HEADER HYDROLASE/DNA 07-JUN-10 3NDH TITLE RESTRICTION ENDONUCLEASE IN COMPLEX WITH SUBSTRATE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESTRICTION ENDONUCLEASE THAI; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PUTATIVE UNCHARACTERIZED PROTEIN TA0828; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*G*GP*TP*AP*CP*GP*CP*GP*AP*TP*G)-3'); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*C*CP*AP*TP*CP*GP*CP*GP*TP*AP*C)-3'); COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOPLASMA ACIDOPHILUM; SOURCE 3 ORGANISM_TAXID: 2303; SOURCE 4 STRAIN: ATCC25905; SOURCE 5 GENE: TA0828; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15BMOD; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, THAI, INTERCALATION, KEYWDS 2 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.FIRCZUK,M.WOJCIECHOWSKI,H.CZAPINSKA,M.BOCHTLER REVDAT 4 20-MAR-24 3NDH 1 REMARK SEQADV REVDAT 3 08-NOV-17 3NDH 1 REMARK REVDAT 2 09-FEB-11 3NDH 1 JRNL REVDAT 1 28-JUL-10 3NDH 0 JRNL AUTH M.FIRCZUK,M.WOJCIECHOWSKI,H.CZAPINSKA,M.BOCHTLER JRNL TITL DNA INTERCALATION WITHOUT FLIPPING IN THE SPECIFIC THAI-DNA JRNL TITL 2 COMPLEX JRNL REF NUCLEIC ACIDS RES. V. 39 744 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 20861000 JRNL DOI 10.1093/NAR/GKQ834 REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 118512 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5962 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8312 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 464 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3478 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.49000 REMARK 3 B22 (A**2) : 1.79000 REMARK 3 B33 (A**2) : -0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.61000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5254 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3516 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7313 ; 1.261 ; 2.168 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8634 ; 3.806 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 551 ; 5.897 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;33.427 ;23.816 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 847 ;15.020 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;18.648 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 760 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5401 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 979 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 909 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3121 ; 0.245 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2318 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2130 ; 0.104 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 395 ; 0.118 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.126 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 15 ; 0.267 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 51 ; 0.211 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.155 ; 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): 2559 ; 0.627 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 996 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4234 ; 1.131 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2695 ; 1.560 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3079 ; 2.302 ; 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 9 A 99 REMARK 3 RESIDUE RANGE : A 124 A 144 REMARK 3 RESIDUE RANGE : A 188 A 201 REMARK 3 RESIDUE RANGE : B 202 B 216 REMARK 3 ORIGIN FOR THE GROUP (A): 4.7650 -0.6720 20.5750 REMARK 3 T TENSOR REMARK 3 T11: 0.0027 T22: -0.0504 REMARK 3 T33: -0.0077 T12: 0.0023 REMARK 3 T13: 0.0170 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.6607 L22: 0.4450 REMARK 3 L33: 0.4312 L12: -0.0977 REMARK 3 L13: 0.0433 L23: 0.0823 REMARK 3 S TENSOR REMARK 3 S11: 0.0088 S12: -0.0683 S13: -0.0717 REMARK 3 S21: -0.0295 S22: 0.0122 S23: -0.0059 REMARK 3 S31: 0.0502 S32: -0.0172 S33: -0.0209 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 9 B 99 REMARK 3 RESIDUE RANGE : B 124 B 144 REMARK 3 RESIDUE RANGE : B 188 B 201 REMARK 3 RESIDUE RANGE : A 202 A 216 REMARK 3 ORIGIN FOR THE GROUP (A): -4.4010 26.8690 9.7360 REMARK 3 T TENSOR REMARK 3 T11: -0.0003 T22: -0.0687 REMARK 3 T33: 0.0185 T12: 0.0037 REMARK 3 T13: 0.0158 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.5008 L22: 0.3482 REMARK 3 L33: 0.8093 L12: -0.1507 REMARK 3 L13: 0.1484 L23: -0.2881 REMARK 3 S TENSOR REMARK 3 S11: 0.0029 S12: -0.0257 S13: 0.1013 REMARK 3 S21: -0.0422 S22: 0.0164 S23: 0.0116 REMARK 3 S31: -0.0130 S32: -0.0161 S33: -0.0193 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 100 A 123 REMARK 3 RESIDUE RANGE : A 145 A 187 REMARK 3 ORIGIN FOR THE GROUP (A): 4.9730 6.6460 41.1450 REMARK 3 T TENSOR REMARK 3 T11: -0.0012 T22: 0.0493 REMARK 3 T33: -0.0594 T12: 0.0117 REMARK 3 T13: 0.0081 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.2244 L22: 1.9610 REMARK 3 L33: 0.4715 L12: -0.2207 REMARK 3 L13: 0.0754 L23: -0.2833 REMARK 3 S TENSOR REMARK 3 S11: -0.0158 S12: -0.1851 S13: 0.0286 REMARK 3 S21: 0.1958 S22: 0.0134 S23: -0.0668 REMARK 3 S31: -0.0084 S32: 0.0061 S33: 0.0024 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 100 B 123 REMARK 3 RESIDUE RANGE : B 145 B 187 REMARK 3 ORIGIN FOR THE GROUP (A): -4.4630 35.6510 29.7840 REMARK 3 T TENSOR REMARK 3 T11: 0.0263 T22: -0.0321 REMARK 3 T33: 0.0215 T12: 0.0475 REMARK 3 T13: 0.0262 T23: -0.0737 REMARK 3 L TENSOR REMARK 3 L11: 0.5928 L22: 1.1872 REMARK 3 L33: 1.6102 L12: -0.0467 REMARK 3 L13: -0.0784 L23: -0.8185 REMARK 3 S TENSOR REMARK 3 S11: -0.0036 S12: -0.1626 S13: 0.1498 REMARK 3 S21: 0.1970 S22: 0.0541 S23: 0.0673 REMARK 3 S31: -0.2912 S32: -0.1454 S33: -0.0505 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 2 C 11 REMARK 3 RESIDUE RANGE : D 2 D 11 REMARK 3 ORIGIN FOR THE GROUP (A): -1.7650 18.6440 29.0940 REMARK 3 T TENSOR REMARK 3 T11: -0.0156 T22: -0.0037 REMARK 3 T33: 0.0006 T12: 0.0163 REMARK 3 T13: 0.0192 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 0.4483 L22: 1.1703 REMARK 3 L33: 1.2031 L12: -0.0352 REMARK 3 L13: 0.0645 L23: -0.1710 REMARK 3 S TENSOR REMARK 3 S11: -0.0438 S12: -0.1494 S13: 0.0599 REMARK 3 S21: 0.0426 S22: 0.0695 S23: 0.0432 REMARK 3 S31: -0.0377 S32: -0.1015 S33: -0.0258 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: REMARK 3 CNS HAS BEEN USED FOR DNA REFINEMENT. NO SUGAR PUCKER CONSTRAINTS REMARK 3 HAVE BEEN APPLIED. REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT REMARK 3 HAS BEEN USED. REMARK 4 REMARK 4 3NDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : TRIANGULAR MONOCHROMATOR REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 118539 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : 0.07400 REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.26600 REMARK 200 R SYM FOR SHELL (I) : 0.26600 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELXCD, SHELXD, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE PH 4.5, 200MM, REMARK 280 AMMONIUM SULFATE, 30% PEG400, 1.5% 1,2,3-HEPTANETRIOL, VAPOR, REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 294K, VAPOR DIFFUSION, REMARK 280 HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 36.45500 REMARK 290 SMTRY3 2 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 300 REMARK: BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A AND B, AND DNA REMARK 300 STRANDS C AND D. THE TETRAMER (ACCORDING TO PDB CONVENTIONS) IS A REMARK 300 COMPLEX OF THE DIMERIC RESTRICTION ENZYME WITH ITS SUBSTRATE, REMARK 300 DOUBLE STRANDED DNA. 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: 10900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 -8 REMARK 465 GLY A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 ASN A 2 REMARK 465 ILE A 3 REMARK 465 ARG A 4 REMARK 465 ASP A 5 REMARK 465 ARG A 6 REMARK 465 MET A 7 REMARK 465 ASN A 8 REMARK 465 MET B -8 REMARK 465 GLY B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 GLU B 0 REMARK 465 PHE B 1 REMARK 465 ASN B 2 REMARK 465 ILE B 3 REMARK 465 ARG B 4 REMARK 465 ASP B 5 REMARK 465 ARG B 6 REMARK 465 MET B 7 REMARK 465 ASN B 8 REMARK 465 DG C 1 REMARK 465 DC D 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DG C 2 P OP1 OP2 REMARK 470 DC D 2 P OP1 OP2 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 GLU A 80 -58.62 72.54 REMARK 500 GLU A 80 -58.62 67.84 REMARK 500 TRP A 107 38.57 -92.94 REMARK 500 ASN A 133 80.94 -150.46 REMARK 500 TYR A 203 127.34 164.70 REMARK 500 GLU B 80 -57.58 77.36 REMARK 500 GLU B 80 -57.58 69.79 REMARK 500 TRP B 107 34.77 -93.86 REMARK 500 ASN B 169 78.42 -114.04 REMARK 500 TYR B 203 139.03 -170.45 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 DG C 6 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE IDENTITY OF THE METAL IONS IS UNCERTAIN. REMARK 600 THE DEPOSITORS SUSPECT THEM TO BE SODIUM OR CALCIUM IONS, REMARK 600 WHICH ARE BOTH PRESENT IN THE BUFFER. REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PGE B 219 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 217, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 219, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 220, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 217, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 12, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 13, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 217, CONFORMER B REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 219, CONFORMER B REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 220, CONFORMER B REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 217, CONFORMER B REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 12, CONFORMER B REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 222 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE B 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE B 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 221 REMARK 999 REMARK 999 SEQUENCE REMARK 999 ALTHOUGH AN N-TERMINAL TAG HAS BEEN ASSIGNED TO CHAIN A, REMARK 999 THE TAG MIGHT BE A PART OF CHAIN A, CHAIN B OR A SYMMETRY MATE. DBREF 3NDH A 2 216 UNP Q9HJY3 Q9HJY3_THEAC 2 216 DBREF 3NDH B 2 216 UNP Q9HJY3 Q9HJY3_THEAC 2 216 DBREF 3NDH C 1 11 PDB 3NDH 3NDH 1 11 DBREF 3NDH D 1 11 PDB 3NDH 3NDH 1 11 SEQADV 3NDH MET A -8 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH GLY A -7 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS A -6 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS A -5 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS A -4 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS A -3 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS A -2 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS A -1 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH GLU A 0 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH PHE A 1 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH MET B -8 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH GLY B -7 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS B -6 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS B -5 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS B -4 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS B -3 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS B -2 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH HIS B -1 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH GLU B 0 UNP Q9HJY3 EXPRESSION TAG SEQADV 3NDH PHE B 1 UNP Q9HJY3 EXPRESSION TAG SEQRES 1 A 225 MET GLY HIS HIS HIS HIS HIS HIS GLU PHE ASN ILE ARG SEQRES 2 A 225 ASP ARG MET ASN ASP HIS LEU LYS ASP LEU PHE ARG ASP SEQRES 3 A 225 ARG LEU ILE ILE ASP LYS VAL GLN ARG ARG LEU PRO TYR SEQRES 4 A 225 MET PHE GLN LEU ALA GLU LEU GLU SER SER ARG ALA GLY SEQRES 5 A 225 LYS VAL GLY MET GLU VAL GLY SER LEU ARG GLU ARG ILE SEQRES 6 A 225 ILE SER SER LEU LEU ILE TYR LYS PHE GLY GLU LYS ASN SEQRES 7 A 225 VAL GLU THR ASP LEU PRO ILE THR GLU PRO GLU ILE ASP SEQRES 8 A 225 VAL LYS LEU PHE GLY SER PRO ILE SER ILE LYS THR ILE SEQRES 9 A 225 THR GLY LYS GLU PRO ALA GLY VAL LYS LEU ILE TRP THR SEQRES 10 A 225 VAL ASP ALA THR LYS ALA ARG GLN PHE LEU GLU THR TRP SEQRES 11 A 225 HIS PRO ARG PHE ASP LEU ILE LEU VAL HIS ILE ASN TRP SEQRES 12 A 225 SER SER LEU GLY GLY VAL TYR TYR ILE PRO ASP TYR VAL SEQRES 13 A 225 GLN GLN ARG ILE PHE ASP GLU ILE GLY LYS ASP LYS TYR SEQRES 14 A 225 ILE LYS LEU PRO LYS GLN GLY THR ASN PRO ARG GLY VAL SEQRES 15 A 225 GLU ILE SER ASN GLU ALA LEU LYS GLU ILE MET THR ASP SEQRES 16 A 225 GLU GLU THR MET SER ILE LYS ILE GLU TRP LYS LYS THR SEQRES 17 A 225 ASN VAL GLN TYR ASN ALA PHE LYS ARG TRP VAL ASP LEU SEQRES 18 A 225 TRP SER GLU GLY SEQRES 1 B 225 MET GLY HIS HIS HIS HIS HIS HIS GLU PHE ASN ILE ARG SEQRES 2 B 225 ASP ARG MET ASN ASP HIS LEU LYS ASP LEU PHE ARG ASP SEQRES 3 B 225 ARG LEU ILE ILE ASP LYS VAL GLN ARG ARG LEU PRO TYR SEQRES 4 B 225 MET PHE GLN LEU ALA GLU LEU GLU SER SER ARG ALA GLY SEQRES 5 B 225 LYS VAL GLY MET GLU VAL GLY SER LEU ARG GLU ARG ILE SEQRES 6 B 225 ILE SER SER LEU LEU ILE TYR LYS PHE GLY GLU LYS ASN SEQRES 7 B 225 VAL GLU THR ASP LEU PRO ILE THR GLU PRO GLU ILE ASP SEQRES 8 B 225 VAL LYS LEU PHE GLY SER PRO ILE SER ILE LYS THR ILE SEQRES 9 B 225 THR GLY LYS GLU PRO ALA GLY VAL LYS LEU ILE TRP THR SEQRES 10 B 225 VAL ASP ALA THR LYS ALA ARG GLN PHE LEU GLU THR TRP SEQRES 11 B 225 HIS PRO ARG PHE ASP LEU ILE LEU VAL HIS ILE ASN TRP SEQRES 12 B 225 SER SER LEU GLY GLY VAL TYR TYR ILE PRO ASP TYR VAL SEQRES 13 B 225 GLN GLN ARG ILE PHE ASP GLU ILE GLY LYS ASP LYS TYR SEQRES 14 B 225 ILE LYS LEU PRO LYS GLN GLY THR ASN PRO ARG GLY VAL SEQRES 15 B 225 GLU ILE SER ASN GLU ALA LEU LYS GLU ILE MET THR ASP SEQRES 16 B 225 GLU GLU THR MET SER ILE LYS ILE GLU TRP LYS LYS THR SEQRES 17 B 225 ASN VAL GLN TYR ASN ALA PHE LYS ARG TRP VAL ASP LEU SEQRES 18 B 225 TRP SER GLU GLY SEQRES 1 C 11 DG DG DT DA DC DG DC DG DA DT DG SEQRES 1 D 11 DC DC DA DT DC DG DC DG DT DA DC HET NA A 217 1 HET CL A 218 1 HET PGE A 219 17 HET ACT A 220 4 HET SO4 A 221 5 HET SO4 A 222 5 HET NA B 217 1 HET CL B 218 1 HET PGE B 219 7 HET PGE B 220 10 HET ACT B 221 4 HET ACT C 12 4 HET ACT C 13 4 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION FORMUL 5 NA 2(NA 1+) FORMUL 6 CL 2(CL 1-) FORMUL 7 PGE 3(C6 H14 O4) FORMUL 8 ACT 4(C2 H3 O2 1-) FORMUL 9 SO4 2(O4 S 2-) FORMUL 18 HOH *470(H2 O) HELIX 1 1 ASP A 9 ASP A 17 1 9 HELIX 2 2 ASP A 17 GLU A 38 1 22 HELIX 3 3 GLU A 48 GLY A 66 1 19 HELIX 4 4 ASP A 110 TRP A 121 1 12 HELIX 5 5 PRO A 144 GLY A 156 1 13 HELIX 6 6 GLY A 156 TYR A 160 1 5 HELIX 7 7 SER A 176 ASP A 186 1 11 HELIX 8 8 PHE A 206 GLU A 215 1 10 HELIX 9 9 HIS B 10 LEU B 14 5 5 HELIX 10 10 ASP B 17 GLU B 38 1 22 HELIX 11 11 GLU B 48 GLY B 66 1 19 HELIX 12 12 ASP B 110 TRP B 121 1 12 HELIX 13 13 PRO B 144 GLY B 156 1 13 HELIX 14 14 GLY B 156 TYR B 160 1 5 HELIX 15 15 SER B 176 ASP B 186 1 11 HELIX 16 16 PHE B 206 GLY B 216 1 11 SHEET 1 A 2 SER A 40 ARG A 41 0 SHEET 2 A 2 LYS A 44 VAL A 45 -1 O LYS A 44 N ARG A 41 SHEET 1 B 6 VAL A 70 GLU A 71 0 SHEET 2 B 6 VAL A 83 LEU A 85 -1 O LYS A 84 N GLU A 71 SHEET 3 B 6 SER A 88 THR A 96 -1 O ILE A 90 N VAL A 83 SHEET 4 B 6 ASP A 126 ILE A 132 1 O ILE A 132 N ILE A 95 SHEET 5 B 6 LEU A 137 ILE A 143 -1 O GLY A 139 N HIS A 131 SHEET 6 B 6 MET A 190 GLU A 195 -1 O ILE A 194 N GLY A 138 SHEET 1 C 3 LYS A 104 ILE A 106 0 SHEET 2 C 3 VAL A 173 ILE A 175 -1 O VAL A 173 N LEU A 105 SHEET 3 C 3 ILE A 161 LYS A 162 -1 N LYS A 162 O GLU A 174 SHEET 1 D 2 SER B 40 ARG B 41 0 SHEET 2 D 2 LYS B 44 VAL B 45 -1 O LYS B 44 N ARG B 41 SHEET 1 E 6 VAL B 70 GLU B 71 0 SHEET 2 E 6 VAL B 83 LEU B 85 -1 O LYS B 84 N GLU B 71 SHEET 3 E 6 SER B 88 THR B 96 -1 O ILE B 90 N VAL B 83 SHEET 4 E 6 ASP B 126 ILE B 132 1 O VAL B 130 N LYS B 93 SHEET 5 E 6 LEU B 137 ILE B 143 -1 O GLY B 139 N HIS B 131 SHEET 6 E 6 MET B 190 GLU B 195 -1 O ILE B 194 N GLY B 138 SHEET 1 F 3 LYS B 104 ILE B 106 0 SHEET 2 F 3 VAL B 173 ILE B 175 -1 O VAL B 173 N LEU B 105 SHEET 3 F 3 ILE B 161 LYS B 162 -1 N LYS B 162 O GLU B 174 SITE 1 AC1 6 ASP A 82 ILE A 92 HOH A 228 HOH A 232 SITE 2 AC1 6 DC C 7 HOH C 17 SITE 1 AC2 2 ASP A 73 LYS A 84 SITE 1 AC3 2 GLU A 38 ARG B 208 SITE 1 AC4 6 ASP B 82 ILE B 92 HOH B 251 HOH B 261 SITE 2 AC4 6 HOH B 362 DC D 7 SITE 1 AC5 5 DG C 11 ACT C 13 DA D 3 DT D 4 SITE 2 AC5 5 HOH D 148 SITE 1 AC6 3 DG C 11 ACT C 12 HOH C 366 SITE 1 BC1 6 ASP A 82 ILE A 92 HOH A 228 HOH A 232 SITE 2 BC1 6 DC D 7 HOH C 17 SITE 1 BC2 1 LYS A 84 SITE 1 BC3 1 GLU A 38 SITE 1 BC4 6 ASP B 82 ILE B 92 HOH B 251 HOH B 261 SITE 2 BC4 6 HOH B 362 DC C 7 SITE 1 BC5 4 DC D 11 DT C 3 DA C 4 HOH D 148 SITE 1 CC1 2 HOH A 248 HOH A 338 SITE 1 CC2 6 HIS A -3 HOH B 310 HOH A 235 HOH A 285 SITE 2 CC2 6 HOH A 294 HOH A 317 SITE 1 CC3 4 HIS A -4 GLU A 67 HOH A 373 HOH A 432 SITE 1 CC4 2 HOH B 357 HOH B 282 SITE 1 CC5 1 ACT B 221 SITE 1 CC6 6 GLU B 71 ASP B 73 GLU B 78 LYS B 84 SITE 2 CC6 6 HOH B 278 HOH B 312 SITE 1 CC7 3 ARG A 208 GLU B 38 PGE B 219 CRYST1 39.310 72.910 88.760 90.00 101.99 90.00 P 1 21 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 0.025439 0.000000 0.005403 0.00000 SCALE2 0.000000 0.013716 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011518 0.00000