PDB Short entry for 3EEO HEADER TRANSFERASE/DNA 05-SEP-08 3EEO TITLE M. HHAI CO-CRYSTALLIZED WITH SYNTHETIC DSDNA CONTAINING A PROPANE DIOL TITLE 2 IN PLACE OF THE DEOXYCYTIDINE RESIDUE TARGETED FOR METHYLATION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3'; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*DGP*DTP*DCP*DAP*DGP*(PDI)P*DGP*DCP*DAP*DTP*DGP*DG)- COMPND 7 3'; COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: MODIFICATION METHYLASE HHAI; COMPND 12 CHAIN: A; COMPND 13 SYNONYM: M.HHAI, CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI; COMPND 14 EC: 2.1.1.37; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HAEMOPHILUS PARAHAEMOLYTICUS; SOURCE 7 ORGANISM_TAXID: 735; SOURCE 8 GENE: HHAIM; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-DNA COMPLEX WITH S-ADENOSYLMETHIONINE CO-FACTOR AND PROPANE KEYWDS 2 DIOL IN PLACE OF TARGETED CYTOSINE., METHYLTRANSFERASE, RESTRICTION KEYWDS 3 SYSTEM, S-ADENOSYL-L-METHIONINE, TRANSFERASE, TRANSFERASE-DNA KEYWDS 4 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.C.PORTA,J.K.CHRISTMAN,G.E.O.BORGSTAHL REVDAT 2 21-FEB-24 3EEO 1 REMARK LINK REVDAT 1 02-MAR-10 3EEO 0 JRNL AUTH J.C.PORTA,J.K.CHRISTMAN,G.E.O.BORGSTAHL JRNL TITL M. HHAI CO-CRYSTALLIZED WITH SYNTHETIC DSDNA CONTAINING A JRNL TITL 2 PROPANE DIOL IN PLACE OF THE DEOXYCYTIDINE RESIDUE TARGETED JRNL TITL 3 FOR METHYLATION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 39593 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) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2107 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) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2838 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 165 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2606 REMARK 3 NUCLEIC ACID ATOMS : 481 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.27000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : 0.40000 REMARK 3 B12 (A**2) : -0.13000 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): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.615 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3217 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4347 ; 2.722 ; 2.141 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 5.884 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;37.985 ;24.462 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 473 ;16.283 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;22.781 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 459 ; 0.201 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2254 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1368 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2153 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 134 ; 0.159 ; 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): 37 ; 0.147 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.172 ; 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): 1684 ; 1.006 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2622 ; 1.540 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1787 ; 2.810 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1725 ; 3.893 ; 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 : 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 3EEO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000049228. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC VARIMAX CONFOCAL MAX-FLUX REMARK 200 OPTIC REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41700 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 40.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 47.73950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.56241 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 106.11767 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 47.73950 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.56241 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 106.11767 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 47.73950 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.56241 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 106.11767 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 47.73950 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 27.56241 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 106.11767 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 47.73950 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 27.56241 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 106.11767 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 47.73950 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 27.56241 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 106.11767 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 55.12483 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 212.23533 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 55.12483 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 212.23533 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 55.12483 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 212.23533 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 55.12483 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 212.23533 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 55.12483 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 212.23533 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 55.12483 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 212.23533 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: 4440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 368 LIES ON A SPECIAL POSITION. 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 O VAL A 64 NH2 ARG A 106 1.99 REMARK 500 O2 DC D 424 O HOH D 71 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DA C 404 C5 DA C 404 C6 -0.087 REMARK 500 DA C 404 C5 DA C 404 N7 -0.038 REMARK 500 DA C 404 N7 DA C 404 C8 0.046 REMARK 500 DA C 404 C8 DA C 404 N9 0.074 REMARK 500 DA C 404 N9 DA C 404 C4 -0.040 REMARK 500 DT C 405 N3 DT C 405 C4 -0.063 REMARK 500 DT C 405 C4 DT C 405 C5 0.065 REMARK 500 DT C 405 C5 DT C 405 C6 -0.061 REMARK 500 DT C 405 C6 DT C 405 N1 -0.087 REMARK 500 DG C 406 N7 DG C 406 C8 0.063 REMARK 500 DC C 407 C5 DC C 407 C6 0.056 REMARK 500 DG C 408 N7 DG C 408 C8 0.039 REMARK 500 DC C 409 C5 DC C 409 C6 0.061 REMARK 500 DT C 410 C4 DT C 410 C5 0.069 REMARK 500 DT C 410 C5 DT C 410 C6 -0.075 REMARK 500 DT C 410 C6 DT C 410 N1 -0.085 REMARK 500 DG C 411 C5 DG C 411 C6 -0.105 REMARK 500 DG C 411 N9 DG C 411 C4 -0.060 REMARK 500 DA C 412 N7 DA C 412 C8 0.049 REMARK 500 DA C 412 C8 DA C 412 N9 0.093 REMARK 500 DC C 413 C5' DC C 413 C4' 0.071 REMARK 500 DG D 422 C2 DG D 422 N3 0.062 REMARK 500 DG D 422 C5 DG D 422 C6 -0.073 REMARK 500 DG D 422 N7 DG D 422 C8 0.049 REMARK 500 DT D 423 C4 DT D 423 C5 0.057 REMARK 500 DT D 423 C5 DT D 423 C6 -0.051 REMARK 500 DT D 423 C6 DT D 423 N1 -0.093 REMARK 500 DT D 423 C2 DT D 423 O2 0.053 REMARK 500 DC D 424 C5 DC D 424 C6 0.066 REMARK 500 DA D 425 C5 DA D 425 C6 -0.130 REMARK 500 DA D 425 N7 DA D 425 C8 0.042 REMARK 500 DA D 425 C8 DA D 425 N9 0.066 REMARK 500 DG D 426 C5' DG D 426 C4' 0.044 REMARK 500 DG D 426 C6 DG D 426 N1 -0.063 REMARK 500 DG D 426 C5 DG D 426 N7 -0.057 REMARK 500 DG D 426 N9 DG D 426 C4 -0.074 REMARK 500 DC D 429 C5 DC D 429 C6 0.052 REMARK 500 DA D 430 C5 DA D 430 C6 -0.081 REMARK 500 DA D 430 C8 DA D 430 N9 0.093 REMARK 500 DA D 430 N9 DA D 430 C4 -0.044 REMARK 500 DT D 431 C4 DT D 431 C5 0.077 REMARK 500 DT D 431 C5 DT D 431 C6 -0.060 REMARK 500 DT D 431 C6 DT D 431 N1 -0.096 REMARK 500 DG D 432 C6 DG D 432 N1 -0.050 REMARK 500 DG D 432 C5 DG D 432 N7 -0.046 REMARK 500 DG D 432 N7 DG D 432 C8 0.064 REMARK 500 DG D 433 C2 DG D 433 N3 0.057 REMARK 500 DG D 433 C5 DG D 433 C6 -0.083 REMARK 500 DG D 433 C5 DG D 433 N7 -0.038 REMARK 500 DG D 433 C2 DG D 433 N2 0.063 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 DC C 402 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC C 402 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC C 402 N3 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC C 402 C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC C 402 N1 - C2 - O2 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC C 402 N3 - C2 - O2 ANGL. DEV. = -9.2 DEGREES REMARK 500 DC C 402 C5 - C4 - N4 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA C 404 N9 - C1' - C2' ANGL. DEV. = -14.3 DEGREES REMARK 500 DA C 404 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DA C 404 C6 - N1 - C2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA C 404 N1 - C2 - N3 ANGL. DEV. = -7.1 DEGREES REMARK 500 DA C 404 C5 - N7 - C8 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA C 404 N7 - C8 - N9 ANGL. DEV. = -7.0 DEGREES REMARK 500 DA C 404 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA C 404 N1 - C6 - N6 ANGL. DEV. = 9.0 DEGREES REMARK 500 DA C 404 C5 - C6 - N6 ANGL. DEV. = -8.8 DEGREES REMARK 500 DT C 405 O3' - P - O5' ANGL. DEV. = -11.6 DEGREES REMARK 500 DT C 405 O3' - P - OP2 ANGL. DEV. = 7.0 DEGREES REMARK 500 DT C 405 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 DT C 405 C6 - N1 - C2 ANGL. DEV. = -18.3 DEGREES REMARK 500 DT C 405 N1 - C2 - N3 ANGL. DEV. = 10.0 DEGREES REMARK 500 DT C 405 C4 - C5 - C6 ANGL. DEV. = -11.6 DEGREES REMARK 500 DT C 405 C5 - C6 - N1 ANGL. DEV. = 22.9 DEGREES REMARK 500 DT C 405 N3 - C2 - O2 ANGL. DEV. = -13.7 DEGREES REMARK 500 DT C 405 N3 - C4 - O4 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT C 405 C5 - C4 - O4 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT C 405 C4 - C5 - C7 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT C 405 C6 - C5 - C7 ANGL. DEV. = 7.0 DEGREES REMARK 500 DT C 405 C6 - N1 - C1' ANGL. DEV. = 14.3 DEGREES REMARK 500 DT C 405 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DG C 406 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG C 406 C6 - N1 - C2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG C 406 C2 - N3 - C4 ANGL. DEV. = 8.7 DEGREES REMARK 500 DG C 406 N3 - C4 - C5 ANGL. DEV. = -9.2 DEGREES REMARK 500 DG C 406 C5 - C6 - N1 ANGL. DEV. = 8.4 DEGREES REMARK 500 DG C 406 C4 - C5 - N7 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG C 406 C5 - N7 - C8 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG C 406 N7 - C8 - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 DG C 406 C8 - N9 - C4 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG C 406 N9 - C4 - C5 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG C 406 N3 - C4 - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 DG C 406 C6 - C5 - N7 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG C 406 C5 - C6 - O6 ANGL. DEV. = -6.9 DEGREES REMARK 500 DG C 408 C6 - N1 - C2 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG C 408 C2 - N3 - C4 ANGL. DEV. = 6.1 DEGREES REMARK 500 DG C 408 N3 - C4 - C5 ANGL. DEV. = -7.8 DEGREES REMARK 500 DG C 408 C5 - C6 - N1 ANGL. DEV. = 7.6 DEGREES REMARK 500 DG C 408 N7 - C8 - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG C 408 C8 - N9 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG C 408 N3 - C4 - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 204 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 ASP A 60 100.41 -12.64 REMARK 500 ASP A 144 40.52 80.02 REMARK 500 LYS A 162 43.63 -75.95 REMARK 500 PHE A 259 48.11 -101.65 REMARK 500 LYS A 261 -28.59 80.02 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 DA C 404 0.15 SIDE CHAIN REMARK 500 DA C 412 0.07 SIDE CHAIN REMARK 500 DA D 425 0.07 SIDE CHAIN REMARK 500 DA D 430 0.13 SIDE CHAIN REMARK 500 DT D 431 0.06 SIDE CHAIN REMARK 500 DG D 432 0.09 SIDE CHAIN REMARK 500 DG D 433 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDI D 427 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 328 DBREF 3EEO A 1 327 UNP P05102 MTH1_HAEPH 1 327 DBREF 3EEO C 402 413 PDB 3EEO 3EEO 402 413 DBREF 3EEO D 422 433 PDB 3EEO 3EEO 422 433 SEQRES 1 C 12 DC DC DA DT DG DC DG DC DT DG DA DC SEQRES 1 D 12 DG DT DC DA DG PDI DG DC DA DT DG DG SEQRES 1 A 327 MET ILE GLU ILE LYS ASP LYS GLN LEU THR GLY LEU ARG SEQRES 2 A 327 PHE ILE ASP LEU PHE ALA GLY LEU GLY GLY PHE ARG LEU SEQRES 3 A 327 ALA LEU GLU SER CYS GLY ALA GLU CYS VAL TYR SER ASN SEQRES 4 A 327 GLU TRP ASP LYS TYR ALA GLN GLU VAL TYR GLU MET ASN SEQRES 5 A 327 PHE GLY GLU LYS PRO GLU GLY ASP ILE THR GLN VAL ASN SEQRES 6 A 327 GLU LYS THR ILE PRO ASP HIS ASP ILE LEU CYS ALA GLY SEQRES 7 A 327 PHE PRO CYS GLN ALA PHE SER ILE SER GLY LYS GLN LYS SEQRES 8 A 327 GLY PHE GLU ASP SER ARG GLY THR LEU PHE PHE ASP ILE SEQRES 9 A 327 ALA ARG ILE VAL ARG GLU LYS LYS PRO LYS VAL VAL PHE SEQRES 10 A 327 MET GLU ASN VAL LYS ASN PHE ALA SER HIS ASP ASN GLY SEQRES 11 A 327 ASN THR LEU GLU VAL VAL LYS ASN THR MET ASN GLU LEU SEQRES 12 A 327 ASP TYR SER PHE HIS ALA LYS VAL LEU ASN ALA LEU ASP SEQRES 13 A 327 TYR GLY ILE PRO GLN LYS ARG GLU ARG ILE TYR MET ILE SEQRES 14 A 327 CYS PHE ARG ASN ASP LEU ASN ILE GLN ASN PHE GLN PHE SEQRES 15 A 327 PRO LYS PRO PHE GLU LEU ASN THR PHE VAL LYS ASP LEU SEQRES 16 A 327 LEU LEU PRO ASP SER GLU VAL GLU HIS LEU VAL ILE ASP SEQRES 17 A 327 ARG LYS ASP LEU VAL MET THR ASN GLN GLU ILE GLU GLN SEQRES 18 A 327 THR THR PRO LYS THR VAL ARG LEU GLY ILE VAL GLY LYS SEQRES 19 A 327 GLY GLY GLN GLY GLU ARG ILE TYR SER THR ARG GLY ILE SEQRES 20 A 327 ALA ILE THR LEU SER ALA TYR GLY GLY GLY ILE PHE ALA SEQRES 21 A 327 LYS THR GLY GLY TYR LEU VAL ASN GLY LYS THR ARG LYS SEQRES 22 A 327 LEU HIS PRO ARG GLU CYS ALA ARG VAL MET GLY TYR PRO SEQRES 23 A 327 ASP SER TYR LYS VAL HIS PRO SER THR SER GLN ALA TYR SEQRES 24 A 327 LYS GLN PHE GLY ASN SER VAL VAL ILE ASN VAL LEU GLN SEQRES 25 A 327 TYR ILE ALA TYR ASN ILE GLY SER SER LEU ASN PHE LYS SEQRES 26 A 327 PRO TYR HET PDI D 427 8 HET SAM A 328 27 HETNAM PDI PHOSPHORIC ACID MONO-(3-HYDROXY-PROPYL) ESTER HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 2 PDI C3 H9 O5 P FORMUL 4 SAM C15 H22 N6 O5 S FORMUL 5 HOH *112(H2 O) HELIX 1 1 GLY A 22 CYS A 31 1 10 HELIX 2 2 ASP A 42 GLY A 54 1 13 HELIX 3 3 ASP A 60 VAL A 64 5 5 HELIX 4 4 ASN A 65 ILE A 69 5 5 HELIX 5 5 LYS A 91 GLY A 98 5 8 HELIX 6 6 THR A 99 LYS A 112 1 14 HELIX 7 7 ASN A 123 ASN A 129 5 7 HELIX 8 8 GLY A 130 LEU A 143 1 14 HELIX 9 9 LEU A 155 TYR A 157 5 3 HELIX 10 10 ASN A 173 ASN A 176 5 4 HELIX 11 11 PHE A 191 LEU A 196 5 6 HELIX 12 12 PRO A 198 HIS A 204 5 7 HELIX 13 13 HIS A 275 MET A 283 1 9 HELIX 14 14 SER A 294 ASN A 304 1 11 HELIX 15 15 VAL A 307 PHE A 324 1 18 SHEET 1 A 6 GLU A 34 ASN A 39 0 SHEET 2 A 6 ARG A 13 LEU A 17 1 N ASP A 16 O TYR A 37 SHEET 3 A 6 ILE A 74 GLY A 78 1 O CYS A 76 N LEU A 17 SHEET 4 A 6 VAL A 115 VAL A 121 1 O PHE A 117 N LEU A 75 SHEET 5 A 6 GLU A 164 PHE A 171 -1 O MET A 168 N MET A 118 SHEET 6 A 6 HIS A 148 ASN A 153 -1 N LYS A 150 O TYR A 167 SHEET 1 B 6 VAL A 206 ILE A 207 0 SHEET 2 B 6 LYS A 270 ARG A 272 -1 O THR A 271 N ILE A 207 SHEET 3 B 6 GLY A 264 VAL A 267 -1 N VAL A 267 O LYS A 270 SHEET 4 B 6 ARG A 240 SER A 243 1 N TYR A 242 O GLY A 264 SHEET 5 B 6 ARG A 228 ILE A 231 -1 N LEU A 229 O ILE A 241 SHEET 6 B 6 VAL A 213 MET A 214 -1 N VAL A 213 O ILE A 231 LINK O3' DG D 426 P PDI D 427 1555 1555 1.63 LINK OG PDI D 427 P DG D 428 1555 1555 1.59 SITE 1 AC1 8 SER A 85 ARG A 165 THR A 250 SER A 252 SITE 2 AC1 8 HOH A 339 HOH D 82 DG D 426 DG D 428 SITE 1 AC2 22 PHE A 18 LEU A 21 GLY A 23 ASN A 39 SITE 2 AC2 22 GLU A 40 TRP A 41 ASP A 42 ASP A 60 SITE 3 AC2 22 ILE A 61 GLY A 78 PRO A 80 LEU A 100 SITE 4 AC2 22 TYR A 285 ASN A 304 SER A 305 VAL A 306 SITE 5 AC2 22 HOH A 343 HOH A 344 HOH A 360 HOH A 386 SITE 6 AC2 22 HOH A 393 HOH A 400 CRYST1 95.479 95.479 318.353 90.00 90.00 120.00 H 3 2 18 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 0.010474 0.006047 0.000000 0.00000 SCALE2 0.000000 0.012094 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003141 0.00000