HEADER HYDROLASE/DNA 13-JAN-10 3LDY TITLE AN EXTRAORDINARY MECHANISM OF DNA PERTURBATION EXHIBITED BY THE RARE- TITLE 2 CUTTING HNH RESTRICTION ENDONUCLEASE PACI COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESTRICTION ENDONUCLEASE PACI; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*A)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*AP*TP*TP*AP*AP*GP*CP*CP*TP*C)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS ALCALIGENES; SOURCE 3 ORGANISM_TAXID: 43263; SOURCE 4 GENE: PACIR; SOURCE 5 EXPRESSION_SYSTEM: PSEUDOMONAS ALCALIGENES; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 43263; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PVS1; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS BETA-BETA-ALPHA-METAL; HNH MOTIF; ZINC CLUSTERS; A-A, AND T-T BASE- KEYWDS 2 PAIRS, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.W.SHEN,D.HEITER,S.-H.CHAN,S.-Y.XU,G.WILSON,B.L.STODDARD REVDAT 4 21-FEB-24 3LDY 1 REMARK DBREF LINK REVDAT 3 17-JUL-13 3LDY 1 REMARK REVDAT 2 20-JUL-11 3LDY 1 JRNL REVDAT 1 21-APR-10 3LDY 0 JRNL AUTH B.W.SHEN,D.F.HEITER,S.H.CHAN,H.WANG,S.Y.XU,R.D.MORGAN, JRNL AUTH 2 G.G.WILSON,B.L.STODDARD JRNL TITL UNUSUAL TARGET SITE DISRUPTION BY THE RARE-CUTTING HNH JRNL TITL 2 RESTRICTION ENDONUCLEASE PACI. JRNL REF STRUCTURE V. 18 734 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20541511 JRNL DOI 10.1016/J.STR.2010.03.009 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0104 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 16445 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 888 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) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 953 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1102 REMARK 3 NUCLEIC ACID ATOMS : 366 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 3.35000 REMARK 3 B33 (A**2) : -3.39000 REMARK 3 B12 (A**2) : 0.00000 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): 0.320 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.790 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1564 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2191 ; 1.542 ; 2.220 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 149 ; 6.338 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 57 ;36.365 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 186 ;16.333 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;21.948 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 230 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1100 ; 0.007 ; 0.020 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): 715 ; 1.163 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1137 ; 2.139 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 849 ; 2.990 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1051 ; 4.493 ; 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): 1564 ; 1.674 ; 3.000 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 142 REMARK 3 ORIGIN FOR THE GROUP (A): 19.7392 33.3662 44.7090 REMARK 3 T TENSOR REMARK 3 T11: 0.0127 T22: 0.0979 REMARK 3 T33: 0.0141 T12: 0.0023 REMARK 3 T13: -0.0031 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.3793 L22: 0.3578 REMARK 3 L33: 2.1776 L12: -0.2210 REMARK 3 L13: -0.2089 L23: 0.0757 REMARK 3 S TENSOR REMARK 3 S11: 0.0085 S12: -0.1285 S13: 0.0161 REMARK 3 S21: 0.0379 S22: 0.0370 S23: -0.0040 REMARK 3 S31: 0.0062 S32: 0.0481 S33: -0.0456 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 : B 1 B 8 REMARK 3 ORIGIN FOR THE GROUP (A): 20.6343 50.2852 44.7205 REMARK 3 T TENSOR REMARK 3 T11: 0.2722 T22: 0.1850 REMARK 3 T33: 0.0611 T12: 0.0386 REMARK 3 T13: 0.0372 T23: -0.1064 REMARK 3 L TENSOR REMARK 3 L11: 3.9729 L22: 2.9019 REMARK 3 L33: 2.4297 L12: 1.7311 REMARK 3 L13: 3.4041 L23: -0.5496 REMARK 3 S TENSOR REMARK 3 S11: -0.2111 S12: -0.7589 S13: 0.4924 REMARK 3 S21: 0.4353 S22: -0.0897 S23: 0.2450 REMARK 3 S31: -0.6510 S32: -0.5739 S33: 0.3008 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 : C 9 C 18 REMARK 3 ORIGIN FOR THE GROUP (A): 22.2009 47.5478 43.0979 REMARK 3 T TENSOR REMARK 3 T11: 0.1301 T22: 0.0893 REMARK 3 T33: 0.0764 T12: 0.0022 REMARK 3 T13: 0.0086 T23: -0.0692 REMARK 3 L TENSOR REMARK 3 L11: 1.4926 L22: -0.0211 REMARK 3 L33: 2.9266 L12: -0.5942 REMARK 3 L13: -0.0881 L23: -0.8479 REMARK 3 S TENSOR REMARK 3 S11: -0.0155 S12: -0.3904 S13: 0.2453 REMARK 3 S21: 0.0926 S22: 0.0444 S23: -0.0532 REMARK 3 S31: -0.5763 S32: 0.0277 S33: -0.0288 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 143 A 145 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9527 33.1902 44.6322 REMARK 3 T TENSOR REMARK 3 T11: 0.0306 T22: 0.0943 REMARK 3 T33: 0.1197 T12: 0.0094 REMARK 3 T13: -0.0979 T23: -0.0630 REMARK 3 L TENSOR REMARK 3 L11: 1.2070 L22: -4.7123 REMARK 3 L33: 3.9678 L12: -2.8272 REMARK 3 L13: -9.9288 L23: -8.5414 REMARK 3 S TENSOR REMARK 3 S11: -0.1801 S12: 0.1769 S13: -0.5469 REMARK 3 S21: -0.3958 S22: 0.1911 S23: 0.2422 REMARK 3 S31: -0.9103 S32: 0.8740 S33: -0.0109 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 146 A 233 REMARK 3 ORIGIN FOR THE GROUP (A): 17.8011 34.2320 41.1581 REMARK 3 T TENSOR REMARK 3 T11: 0.0521 T22: 0.0636 REMARK 3 T33: 0.0436 T12: -0.0029 REMARK 3 T13: 0.0101 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 0.9432 L22: 0.6764 REMARK 3 L33: 1.6394 L12: -0.2543 REMARK 3 L13: 0.2680 L23: -0.9012 REMARK 3 S TENSOR REMARK 3 S11: -0.0194 S12: -0.1697 S13: 0.0234 REMARK 3 S21: 0.0452 S22: 0.0166 S23: 0.0474 REMARK 3 S31: -0.0516 S32: -0.1417 S33: 0.0028 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 3LDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000057158. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-09; 01-JAN-09; 01-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100; 100; 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N; Y REMARK 200 RADIATION SOURCE : ALS; ROTATING ANODE; ALS REMARK 200 BEAMLINE : 5.0.1; NULL; 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU MICROMAX-007 HF; REMARK 200 NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774; 1.5418; 1.0719 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220); MIRRORS; DOUBLE- REMARK 200 CRYSTAL, SI(111) REMARK 200 OPTICS : MIRRORS; NULL; MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; RIGAKU SATURN REMARK 200 944; ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19597 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 39.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25000 REMARK 200 FOR SHELL : 2.260 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH; SINGLE REMARK 200 WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-24% PEG 3000, 2-5% ETHYLENE GLYCOL, REMARK 280 0.1M SODIUM CITRATE., PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 57.34450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.34450 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 18.45400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.89400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.45400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.89400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.34450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.45400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.89400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.34450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.45400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.89400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY REMARK 300 THE OPERATION -X+1, Y, -Z+1/2 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 36.90800 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 57.34450 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 HOH A 147 O HOH A 208 2.13 REMARK 500 O HOH A 212 O HOH A 222 2.14 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 O3' DA B 8 P DA C 9 3655 1.65 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 DT B 7 C5 DT B 7 C7 0.042 REMARK 500 DA C 9 N3 DA C 9 C4 0.039 REMARK 500 DA C 9 C6 DA C 9 N1 0.044 REMARK 500 DA C 9 C5 DA C 9 N7 0.063 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 B 7 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT B 7 C5 - C4 - O4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT C 10 N1 - C2 - N3 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT C 10 C2 - N3 - C4 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT C 17 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC C 18 O4' - C1' - N1 ANGL. DEV. = 3.9 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 ARG A 6 -63.11 -101.37 REMARK 500 GLN A 8 15.46 56.66 REMARK 500 SER A 117 -135.64 44.04 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 ZN A 144 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 4 SG REMARK 620 2 CYS A 7 SG 104.0 REMARK 620 3 CYS A 24 SG 112.3 110.9 REMARK 620 4 CYS A 27 SG 111.0 107.8 110.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 143 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 63 SG REMARK 620 2 CYS A 66 SG 108.6 REMARK 620 3 CYS A 109 SG 107.4 111.9 REMARK 620 4 CYS A 112 SG 108.5 112.9 107.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 145 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 92 OD1 REMARK 620 2 ASN A 113 OD1 94.0 REMARK 620 3 HOH A 167 O 83.1 169.4 REMARK 620 4 HOH A 168 O 95.4 84.2 86.0 REMARK 620 5 DT C 10 O3' 167.5 91.2 93.7 96.3 REMARK 620 6 DT C 11 OP1 108.7 99.8 90.8 155.1 59.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 143 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 144 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 145 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M7K RELATED DB: PDB DBREF 3LDY A 1 142 PDB 3LDY 3LDY 1 142 DBREF 3LDY B 1 8 PDB 3LDY 3LDY 1 8 DBREF 3LDY C 9 18 PDB 3LDY 3LDY 9 18 SEQRES 1 A 142 MET THR GLN CYS PRO ARG CYS GLN ARG ASN LEU ALA ALA SEQRES 2 A 142 ASP GLU PHE TYR ALA GLY SER SER LYS MET CYS LYS GLY SEQRES 3 A 142 CYS MET THR TRP GLN ASN LEU SER TYR ASN ALA ASN LYS SEQRES 4 A 142 GLU GLY HIS ALA ASN THR PHE THR LYS ALA THR PHE LEU SEQRES 5 A 142 ALA TRP TYR GLY LEU SER ALA GLN ARG HIS CYS GLY TYR SEQRES 6 A 142 CYS GLY ILE SER GLU ALA GLY PHE THR SER LEU HIS ARG SEQRES 7 A 142 THR ASN PRO ARG GLY TYR HIS ILE GLN CYS LEU GLY VAL SEQRES 8 A 142 ASP ARG SER ASP SER PHE GLU GLY TYR SER PRO GLN ASN SEQRES 9 A 142 ALA ARG LEU ALA CYS PHE ILE CYS ASN ARG ILE LYS SER SEQRES 10 A 142 ASN ILE PHE SER ALA SER GLU MET ASP VAL LEU GLY GLU SEQRES 11 A 142 ALA ILE SER LYS ALA TRP HIS GLY ARG GLY ILE ALA SEQRES 1 B 8 DG DA DG DG DC DT DT DA SEQRES 1 C 10 DA DT DT DA DA DG DC DC DT DC HET ZN A 143 1 HET ZN A 144 1 HET CA A 145 1 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 4 ZN 2(ZN 2+) FORMUL 6 CA CA 2+ FORMUL 7 HOH *89(H2 O) HELIX 1 1 ALA A 12 PHE A 16 5 5 HELIX 2 2 CYS A 24 GLY A 41 1 18 HELIX 3 3 THR A 47 GLY A 56 1 10 HELIX 4 4 LEU A 57 ARG A 61 5 5 HELIX 5 5 SER A 69 SER A 75 1 7 HELIX 6 6 CYS A 109 SER A 117 1 9 HELIX 7 7 SER A 121 ARG A 139 1 19 SHEET 1 A 2 THR A 2 GLN A 3 0 SHEET 2 A 2 ASN A 10 LEU A 11 -1 O LEU A 11 N THR A 2 SHEET 1 B 2 GLY A 90 ARG A 93 0 SHEET 2 B 2 ALA A 105 ALA A 108 -1 O ARG A 106 N ASP A 92 LINK SG CYS A 4 ZN ZN A 144 1555 1555 2.32 LINK SG CYS A 7 ZN ZN A 144 1555 1555 2.39 LINK SG CYS A 24 ZN ZN A 144 1555 1555 2.37 LINK SG CYS A 27 ZN ZN A 144 1555 1555 2.30 LINK SG CYS A 63 ZN ZN A 143 1555 1555 2.36 LINK SG CYS A 66 ZN ZN A 143 1555 1555 2.35 LINK OD1 ASP A 92 CA CA A 145 1555 1555 2.45 LINK SG CYS A 109 ZN ZN A 143 1555 1555 2.00 LINK SG CYS A 112 ZN ZN A 143 1555 1555 2.41 LINK OD1 ASN A 113 CA CA A 145 1555 1555 2.37 LINK CA CA A 145 O HOH A 167 1555 1555 2.50 LINK CA CA A 145 O HOH A 168 1555 1555 2.51 LINK CA CA A 145 O3' DT C 10 1555 1555 2.62 LINK CA CA A 145 OP1 DT C 11 1555 1555 2.34 CISPEP 1 ARG A 82 GLY A 83 0 -25.20 SITE 1 AC1 4 CYS A 63 CYS A 66 CYS A 109 CYS A 112 SITE 1 AC2 4 CYS A 4 CYS A 7 CYS A 24 CYS A 27 SITE 1 AC3 6 ASP A 92 ASN A 113 HOH A 167 HOH A 168 SITE 2 AC3 6 DT C 10 DT C 11 CRYST1 36.908 115.788 114.689 90.00 90.00 90.00 C 2 2 21 8 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 0.027094 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008636 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008719 0.00000