 LEU ILE MET GLN ASN LYS ASN HIS LEU THR PRO GLU GLY SEQRES 23 A 302 LEU ASN GLU ILE ARG ALA LEU LYS GLY GLY MET ASN LYS SEQRES 24 A 302 GLY ARG LEU SEQRES 1 B 14 DC DG DT DA DC DA DC DC DT DG DA DT DA SEQRES 2 B 14 DA SEQRES 1 C 11 DT DG DG DA DG DG DA DT DA DC DC SEQRES 1 D 15 DG DG DT DA DT DC DC DT DC DC DA DT DT SEQRES 2 D 15 DA DT SEQRES 1 E 10 DC DA DG DG DT DG DT DA DC DG HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HET MXE A 404 5 HET PG0 E 101 16 HETNAM MG MAGNESIUM ION HETNAM MXE 2-METHOXYETHANOL HETNAM PG0 2-(2-METHOXYETHOXY)ETHANOL HETSYN PG0 PEG 6000 FORMUL 6 MG 3(MG 2+) FORMUL 9 MXE C3 H8 O2 FORMUL 10 PG0 C5 H12 O3 FORMUL 11 HOH *49(H2 O) HELIX 1 AA1 ASN A 9 GLU A 20 1 12 HELIX 2 AA2 ASP A 51 PHE A 62 1 12 HELIX 3 AA3 SER A 82 ILE A 89 1 8 HELIX 4 AA4 ILE A 89 TYR A 97 1 9 HELIX 5 AA5 GLU A 102 THR A 119 1 18 HELIX 6 AA6 LYS A 120 LEU A 123 5 4 HELIX 7 AA7 THR A 124 ALA A 136 1 13 HELIX 8 AA8 SER A 143 PHE A 150 1 8 HELIX 9 AA9 ASP A 168 ASP A 179 1 12 HELIX 10 AB1 ASP A 210 GLY A 222 1 13 HELIX 11 AB2 ASN A 241 LYS A 248 1 8 HELIX 12 AB3 LYS A 248 TYR A 256 1 9 HELIX 13 AB4 SER A 261 ASN A 278 1 18 HELIX 14 AB5 LYS A 279 LEU A 282 5 4 HELIX 15 AB6 THR A 283 MET A 297 1 15 SHEET 1 AA1 4 GLY A 21 LYS A 29 0 SHEET 2 AA1 4 TRP A 37 ASP A 48 -1 O VAL A 40 N ARG A 26 SHEET 3 AA1 4 THR A 75 ILE A 80 -1 O TYR A 78 N VAL A 45 SHEET 4 AA1 4 SER A 67 LYS A 70 -1 N LYS A 69 O SER A 77 SHEET 1 AA2 4 GLY A 180 LYS A 188 0 SHEET 2 AA2 4 PHE A 196 HIS A 207 -1 O VAL A 201 N LYS A 183 SHEET 3 AA2 4 TRP A 234 VAL A 239 -1 O LEU A 235 N GLN A 206 SHEET 4 AA2 4 PHE A 225 LYS A 228 -1 N PHE A 225 O THR A 238 LINK O ALA A 19 MG MG A 402 1555 1555 2.21 LINK OE1 GLU A 20 MG MG A 401 1555 1555 2.72 LINK OE2 GLU A 20 MG MG A 401 1555 1555 2.85 LINK O GLY A 178 MG MG A 403 1555 1555 2.41 LINK OD1 ASP A 179 MG MG A 401 1555 1555 2.22 LINK OD2 ASP A 179 MG MG A 402 1555 1555 2.12 LINK O3' DA B 14 MG MG A 401 1555 1555 2.42 LINK OP3 DT C 15 MG MG A 401 1555 1555 1.84 LINK OP3 DT C 15 MG MG A 402 1555 1555 2.03 LINK OP1 DT C 15 MG MG A 402 1555 1555 2.10 LINK OP1 DT D 15 MG MG A 402 1555 1555 1.82 LINK O3' DT D 15 MG MG A 401 1555 1555 2.66 LINK OP1 DC E 16 MG MG A 401 1555 1555 2.35 LINK OP2 DC E 16 MG MG A 403 1555 1555 1.90 LINK MG MG A 402 O HOH D 101 1555 1555 2.22 CISPEP 1 LYS A 299 GLY A 300 0 -25.57 SITE 1 AC1 8 ALA A 19 GLU A 20 ASP A 179 MG A 402 SITE 2 AC1 8 DA B 14 DT C 15 DT D 15 DC E 16 SITE 1 AC2 6 ALA A 19 ASP A 179 MG A 401 DT C 15 SITE 2 AC2 6 DT D 15 HOH D 101 SITE 1 AC3 5 GLU A 20 SER A 177 GLY A 178 DA B 14 SITE 2 AC3 5 DC E 16 SITE 1 AC4 3 LYS A 49 DC C 25 DG D 1 SITE 1 AC5 4 DG B 2 DT B 3 DC E 24 DG E 25 CRYST1 59.835 67.694 97.780 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 0.016713 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010227 0.00000