HEADER DNA BINDING PROTEIN/DNA 01-APR-09 3GX4 TITLE CRYSTAL STRUCTURE ANALYSIS OF S. POMBE ATL IN COMPLEX WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKYLTRANSFERASE-LIKE PROTEIN 1; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3'); COMPND 7 CHAIN: Y; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3'); COMPND 11 CHAIN: Z; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 GENE: ATL1, SPAC1250.04C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES KEYWDS ALKYLATED DNA DAMAGE REPAIR METHYLGUANINE, DNA DAMAGE, DNA REPAIR, KEYWDS 2 DNA-BINDING, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.L.TUBBS,A.S.ARVAI,J.A.TAINER REVDAT 4 21-FEB-24 3GX4 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3GX4 1 VERSN REVDAT 2 28-JUL-09 3GX4 1 JRNL REVDAT 1 09-JUN-09 3GX4 0 JRNL AUTH J.L.TUBBS,V.LATYPOV,S.KANUGULA,A.BUTT,M.MELIKISHVILI, JRNL AUTH 2 R.KRAEHENBUEHL,O.FLECK,A.MARRIOTT,A.J.WATSON,B.VERBEEK, JRNL AUTH 3 G.MCGOWN,M.THORNCROFT,M.F.SANTIBANEZ-KOREF,C.MILLINGTON, JRNL AUTH 4 A.S.ARVAI,M.D.KROEGER,L.A.PETERSON,D.M.WILLIAMS,M.G.FRIED, JRNL AUTH 5 G.P.MARGISON,A.E.PEGG,J.A.TAINER JRNL TITL FLIPPING OF ALKYLATED DNA DAMAGE BRIDGES BASE AND NUCLEOTIDE JRNL TITL 2 EXCISION REPAIR. JRNL REF NATURE V. 459 808 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 19516334 JRNL DOI 10.1038/NATURE08076 REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 6342 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) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 373 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) : 286 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.3840 REMARK 3 BIN FREE R VALUE SET COUNT : 21 REMARK 3 BIN FREE R VALUE : 0.4520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 890 REMARK 3 NUCLEIC ACID ATOMS : 528 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.44000 REMARK 3 B22 (A**2) : 2.44000 REMARK 3 B33 (A**2) : -3.66000 REMARK 3 B12 (A**2) : 1.22000 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): 1.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.400 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.348 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.836 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.882 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1515 ; 0.042 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2164 ; 4.544 ; 2.404 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 107 ;11.007 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 46 ;42.677 ;23.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 163 ;24.865 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;26.183 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 225 ; 0.203 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 980 ; 0.018 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 846 ; 0.359 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 992 ; 0.390 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 97 ; 0.234 ; 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): 49 ; 0.380 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.202 ; 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): 558 ; 1.811 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 871 ; 2.942 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1291 ; 4.409 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1287 ; 5.973 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 5 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 1 X 108 REMARK 3 RESIDUE RANGE : Y 201 Y 213 REMARK 3 RESIDUE RANGE : Z 214 Z 226 REMARK 3 RESIDUE RANGE : X 403 X 425 REMARK 3 RESIDUE RANGE : Y 302 Y 302 REMARK 3 ORIGIN FOR THE GROUP (A): 29.0633 -27.9930 3.7723 REMARK 3 T TENSOR REMARK 3 T11: 0.0593 T22: 0.2120 REMARK 3 T33: 0.0590 T12: -0.0016 REMARK 3 T13: 0.0463 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.7165 L22: 1.2365 REMARK 3 L33: 2.0735 L12: -0.2181 REMARK 3 L13: 0.4100 L23: -0.0609 REMARK 3 S TENSOR REMARK 3 S11: -0.0611 S12: -0.0173 S13: -0.0012 REMARK 3 S21: -0.0088 S22: 0.0473 S23: 0.0033 REMARK 3 S31: 0.1335 S32: -0.1118 S33: 0.0138 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 3GX4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6342 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 79.34267 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 158.68533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 119.01400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 198.35667 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 39.67133 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.34267 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 158.68533 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 198.35667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 119.01400 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 39.67133 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: 4140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Y, Z 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 X 404 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY X 109 REMARK 465 SER X 110 REMARK 465 HIS X 111 REMARK 465 HIS X 112 REMARK 465 HIS X 113 REMARK 465 HIS X 114 REMARK 465 HIS X 115 REMARK 465 HIS X 116 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 ASP X 70 N SER X 72 2.11 REMARK 500 O LYS X 68 N ASP X 70 2.16 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 ARG X 2 CG ARG X 2 CD 0.164 REMARK 500 TYR X 7 CZ TYR X 7 CE2 0.089 REMARK 500 TYR X 11 CE2 TYR X 11 CD2 0.101 REMARK 500 VAL X 22 CB VAL X 22 CG2 0.149 REMARK 500 GLU X 27 CD GLU X 27 OE1 0.075 REMARK 500 ARG X 39 CB ARG X 39 CG -0.167 REMARK 500 ARG X 39 CZ ARG X 39 NH1 0.084 REMARK 500 GLN X 40 C GLN X 40 O 0.142 REMARK 500 TRP X 56 CB TRP X 56 CG -0.129 REMARK 500 GLU X 75 N GLU X 75 CA 0.151 REMARK 500 GLU X 75 CG GLU X 75 CD 0.091 REMARK 500 GLU X 75 CD GLU X 75 OE1 0.068 REMARK 500 GLU X 84 CG GLU X 84 CD 0.124 REMARK 500 GLU X 84 CD GLU X 84 OE1 0.094 REMARK 500 GLU X 84 CD GLU X 84 OE2 0.075 REMARK 500 TYR X 90 CG TYR X 90 CD1 0.084 REMARK 500 TYR X 90 CE1 TYR X 90 CZ 0.117 REMARK 500 TYR X 90 CZ TYR X 90 CE2 0.125 REMARK 500 LYS X 98 CB LYS X 98 CG -0.212 REMARK 500 GLU X 103 CG GLU X 103 CD 0.100 REMARK 500 MET X 105 CA MET X 105 CB -0.133 REMARK 500 DG Y 201 O3' DG Y 201 C3' -0.055 REMARK 500 DG Y 201 C5 DG Y 201 N7 -0.037 REMARK 500 DG Y 201 C8 DG Y 201 N9 -0.048 REMARK 500 DC Y 202 O3' DC Y 202 C3' -0.054 REMARK 500 DC Y 203 O3' DC Y 203 C3' -0.038 REMARK 500 DA Y 204 N3 DA Y 204 C4 -0.037 REMARK 500 DA Y 204 C6 DA Y 204 N1 -0.045 REMARK 500 DT Y 205 O3' DT Y 205 C3' -0.065 REMARK 500 DT Y 205 C4 DT Y 205 C5 -0.056 REMARK 500 DG Y 206 O3' DG Y 206 C3' -0.073 REMARK 500 DG Y 206 C5 DG Y 206 N7 -0.041 REMARK 500 6OG Y 207 O3' DC Y 208 P -0.162 REMARK 500 DC Y 208 P DC Y 208 O5' -0.071 REMARK 500 DC Y 208 C2 DC Y 208 O2 -0.059 REMARK 500 DC Y 208 N1 DC Y 208 C6 -0.041 REMARK 500 DC Y 208 C2 DC Y 208 N3 -0.054 REMARK 500 DC Y 208 N3 DC Y 208 C4 -0.049 REMARK 500 DT Y 209 P DT Y 209 O5' -0.075 REMARK 500 DT Y 209 N1 DT Y 209 C2 -0.052 REMARK 500 DT Y 209 C6 DT Y 209 N1 -0.042 REMARK 500 DT Y 209 C2 DT Y 209 O2 -0.048 REMARK 500 DA Y 210 P DA Y 210 O5' -0.088 REMARK 500 DA Y 210 O3' DA Y 210 C3' -0.058 REMARK 500 DA Y 210 N3 DA Y 210 C4 -0.038 REMARK 500 DA Y 210 C4 DA Y 210 C5 -0.043 REMARK 500 DG Y 211 O3' DG Y 211 C3' -0.055 REMARK 500 DG Y 211 N9 DG Y 211 C4 -0.049 REMARK 500 DT Y 212 C4 DT Y 212 C5 -0.057 REMARK 500 DA Y 213 O3' DA Y 213 C3' -0.060 REMARK 500 REMARK 500 THIS ENTRY HAS 91 BOND DEVIATIONS. 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 ARG X 2 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG X 2 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASP X 4 CB - CG - OD1 ANGL. DEV. = 8.5 DEGREES REMARK 500 ASP X 4 CB - CG - OD2 ANGL. DEV. = -9.1 DEGREES REMARK 500 CYS X 15 CA - CB - SG ANGL. DEV. = -15.3 DEGREES REMARK 500 ARG X 39 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 HIS X 47 CB - CA - C ANGL. DEV. = -12.7 DEGREES REMARK 500 PRO X 50 C - N - CA ANGL. DEV. = -15.5 DEGREES REMARK 500 PRO X 50 C - N - CD ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG X 58 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG X 63 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG X 69 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 GLY X 74 N - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 GLU X 75 CB - CA - C ANGL. DEV. = -14.8 DEGREES REMARK 500 MET X 105 CA - CB - CG ANGL. DEV. = -10.6 DEGREES REMARK 500 DC Y 202 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DC Y 203 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA Y 204 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DA Y 204 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DT Y 205 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DT Y 205 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DT Y 205 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT Y 205 N3 - C4 - O4 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT Y 205 C5 - C4 - O4 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG Y 206 O4' - C4' - C3' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG Y 206 C4' - C3' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 DG Y 206 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 6OG Y 207 O3' - P - OP2 ANGL. DEV. = 8.1 DEGREES REMARK 500 6OG Y 207 C3' - O3' - P ANGL. DEV. = -21.9 DEGREES REMARK 500 DC Y 208 O3' - P - OP2 ANGL. DEV. = 24.0 DEGREES REMARK 500 DC Y 208 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 DC Y 208 O4' - C1' - C2' ANGL. DEV. = -6.4 DEGREES REMARK 500 DT Y 209 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 DA Y 210 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA Y 210 O4' - C1' - N9 ANGL. DEV. = 8.6 DEGREES REMARK 500 DG Y 211 O4' - C4' - C3' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG Y 211 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG Y 211 C4 - C5 - N7 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT Y 212 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DT Y 212 O4' - C1' - N1 ANGL. DEV. = -7.2 DEGREES REMARK 500 DA Y 213 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA Y 213 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC Z 214 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES REMARK 500 DC Z 214 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT Z 215 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT Z 215 N3 - C4 - O4 ANGL. DEV. = 6.0 DEGREES REMARK 500 DT Z 215 C5 - C4 - O4 ANGL. DEV. = -8.3 DEGREES REMARK 500 DT Z 215 C4 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA Z 216 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DA Z 216 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 68 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 TYR X 19 134.07 -33.68 REMARK 500 MET X 34 62.84 -119.04 REMARK 500 TYR X 37 38.67 -92.39 REMARK 500 HIS X 47 38.31 -81.43 REMARK 500 PRO X 50 31.07 -70.15 REMARK 500 PRO X 55 49.10 -70.48 REMARK 500 ARG X 69 20.77 46.17 REMARK 500 ASP X 70 -115.42 14.01 REMARK 500 ILE X 71 91.25 -6.23 REMARK 500 SER X 72 161.84 61.26 REMARK 500 GLU X 75 -2.28 -34.52 REMARK 500 TYR X 90 -161.74 -125.62 REMARK 500 SER X 93 119.24 -37.20 REMARK 500 LEU X 94 82.89 73.99 REMARK 500 GLU X 96 94.88 -3.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY X 74 GLU X 75 147.42 REMARK 500 GLU X 75 GLN X 76 145.83 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 NCO Y 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO Z 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GVA RELATED DB: PDB REMARK 900 SAME PROTEIN WITHOUT DNA REMARK 900 RELATED ID: 3GYH RELATED DB: PDB REMARK 900 SAME PROTEIN WITH DNA DBREF 3GX4 X 1 108 UNP Q9UTN9 ATL1_SCHPO 1 108 DBREF 3GX4 Y 201 213 PDB 3GX4 3GX4 201 213 DBREF 3GX4 Z 214 226 PDB 3GX4 3GX4 214 226 SEQADV 3GX4 GLY X 109 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GX4 SER X 110 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GX4 HIS X 111 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GX4 HIS X 112 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GX4 HIS X 113 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GX4 HIS X 114 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GX4 HIS X 115 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GX4 HIS X 116 UNP Q9UTN9 EXPRESSION TAG SEQRES 1 X 116 MET ARG MET ASP GLU PHE TYR THR LYS VAL TYR ASP ALA SEQRES 2 X 116 VAL CYS GLU ILE PRO TYR GLY LYS VAL SER THR TYR GLY SEQRES 3 X 116 GLU ILE ALA ARG TYR VAL GLY MET PRO SER TYR ALA ARG SEQRES 4 X 116 GLN VAL GLY GLN ALA MET LYS HIS LEU HIS PRO GLU THR SEQRES 5 X 116 HIS VAL PRO TRP HIS ARG VAL ILE ASN SER ARG GLY THR SEQRES 6 X 116 ILE SER LYS ARG ASP ILE SER ALA GLY GLU GLN ARG GLN SEQRES 7 X 116 LYS ASP ARG LEU GLU GLU GLU GLY VAL GLU ILE TYR GLN SEQRES 8 X 116 THR SER LEU GLY GLU TYR LYS LEU ASN LEU PRO GLU TYR SEQRES 9 X 116 MET TRP LYS PRO GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 Y 13 DG DC DC DA DT DG 6OG DC DT DA DG DT DA SEQRES 1 Z 13 DC DT DA DC DT DA DG DC DC DA DT DG DG MODRES 3GX4 6OG Y 207 DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HET 6OG Y 207 23 HET NCO Y 302 7 HET NCO Z 303 7 HETNAM 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HETNAM NCO COBALT HEXAMMINE(III) FORMUL 2 6OG C11 H16 N5 O7 P FORMUL 4 NCO 2(CO H18 N6 3+) FORMUL 6 HOH *23(H2 O) HELIX 1 1 ARG X 2 GLU X 16 1 15 HELIX 2 2 TYR X 25 VAL X 32 1 8 HELIX 3 3 TYR X 37 HIS X 47 1 11 HELIX 4 4 PRO X 55 HIS X 57 5 3 HELIX 5 5 GLU X 75 GLU X 83 1 9 HELIX 6 6 GLU X 84 GLY X 86 5 3 HELIX 7 7 ASN X 100 MET X 105 1 6 SHEET 1 A 2 SER X 23 THR X 24 0 SHEET 2 A 2 VAL X 59 ILE X 60 1 O ILE X 60 N SER X 23 LINK O3' DG Y 206 P 6OG Y 207 1555 1555 1.55 LINK O3' 6OG Y 207 P DC Y 208 1555 1555 1.45 SITE 1 AC1 5 ARG X 39 GLN X 43 DG Y 206 6OG Y 207 SITE 2 AC1 5 DC Y 208 SITE 1 AC2 6 GLU X 51 DG Y 201 DC Y 202 DC Z 214 SITE 2 AC2 6 DG Z 225 DG Z 226 CRYST1 59.728 59.728 238.028 90.00 90.00 120.00 P 61 2 2 12 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 0.016743 0.009666 0.000000 0.00000 SCALE2 0.000000 0.019333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004201 0.00000