HEADER DNA BINDING PROTEIN/DNA 03-APR-09 3GYH TITLE CRYSTAL STRUCTURE ANALYSIS OF S. POMBE ATL IN COMPLEX WITH DAMAGED DNA TITLE 2 CONTAINING POB 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*GP*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 DNA DAMAGE, DNA REPAIR, DNA-BINDING, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.L.TUBBS,A.S.ARVAI,J.A.TAINER,D.S.SHIN REVDAT 4 21-FEB-24 3GYH 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3GYH 1 VERSN REVDAT 2 28-JUL-09 3GYH 1 JRNL REVDAT 1 16-JUN-09 3GYH 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. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 6078 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 341 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 225 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.4450 REMARK 3 BIN FREE R VALUE SET COUNT : 6 REMARK 3 BIN FREE R VALUE : 0.6380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 890 REMARK 3 NUCLEIC ACID ATOMS : 527 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 2 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) : 84.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.59000 REMARK 3 B22 (A**2) : 5.59000 REMARK 3 B33 (A**2) : -8.38000 REMARK 3 B12 (A**2) : 2.79000 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): 6.232 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.414 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.352 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 42.393 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1515 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2146 ; 1.308 ; 2.398 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 107 ; 9.552 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 46 ;39.370 ;23.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 163 ;24.108 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;22.091 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 225 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 987 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 537 ; 1.000 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 869 ; 1.951 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 978 ; 2.840 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1277 ; 4.494 ; 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 : 3 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 : X 1 X 108 REMARK 3 ORIGIN FOR THE GROUP (A): 28.7896 -21.3040 1.8135 REMARK 3 T TENSOR REMARK 3 T11: 0.1113 T22: 0.2578 REMARK 3 T33: 0.2130 T12: 0.0865 REMARK 3 T13: 0.0618 T23: 0.0360 REMARK 3 L TENSOR REMARK 3 L11: 2.0731 L22: 1.4976 REMARK 3 L33: 4.4228 L12: -1.0662 REMARK 3 L13: 0.3162 L23: -0.7987 REMARK 3 S TENSOR REMARK 3 S11: -0.0770 S12: 0.2720 S13: 0.0127 REMARK 3 S21: 0.0728 S22: 0.0276 S23: -0.0510 REMARK 3 S31: -0.4299 S32: -0.1499 S33: 0.0493 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 : Y 201 Y 213 REMARK 3 ORIGIN FOR THE GROUP (A): 29.7547 -38.3685 6.7585 REMARK 3 T TENSOR REMARK 3 T11: 0.2658 T22: 0.2788 REMARK 3 T33: 0.2015 T12: -0.0357 REMARK 3 T13: 0.1401 T23: -0.0390 REMARK 3 L TENSOR REMARK 3 L11: 1.3533 L22: 3.5641 REMARK 3 L33: 6.1664 L12: 0.7280 REMARK 3 L13: 1.1953 L23: 1.5781 REMARK 3 S TENSOR REMARK 3 S11: -0.3327 S12: 0.0133 S13: 0.0125 REMARK 3 S21: -0.1573 S22: 0.2228 S23: -0.0374 REMARK 3 S31: 0.4091 S32: -0.2994 S33: 0.1099 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 : Z 214 Z 226 REMARK 3 ORIGIN FOR THE GROUP (A): 29.8901 -38.9211 6.0434 REMARK 3 T TENSOR REMARK 3 T11: 0.1132 T22: 0.1479 REMARK 3 T33: 0.1272 T12: 0.0223 REMARK 3 T13: 0.0379 T23: 0.0278 REMARK 3 L TENSOR REMARK 3 L11: 1.3445 L22: 1.5510 REMARK 3 L33: 10.1397 L12: 0.1743 REMARK 3 L13: -1.9671 L23: 0.4917 REMARK 3 S TENSOR REMARK 3 S11: 0.0126 S12: 0.2219 S13: 0.2456 REMARK 3 S21: 0.0988 S22: -0.0488 S23: -0.1716 REMARK 3 S31: 0.6378 S32: -0.6942 S33: 0.0362 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES: RESIDUAL ONLY REMARK 4 REMARK 4 3GYH 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_1000052464. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : NULL 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 : 6078 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 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 (%): 56.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 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 78.51533 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 157.03067 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 117.77300 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 196.28833 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 39.25767 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 78.51533 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 157.03067 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 196.28833 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 117.77300 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 39.25767 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: 3530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 NH2 ARG X 39 N3 DC Z 221 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG X 2 OD2 ASP X 12 12545 2.11 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 DG Y 207 C6 DG Y 207 N1 -0.045 REMARK 500 DG Y 207 C5 DG Y 207 N7 -0.038 REMARK 500 DG Y 207 N7 DG Y 207 C8 0.055 REMARK 500 DG Y 207 C6 DG Y 207 O6 0.135 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 DT Y 205 O4' - C1' - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG Y 206 C3' - O3' - P ANGL. DEV. = -8.3 DEGREES REMARK 500 DG Y 207 O3' - P - OP2 ANGL. DEV. = 28.6 DEGREES REMARK 500 DG Y 207 O3' - P - OP1 ANGL. DEV. = -27.4 DEGREES REMARK 500 DG Y 207 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG Y 207 C6 - N1 - C2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG Y 207 C2 - N3 - C4 ANGL. DEV. = 7.8 DEGREES REMARK 500 DG Y 207 N3 - C4 - C5 ANGL. DEV. = -9.2 DEGREES REMARK 500 DG Y 207 C5 - C6 - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 DG Y 207 C4 - C5 - N7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG Y 207 C5 - N7 - C8 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG Y 207 N7 - C8 - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG Y 207 N9 - C4 - C5 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG Y 207 N3 - C4 - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG Y 207 C5 - C6 - O6 ANGL. DEV. = -8.2 DEGREES REMARK 500 DG Y 207 C3' - O3' - P ANGL. DEV. = -12.8 DEGREES REMARK 500 DC Y 208 O3' - P - OP2 ANGL. DEV. = 16.1 DEGREES REMARK 500 DC Y 208 O3' - P - OP1 ANGL. DEV. = -15.9 DEGREES REMARK 500 DG Y 211 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC Z 214 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT Z 218 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT Z 224 N3 - C4 - O4 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG Z 225 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG Z 226 O4' - C4' - C3' ANGL. DEV. = -2.8 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 TYR X 25 -64.48 -29.69 REMARK 500 HIS X 47 36.11 -98.31 REMARK 500 HIS X 53 47.22 -104.84 REMARK 500 ILE X 60 -163.58 -103.02 REMARK 500 ILE X 71 46.72 -96.23 REMARK 500 SER X 72 163.35 40.39 REMARK 500 THR X 92 -144.18 -104.27 REMARK 500 LEU X 94 52.47 -140.22 REMARK 500 GLU X 96 76.52 -7.11 REMARK 500 TYR X 97 129.23 -38.59 REMARK 500 GLU X 103 -82.14 -54.45 REMARK 500 LYS X 107 85.65 -156.40 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 SER X 93 LEU X 94 123.74 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 PBO Y 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GVA RELATED DB: PDB REMARK 900 SAME PROTEIN WITHOUT DNA REMARK 900 RELATED ID: 3GX4 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH DNA DBREF 3GYH X 1 108 UNP Q9UTN9 ATL1_SCHPO 1 108 DBREF 3GYH Y 201 213 PDB 3GYH 3GYH 201 213 DBREF 3GYH Z 214 226 PDB 3GYH 3GYH 214 226 SEQADV 3GYH GLY X 109 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GYH SER X 110 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GYH HIS X 111 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GYH HIS X 112 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GYH HIS X 113 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GYH HIS X 114 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GYH HIS X 115 UNP Q9UTN9 EXPRESSION TAG SEQADV 3GYH 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 DG DC DT DA DG DT DA SEQRES 1 Z 13 DC DT DA DC DT DA DG DC DC DA DT DG DG HET PBO Y 200 11 HETNAM PBO 1-PYRIDIN-3-YLBUTAN-1-ONE FORMUL 4 PBO C9 H11 N O FORMUL 5 HOH *2(H2 O) HELIX 1 1 ARG X 2 CYS X 15 1 14 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 SER X 72 GLY X 74 5 3 HELIX 6 6 GLU X 75 GLY X 86 1 12 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 C10 PBO Y 200 O6 DG Y 207 1555 1555 1.43 SITE 1 AC1 8 MET X 45 LEU X 48 PRO X 50 TRP X 56 SITE 2 AC1 8 ARG X 77 ARG X 81 DG Y 207 DG Y 211 CRYST1 60.180 60.180 235.546 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 0.016617 0.009594 0.000000 0.00000 SCALE2 0.000000 0.019187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004245 0.00000