HEADER HYDROLASE/DNA 17-OCT-08 3EY1 TITLE A CONFORMATIONAL TRANSITION IN THE STRUCTURE OF A 2'-THIOMETHYL- TITLE 2 MODIFIED DNA VISUALIZED AT HIGH RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNASE H DOMAIN, UNP RESIDUES 59-196; COMPND 5 SYNONYM: RNASE H; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: 2'-THIOMETHYL URIDINE (USM) MODIFIED DECAMER NUCLEIC COMPND 14 ACID 5'-DC DG DC DG DA DA USM USM DC DG DC DG-3' SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 86665; SOURCE 4 GENE: RNHA, BH0863; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: CHEMICALLY SYNTHESIZED MODIFIED DODECAMER DNA SOURCE 8 (OLIGONUCLEOTIDE) KEYWDS RNASE H-DNA COMPLEX, PROTEIN-DNA COMPLEX, ENDONUCLEASE, 2'-THIOMETHYL KEYWDS 2 URIDINE RIBONUCLEIC ACID, HYDROLASE, MAGNESIUM, MANGANESE, METAL- KEYWDS 3 BINDING, NUCLEASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.EGLI,P.S.PALLAN REVDAT 7 06-SEP-23 3EY1 1 REMARK REVDAT 6 20-OCT-21 3EY1 1 REMARK SEQADV LINK REVDAT 5 25-OCT-17 3EY1 1 REMARK REVDAT 4 13-JUL-11 3EY1 1 VERSN REVDAT 3 26-MAY-09 3EY1 1 REMARK REVDAT 2 05-MAY-09 3EY1 1 JRNL REVDAT 1 28-APR-09 3EY1 0 JRNL AUTH P.S.PALLAN,T.P.PRAKASH,F.LI,R.L.EOFF,M.MANOHARAN,M.EGLI JRNL TITL A CONFORMATIONAL TRANSITION IN THE STRUCTURE OF A JRNL TITL 2 2'-THIOMETHYL-MODIFIED DNA VISUALIZED AT HIGH RESOLUTION. JRNL REF CHEM.COMMUN.(CAMB.) V. 15 2017 2009 JRNL REFN ISSN 1359-7345 JRNL PMID 19333476 JRNL DOI 10.1039/B822781K REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.193 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2634 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 26449 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1114 REMARK 3 NUCLEIC ACID ATOMS : 245 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 103 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.026 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3EY1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26499 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 363.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3D0P, USING THE PROTEIN MOLECULE ALONE. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE (PH 4.6), 0.2 M REMARK 280 AMMONIUM SULPHATE, 25% PEG 4000., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 40.96500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.31000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.96500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.31000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 LYS A 196 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 GLN A 75 C - N - CA ANGL. DEV. = 16.9 DEGREES REMARK 500 ARG A 97 NE - CZ - NH1 ANGL. DEV. = -6.0 DEGREES REMARK 500 GLU A 154 OE1 - CD - OE2 ANGL. DEV. = -8.1 DEGREES REMARK 500 GLY A 194 C - N - CA ANGL. DEV. = 13.1 DEGREES REMARK 500 DC B 301 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC B 303 O4' - C1' - N1 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG B 304 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 304 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DA B 305 O4' - C1' - N9 ANGL. DEV. = -6.1 DEGREES REMARK 500 DG B 312 O4' - C1' - N9 ANGL. DEV. = 2.0 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 LYS A 60 60.18 -69.69 REMARK 500 GLU A 62 -78.23 -36.02 REMARK 500 SER A 74 -111.62 -125.51 REMARK 500 GLN A 75 -108.62 102.79 REMARK 500 ASN A 124 -2.18 74.50 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 GOL B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EY2 RELATED DB: PDB REMARK 900 RELATED ID: 3EY3 RELATED DB: PDB DBREF 3EY1 A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 3EY1 B 301 312 PDB 3EY1 3EY1 301 312 SEQADV 3EY1 ASN A 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQRES 1 A 138 ALA LYS GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP SEQRES 2 A 138 VAL GLY SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS SEQRES 3 A 138 GLY VAL ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG SEQRES 4 A 138 GLU PRO ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE SEQRES 5 A 138 LEU ALA ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG SEQRES 6 A 138 ASN SER ARG LYS PRO ILE TYR SER ASN SER GLN THR ALA SEQRES 7 A 138 ILE LYS TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU SEQRES 8 A 138 VAL ARG ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL SEQRES 9 A 138 ASP GLU ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU SEQRES 10 A 138 THR PRO ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU SEQRES 11 A 138 ILE LYS ALA ASP TYR GLY ARG LYS SEQRES 1 B 12 DC DG DC DG DA DA USM USM DC DG DC DG MODRES 3EY1 USM B 307 DU MODRES 3EY1 USM B 308 DU HET USM B 307 21 HET USM B 308 21 HET GOL B 601 6 HET GOL B 602 6 HET GOL B 603 6 HETNAM USM 2'-S-METHYL-2'-THIOURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 USM 2(C10 H15 N2 O8 P S) FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 HOH *103(H2 O) HELIX 1 1 THR A 104 ARG A 123 1 20 HELIX 2 2 SER A 133 LYS A 143 1 11 HELIX 3 3 THR A 155 ASN A 170 1 16 HELIX 4 4 GLN A 182 GLY A 187 1 6 SHEET 1 A 5 VAL A 93 GLY A 103 0 SHEET 2 A 5 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 A 5 LEU A 68 GLY A 73 -1 N GLY A 73 O GLU A 82 SHEET 4 A 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 A 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 LINK O3' DA B 306 P USM B 307 1555 1555 1.59 LINK O3' USM B 307 P USM B 308 1555 1555 1.60 LINK O3' USM B 308 P DC B 309 1555 1555 1.57 CISPEP 1 ASN A 77 PRO A 78 0 4.01 CISPEP 2 TYR A 193 GLY A 194 0 8.83 SITE 1 AC1 4 GLY A 76 ASN A 77 DC B 301 DG B 302 SITE 1 AC2 2 USM B 307 USM B 308 SITE 1 AC3 3 LYS A 138 DA B 305 DA B 306 CRYST1 81.930 66.620 38.770 90.00 103.30 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 0.012206 0.000000 0.002885 0.00000 SCALE2 0.000000 0.015011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026504 0.00000