HEADER ISOMERASE/DNA 10-MAR-10 3M4A TITLE CRYSTAL STRUCTURE OF A BACTERIAL TOPOISOMERASE IB IN COMPLEX WITH DNA TITLE 2 REVEALS A SECONDARY DNA BINDING SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE TYPE I TOPOISOMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*C)-3'); COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(*GP*CP*GP*CP*CP*CP*TP*TP*AP*TP*TP*C)-3'); COMPND 11 CHAIN: E; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 GENE: DR_0690; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS TYPE IB, TOPIB, PROTEIN-DNA COMPLEX, ISOMERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PATEL,L.YAKOVLEVA,S.SHUMAN,A.MONDRAGON REVDAT 2 06-SEP-23 3M4A 1 REMARK LINK REVDAT 1 14-JUL-10 3M4A 0 JRNL AUTH A.PATEL,L.YAKOVLEVA,S.SHUMAN,A.MONDRAGON JRNL TITL CRYSTAL STRUCTURE OF A BACTERIAL TOPOISOMERASE IB IN COMPLEX JRNL TITL 2 WITH DNA REVEALS A SECONDARY DNA BINDING SITE. JRNL REF STRUCTURE V. 18 725 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20541510 JRNL DOI 10.1016/J.STR.2010.03.007 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 53565 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2820 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3633 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 209 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2420 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 281 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.30000 REMARK 3 B22 (A**2) : -0.72000 REMARK 3 B33 (A**2) : 0.43000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.617 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3107 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2046 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4311 ; 1.290 ; 2.168 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4967 ; 0.947 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 325 ; 4.818 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;32.368 ;21.885 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 457 ;12.094 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;11.133 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 483 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3096 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 562 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 529 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2116 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1404 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1462 ; 0.078 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 205 ; 0.141 ; 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): 15 ; 0.188 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 44 ; 0.242 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.233 ; 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): 2037 ; 0.936 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 631 ; 0.154 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2514 ; 1.017 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1958 ; 1.743 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1784 ; 2.479 ; 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 : 1.40 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 REMARK 4 REMARK 4 3M4A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058089. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-06; 01-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; NULL REMARK 200 BEAMLINE : NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 1.00 REMARK 200 MONOCHROMATOR : FRANKS MIRRORS; SI(111) REMARK 200 OPTICS : FRANKS MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE; MAR REMARK 200 CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56385 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 76.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.32500 REMARK 200 R SYM FOR SHELL (I) : 0.27600 REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2F4Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 400 (W/V), 0.1 M SODIUM REMARK 280 ACETATE (PH 4.5), 0.2 M CALCIUM CHLORIDE. 1:1 MOLAR RATIO OF REMARK 280 PROTEIN AND DNA, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K 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 59.83500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.72000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.83500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.72000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 GLU A 10 REMARK 465 GLU A 11 REMARK 465 TYR A 12 REMARK 465 LEU A 13 REMARK 465 GLU A 16 REMARK 465 GLY A 17 REMARK 465 HIS A 18 REMARK 465 ASP A 19 REMARK 465 PRO A 20 REMARK 465 GLN A 21 REMARK 465 LYS A 22 REMARK 465 PHE A 23 REMARK 465 ARG A 24 REMARK 465 TYR A 25 REMARK 465 VAL A 26 REMARK 465 HIS A 27 REMARK 465 PRO A 28 REMARK 465 ASP A 29 REMARK 465 GLY A 30 REMARK 465 THR A 31 REMARK 465 PRO A 32 REMARK 465 TYR A 33 REMARK 465 THR A 34 REMARK 465 ASP A 35 REMARK 465 ALA A 36 REMARK 465 ASP A 37 REMARK 465 GLY A 38 REMARK 465 LEU A 39 REMARK 465 GLY A 73 REMARK 465 GLN A 85 REMARK 465 ALA A 86 REMARK 465 GLY A 87 REMARK 465 GLY A 210 REMARK 465 ARG A 339 REMARK 465 GLN A 340 REMARK 465 ARG A 341 REMARK 465 GLY A 342 REMARK 465 ARG A 343 REMARK 465 ALA A 344 REMARK 465 LEU A 345 REMARK 465 LYS A 346 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 OD1 ASP A 197 O HOH A 545 2555 2.17 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 DA D 7 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 DG D 10 O4' - C1' - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 DC E 111 O4' - C1' - N1 ANGL. DEV. = -6.4 DEGREES REMARK 500 DC E 113 O4' - C1' - N1 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC E 114 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT E 116 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES REMARK 500 DT E 117 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC E 121 O4' - C1' - N1 ANGL. DEV. = 2.4 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 PRO A 58 30.92 -82.46 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 D 808 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 14 O REMARK 620 2 HOH D 15 O 82.1 REMARK 620 3 HOH D 266 O 65.5 146.0 REMARK 620 4 HOH E 122 O 90.0 87.1 102.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 808 DBREF 3M4A A 1 346 UNP Q9RWH8 Q9RWH8_DEIRA 1 346 DBREF 3M4A D 2 13 PDB 3M4A 3M4A 2 13 DBREF 3M4A E 110 121 PDB 3M4A 3M4A 110 121 SEQRES 1 A 346 MET PRO SER ARG THR GLU LEU LEU ALA GLU GLU TYR LEU SEQRES 2 A 346 ARG ARG GLU GLY HIS ASP PRO GLN LYS PHE ARG TYR VAL SEQRES 3 A 346 HIS PRO ASP GLY THR PRO TYR THR ASP ALA ASP GLY LEU SEQRES 4 A 346 ALA ARG ILE ALA ARG LEU ALA VAL PRO PRO ALA TYR GLN SEQRES 5 A 346 ASP VAL TYR VAL SER PRO ASP ALA GLU ASN GLU LEU GLN SEQRES 6 A 346 ALA PHE GLY ARG ASP ALA ALA GLY ARG LEU GLN TYR ARG SEQRES 7 A 346 TYR HIS PRO ASP PHE VAL GLN ALA GLY ALA LEU LYS LYS SEQRES 8 A 346 TRP GLN ARG LEU THR ARG PHE ALA GLY ALA LEU PRO THR SEQRES 9 A 346 LEU LYS VAL ALA THR THR ALA ASP LEU ARG ALA SER GLY SEQRES 10 A 346 LEU PRO PRO ARG LYS VAL MET ALA LEU MET THR ARG LEU SEQRES 11 A 346 LEU HIS VAL ALA ARG PHE ARG VAL GLY SER ASP ILE TYR SEQRES 12 A 346 ALA ARG GLN HIS LYS THR TYR GLY LEU SER THR LEU ARG SEQRES 13 A 346 GLN ARG HIS VAL VAL VAL ASP GLY ASN THR VAL THR PHE SEQRES 14 A 346 ARG PHE LYS GLY LYS HIS GLY VAL SER GLN HIS LYS ALA SEQRES 15 A 346 THR SER ASP ARG THR LEU ALA ALA ASN MET GLN LYS LEU SEQRES 16 A 346 LEU ASP LEU PRO GLY PRO TRP LEU PHE GLN THR VAL ASP SEQRES 17 A 346 ALA GLY GLY GLY GLU ARG ARG ARG ILE HIS SER THR GLU SEQRES 18 A 346 LEU ASN ALA TYR LEU ARG GLU VAL ILE GLY PRO PHE THR SEQRES 19 A 346 ALA LYS ASP PHE ARG THR TRP GLY GLY THR LEU LEU ALA SEQRES 20 A 346 ALA GLU TYR LEU ALA GLN GLN GLY THR GLU SER SER GLU SEQRES 21 A 346 ARG GLN ALA LYS LYS VAL LEU VAL ASP CYS VAL LYS PHE SEQRES 22 A 346 VAL ALA ASP ASP LEU GLY ASN THR PRO ALA VAL THR ARG SEQRES 23 A 346 GLY SER TYR ILE CYS PRO VAL ILE PHE ASP ARG TYR LEU SEQRES 24 A 346 ASP GLY LYS VAL LEU ASP ASP TYR GLU PRO ARG THR GLU SEQRES 25 A 346 ARG GLN GLU ALA GLU LEU GLU GLY LEU THR ARG SER GLU SEQRES 26 A 346 GLY ALA LEU LYS ARG MET LEU GLU SER GLU ARG THR LEU SEQRES 27 A 346 ARG GLN ARG GLY ARG ALA LEU LYS SEQRES 1 D 12 DG DA DA DT DA DA DG DG DG DC DG DC SEQRES 1 E 12 DG DC DG DC DC DC DT DT DA DT DT DC HET ACY A 804 4 HET ACY A 805 4 HET MG D 808 1 HETNAM ACY ACETIC ACID HETNAM MG MAGNESIUM ION FORMUL 4 ACY 2(C2 H4 O2) FORMUL 6 MG MG 2+ FORMUL 7 HOH *281(H2 O) HELIX 1 1 SER A 3 ALA A 9 1 7 HELIX 2 2 ALA A 40 ALA A 46 1 7 HELIX 3 3 PRO A 81 VAL A 84 5 4 HELIX 4 4 LYS A 90 ARG A 114 1 25 HELIX 5 5 PRO A 119 ARG A 135 1 17 HELIX 6 6 SER A 140 LYS A 148 1 9 HELIX 7 7 GLY A 151 LEU A 155 5 5 HELIX 8 8 ARG A 156 ARG A 158 5 3 HELIX 9 9 LYS A 174 GLY A 176 5 3 HELIX 10 10 ASP A 185 ASP A 197 1 13 HELIX 11 11 HIS A 218 GLY A 231 1 14 HELIX 12 12 THR A 234 GLY A 255 1 22 HELIX 13 13 SER A 259 GLY A 279 1 21 HELIX 14 14 THR A 281 TYR A 289 1 9 HELIX 15 15 CYS A 291 ASP A 300 1 10 HELIX 16 16 VAL A 303 GLU A 308 5 6 HELIX 17 17 THR A 311 GLU A 317 1 7 HELIX 18 18 THR A 322 LEU A 338 1 17 SHEET 1 A 3 GLN A 52 VAL A 56 0 SHEET 2 A 3 LEU A 64 ARG A 69 -1 O ARG A 69 N GLN A 52 SHEET 3 A 3 LEU A 75 TYR A 79 -1 O ARG A 78 N ALA A 66 SHEET 1 B 3 VAL A 160 ASP A 163 0 SHEET 2 B 3 THR A 166 LYS A 172 -1 O THR A 166 N ASP A 163 SHEET 3 B 3 SER A 178 THR A 183 -1 O GLN A 179 N PHE A 171 SHEET 1 C 2 GLN A 205 VAL A 207 0 SHEET 2 C 2 ARG A 214 ARG A 216 -1 O ARG A 215 N THR A 206 LINK O HOH D 14 MG MG D 808 1555 1555 2.19 LINK O HOH D 15 MG MG D 808 1555 1555 2.19 LINK O HOH D 266 MG MG D 808 1555 1555 2.43 LINK MG MG D 808 O HOH E 122 1555 1555 2.17 CISPEP 1 GLY A 200 PRO A 201 0 4.06 CISPEP 2 GLY A 231 PRO A 232 0 9.32 SITE 1 AC1 7 LEU A 105 LYS A 106 THR A 109 ARG A 129 SITE 2 AC1 7 HIS A 132 HOH A 356 HOH A 535 SITE 1 AC2 5 HIS A 132 ASP A 163 GLU A 325 HOH A 362 SITE 2 AC2 5 HOH A 539 SITE 1 AC3 4 HOH D 14 HOH D 15 HOH D 266 HOH E 122 CRYST1 119.670 53.440 77.360 90.00 96.33 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 0.008356 0.000000 0.000928 0.00000 SCALE2 0.000000 0.018713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013006 0.00000