PDB Short entry for 3E3Y HEADER HYDROLASE/DNA 08-AUG-08 3E3Y TITLE Q138F HINCII BOUND TO GTTAAC AND COCRYSTALLIZED WITH 5 MM CA2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE-2 RESTRICTION ENZYME HINDII; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: R.HINDII, TYPE II RESTRICTION ENZYME HINDII, ENDONUCLEASE COMPND 5 HINDII; COMPND 6 EC: 3.1.21.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DTP*DAP*DAP*DCP*DCP*DGP*DGP*D COMPND 11 C)-3'; COMPND 12 CHAIN: E, F; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 GENE: HINDIIR, HI0512; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, ENDONUCLEASE, INDIRECT READOUT, HYDROLASE, KEYWDS 2 NUCLEASE, RESTRICTION SYSTEM, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.C.HORTON,A.C.BABIC,E.J.LITTLE,V.M.MANOHAR REVDAT 4 21-FEB-24 3E3Y 1 REMARK REVDAT 3 20-OCT-21 3E3Y 1 REMARK SEQADV LINK REVDAT 2 20-JAN-09 3E3Y 1 JRNL VERSN REVDAT 1 26-AUG-08 3E3Y 0 JRNL AUTH A.C.BABIC,E.J.LITTLE,V.M.MANOHAR,J.BITINAITE,N.C.HORTON JRNL TITL DNA DISTORTION AND SPECIFICITY IN A SEQUENCE-SPECIFIC JRNL TITL 2 ENDONUCLEASE. JRNL REF J.MOL.BIOL. V. 383 186 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18762194 JRNL DOI 10.1016/J.JMB.2008.08.032 REMARK 2 REMARK 2 RESOLUTION. 2.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32369 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1606 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.0670 - 4.7350 0.99 2824 152 0.2060 0.2200 REMARK 3 2 4.7350 - 3.7590 1.00 2842 128 0.1440 0.2030 REMARK 3 3 3.7590 - 3.2840 1.00 2776 161 0.1530 0.1930 REMARK 3 4 3.2840 - 2.9840 1.00 2769 155 0.1610 0.2230 REMARK 3 5 2.9840 - 2.7700 1.00 2808 149 0.1790 0.2470 REMARK 3 6 2.7700 - 2.6070 1.00 2835 135 0.1800 0.2570 REMARK 3 7 2.6070 - 2.4760 1.00 2788 144 0.1830 0.2620 REMARK 3 8 2.4760 - 2.3680 1.00 2784 149 0.1910 0.2550 REMARK 3 9 2.3680 - 2.2770 1.00 2770 155 0.2020 0.2720 REMARK 3 10 2.2770 - 2.1990 1.00 2760 149 0.2150 0.2980 REMARK 3 11 2.1990 - 2.1300 1.00 2807 129 0.2100 0.2850 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 66.11 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.52200 REMARK 3 B22 (A**2) : 2.41500 REMARK 3 B33 (A**2) : -1.89300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.67900 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 4594 REMARK 3 ANGLE : 0.992 6347 REMARK 3 CHIRALITY : 0.060 709 REMARK 3 PLANARITY : 0.003 713 REMARK 3 DIHEDRAL : 19.629 1641 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3E3Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048844. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32390 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.130 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.08500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, 150 MM NACL, 10 MM HEPES PH REMARK 280 7.5, 5 MM CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K 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 45.82000 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 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: 9070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, F 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 PRO A 23 REMARK 465 LYS A 24 REMARK 465 SER A 25 REMARK 465 GLY A 26 REMARK 465 THR A 27 REMARK 465 LEU A 28 REMARK 465 SER A 29 REMARK 465 GLY A 30 REMARK 465 HIS A 31 REMARK 465 ALA A 32 REMARK 465 ALA A 33 REMARK 465 GLY A 34 REMARK 465 GLU A 35 REMARK 465 PRO A 36 REMARK 465 GLN A 109 REMARK 465 ARG B 22 REMARK 465 PRO B 23 REMARK 465 LYS B 24 REMARK 465 SER B 25 REMARK 465 GLY B 26 REMARK 465 THR B 27 REMARK 465 LEU B 28 REMARK 465 SER B 29 REMARK 465 GLY B 30 REMARK 465 HIS B 31 REMARK 465 ALA B 32 REMARK 465 ALA B 33 REMARK 465 GLY B 34 REMARK 465 GLU B 35 REMARK 465 PRO B 36 REMARK 465 LEU B 258 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 LYS A 19 CD CE NZ REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 ARG A 22 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 39 CG CD CE NZ REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 SER A 50 OG REMARK 470 LYS A 66 CD CE NZ REMARK 470 ASN A 81 CG OD1 ND2 REMARK 470 GLU A 107 CD OE1 OE2 REMARK 470 LYS A 119 CD CE NZ REMARK 470 GLN A 121 CG CD OE1 NE2 REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 ASN A 176 CG OD1 ND2 REMARK 470 GLU A 178 CG CD OE1 OE2 REMARK 470 LYS A 228 CE NZ REMARK 470 LYS A 232 CG CD CE NZ REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 251 CG CD CE NZ REMARK 470 LYS A 254 CG CD CE NZ REMARK 470 LYS A 255 CG CD CE NZ REMARK 470 LEU A 258 CG CD1 CD2 REMARK 470 GLN B 9 CD OE1 NE2 REMARK 470 GLN B 18 CG CD OE1 NE2 REMARK 470 LYS B 19 CG CD CE NZ REMARK 470 VAL B 20 CG1 CG2 REMARK 470 LYS B 21 CG CD CE NZ REMARK 470 PHE B 37 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 SER B 50 OG REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 LYS B 78 CD CE NZ REMARK 470 ILE B 101 CG1 CG2 CD1 REMARK 470 GLU B 102 CG CD OE1 OE2 REMARK 470 LYS B 119 CE NZ REMARK 470 GLN B 121 CG CD OE1 NE2 REMARK 470 LYS B 135 CG CD CE NZ REMARK 470 LYS B 159 CG CD CE NZ REMARK 470 LEU B 175 CG CD1 CD2 REMARK 470 ASN B 176 CG OD1 ND2 REMARK 470 GLU B 178 CG CD OE1 OE2 REMARK 470 ASP B 179 CG OD1 OD2 REMARK 470 LYS B 192 CE NZ REMARK 470 LYS B 232 CD CE NZ 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 E 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG E 12 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DG E 12 O4' - C1' - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 DC E 14 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA F 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG F 12 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 DC F 14 O4' - C1' - N1 ANGL. DEV. = 2.2 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 LEU A 49 52.78 -141.63 REMARK 500 SER A 82 118.45 -168.98 REMARK 500 ASP A 162 44.09 -141.61 REMARK 500 VAL A 250 -62.66 -107.14 REMARK 500 LYS B 39 27.42 -62.72 REMARK 500 SER B 82 113.85 -173.70 REMARK 500 VAL B 250 -63.13 -109.58 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 CA A 259 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 114 OD1 REMARK 620 2 ASP A 127 OD2 78.9 REMARK 620 3 VAL A 128 O 93.4 76.5 REMARK 620 4 HOH A 410 O 76.3 150.1 121.2 REMARK 620 5 DA F 8 OP1 100.5 85.3 154.6 83.1 REMARK 620 6 DA F 9 OP2 172.2 106.5 82.5 100.0 85.8 REMARK 620 7 HOH F 391 O 94.4 146.9 71.6 52.4 127.7 78.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA F 15 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 114 OD2 REMARK 620 2 HOH A 309 O 85.0 REMARK 620 3 HOH A 366 O 112.8 93.1 REMARK 620 4 HOH A 367 O 91.3 165.6 101.1 REMARK 620 5 DT F 7 O3' 138.6 84.1 107.6 89.7 REMARK 620 6 DA F 8 OP1 87.6 73.2 154.8 92.8 51.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 260 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 127 OD1 REMARK 620 2 ILE A 142 O 89.1 REMARK 620 3 HOH A 297 O 169.0 85.0 REMARK 620 4 HOH A 459 O 90.6 102.2 99.6 REMARK 620 5 DA F 8 OP2 90.7 118.7 84.0 139.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 259 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 114 OD2 REMARK 620 2 ASP B 127 OD1 80.9 REMARK 620 3 VAL B 128 O 91.0 78.7 REMARK 620 4 HOH B 389 O 75.4 149.4 120.3 REMARK 620 5 DA E 8 OP1 99.5 86.1 159.9 79.1 REMARK 620 6 DA E 9 OP2 166.3 107.8 80.6 99.4 91.8 REMARK 620 7 HOH E 34 O 89.2 149.7 72.9 49.6 123.9 78.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 260 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 127 OD2 REMARK 620 2 ILE B 142 O 80.1 REMARK 620 3 HOH B 302 O 164.0 88.2 REMARK 620 4 DA E 8 OP2 91.5 120.2 85.0 REMARK 620 5 HOH E 17 O 95.3 98.9 97.3 140.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA F 15 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TX3 RELATED DB: PDB REMARK 900 WILD TYPE HINCII BOUND TO GTCGAC REMARK 900 RELATED ID: 2GIJ RELATED DB: PDB REMARK 900 Q138F HINCII BOUND TO GTTAAC AND CA2+ (FROM SOAKING CA2+ INTO REMARK 900 PREFORMED CRYSTALS) REMARK 900 RELATED ID: 3E40 RELATED DB: PDB REMARK 900 RELATED ID: 3E41 RELATED DB: PDB REMARK 900 RELATED ID: 3E42 RELATED DB: PDB REMARK 900 RELATED ID: 3E43 RELATED DB: PDB REMARK 900 RELATED ID: 3E44 RELATED DB: PDB REMARK 900 RELATED ID: 3E45 RELATED DB: PDB DBREF 3E3Y A 2 258 UNP P44413 T2D2_HAEIN 2 258 DBREF 3E3Y B 2 258 UNP P44413 T2D2_HAEIN 2 258 DBREF 3E3Y E 1 14 PDB 3E3Y 3E3Y 1 14 DBREF 3E3Y F 1 14 PDB 3E3Y 3E3Y 1 14 SEQADV 3E3Y ASN A 67 UNP P44413 LYS 67 CONFLICT SEQADV 3E3Y PHE A 138 UNP P44413 GLN 138 ENGINEERED MUTATION SEQADV 3E3Y ASN B 67 UNP P44413 LYS 67 CONFLICT SEQADV 3E3Y PHE B 138 UNP P44413 GLN 138 ENGINEERED MUTATION SEQRES 1 A 257 SER PHE ILE LYS PRO ILE TYR GLN ASP ILE ASN SER ILE SEQRES 2 A 257 LEU ILE GLY GLN LYS VAL LYS ARG PRO LYS SER GLY THR SEQRES 3 A 257 LEU SER GLY HIS ALA ALA GLY GLU PRO PHE GLU LYS LEU SEQRES 4 A 257 VAL TYR LYS PHE LEU LYS GLU ASN LEU SER ASP LEU THR SEQRES 5 A 257 PHE LYS GLN TYR GLU TYR LEU ASN ASP LEU PHE MET LYS SEQRES 6 A 257 ASN PRO ALA ILE ILE GLY HIS GLU ALA ARG TYR LYS LEU SEQRES 7 A 257 PHE ASN SER PRO THR LEU LEU PHE LEU LEU SER ARG GLY SEQRES 8 A 257 LYS ALA ALA THR GLU ASN TRP SER ILE GLU ASN LEU PHE SEQRES 9 A 257 GLU GLU LYS GLN ASN ASP THR ALA ASP ILE LEU LEU VAL SEQRES 10 A 257 LYS ASP GLN PHE TYR GLU LEU LEU ASP VAL LYS THR ARG SEQRES 11 A 257 ASN ILE SER LYS SER ALA PHE ALA PRO ASN ILE ILE SER SEQRES 12 A 257 ALA TYR LYS LEU ALA GLN THR CYS ALA LYS MET ILE ASP SEQRES 13 A 257 ASN LYS GLU PHE ASP LEU PHE ASP ILE ASN TYR LEU GLU SEQRES 14 A 257 VAL ASP TRP GLU LEU ASN GLY GLU ASP LEU VAL CYS VAL SEQRES 15 A 257 SER THR SER PHE ALA GLU LEU PHE LYS SER GLU PRO SER SEQRES 16 A 257 GLU LEU TYR ILE ASN TRP ALA ALA ALA MET GLN ILE GLN SEQRES 17 A 257 PHE HIS VAL ARG ASP LEU ASP GLN GLY PHE ASN GLY THR SEQRES 18 A 257 ARG GLU GLU TRP ALA LYS SER TYR LEU LYS HIS PHE VAL SEQRES 19 A 257 THR GLN ALA GLU GLN ARG ALA ILE SER MET ILE ASP LYS SEQRES 20 A 257 PHE VAL LYS PRO PHE LYS LYS TYR ILE LEU SEQRES 1 B 257 SER PHE ILE LYS PRO ILE TYR GLN ASP ILE ASN SER ILE SEQRES 2 B 257 LEU ILE GLY GLN LYS VAL LYS ARG PRO LYS SER GLY THR SEQRES 3 B 257 LEU SER GLY HIS ALA ALA GLY GLU PRO PHE GLU LYS LEU SEQRES 4 B 257 VAL TYR LYS PHE LEU LYS GLU ASN LEU SER ASP LEU THR SEQRES 5 B 257 PHE LYS GLN TYR GLU TYR LEU ASN ASP LEU PHE MET LYS SEQRES 6 B 257 ASN PRO ALA ILE ILE GLY HIS GLU ALA ARG TYR LYS LEU SEQRES 7 B 257 PHE ASN SER PRO THR LEU LEU PHE LEU LEU SER ARG GLY SEQRES 8 B 257 LYS ALA ALA THR GLU ASN TRP SER ILE GLU ASN LEU PHE SEQRES 9 B 257 GLU GLU LYS GLN ASN ASP THR ALA ASP ILE LEU LEU VAL SEQRES 10 B 257 LYS ASP GLN PHE TYR GLU LEU LEU ASP VAL LYS THR ARG SEQRES 11 B 257 ASN ILE SER LYS SER ALA PHE ALA PRO ASN ILE ILE SER SEQRES 12 B 257 ALA TYR LYS LEU ALA GLN THR CYS ALA LYS MET ILE ASP SEQRES 13 B 257 ASN LYS GLU PHE ASP LEU PHE ASP ILE ASN TYR LEU GLU SEQRES 14 B 257 VAL ASP TRP GLU LEU ASN GLY GLU ASP LEU VAL CYS VAL SEQRES 15 B 257 SER THR SER PHE ALA GLU LEU PHE LYS SER GLU PRO SER SEQRES 16 B 257 GLU LEU TYR ILE ASN TRP ALA ALA ALA MET GLN ILE GLN SEQRES 17 B 257 PHE HIS VAL ARG ASP LEU ASP GLN GLY PHE ASN GLY THR SEQRES 18 B 257 ARG GLU GLU TRP ALA LYS SER TYR LEU LYS HIS PHE VAL SEQRES 19 B 257 THR GLN ALA GLU GLN ARG ALA ILE SER MET ILE ASP LYS SEQRES 20 B 257 PHE VAL LYS PRO PHE LYS LYS TYR ILE LEU SEQRES 1 E 14 DG DC DC DG DG DT DT DA DA DC DC DG DG SEQRES 2 E 14 DC SEQRES 1 F 14 DG DC DC DG DG DT DT DA DA DC DC DG DG SEQRES 2 F 14 DC HET CA A 259 1 HET NA A 260 1 HET CA B 259 1 HET NA B 260 1 HET NA F 15 1 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 5 CA 2(CA 2+) FORMUL 6 NA 3(NA 1+) FORMUL 10 HOH *448(H2 O) HELIX 1 1 ILE A 4 PRO A 6 5 3 HELIX 2 2 ILE A 7 ILE A 16 1 10 HELIX 3 3 PHE A 37 LEU A 49 1 13 HELIX 4 4 GLN A 56 LYS A 66 1 11 HELIX 5 5 GLY A 72 LYS A 78 1 7 HELIX 6 6 LEU A 79 ASN A 81 5 3 HELIX 7 7 SER A 82 SER A 90 1 9 HELIX 8 8 GLY A 92 TRP A 99 1 8 HELIX 9 9 ALA A 145 ASN A 158 1 14 HELIX 10 10 PHE A 191 SER A 193 5 3 HELIX 11 11 GLU A 194 LEU A 198 5 5 HELIX 12 12 HIS A 211 LEU A 215 5 5 HELIX 13 13 THR A 222 VAL A 250 1 29 HELIX 14 14 VAL A 250 LYS A 255 1 6 HELIX 15 15 ILE B 4 PRO B 6 5 3 HELIX 16 16 ILE B 7 ILE B 16 1 10 HELIX 17 17 LEU B 40 LEU B 49 1 10 HELIX 18 18 GLN B 56 LYS B 66 1 11 HELIX 19 19 GLY B 72 LEU B 79 1 8 HELIX 20 20 SER B 82 SER B 90 1 9 HELIX 21 21 GLY B 92 TRP B 99 1 8 HELIX 22 22 ALA B 145 ASN B 158 1 14 HELIX 23 23 PHE B 191 SER B 193 5 3 HELIX 24 24 GLU B 194 LEU B 198 5 5 HELIX 25 25 HIS B 211 LEU B 215 5 5 HELIX 26 26 THR B 222 VAL B 250 1 29 HELIX 27 27 VAL B 250 LYS B 255 1 6 SHEET 1 A 6 LYS A 19 LYS A 21 0 SHEET 2 A 6 ASP A 179 GLU A 189 -1 O LEU A 180 N VAL A 20 SHEET 3 A 6 PHE A 164 ASN A 176 -1 N TYR A 168 O ALA A 188 SHEET 4 A 6 PHE A 122 ASN A 132 1 N LEU A 125 O ASP A 165 SHEET 5 A 6 ILE A 115 LYS A 119 -1 N ILE A 115 O LEU A 126 SHEET 6 A 6 THR A 53 LYS A 55 -1 N PHE A 54 O LEU A 116 SHEET 1 B 3 ASN A 141 SER A 144 0 SHEET 2 B 3 GLN A 207 GLN A 209 -1 O ILE A 208 N ILE A 142 SHEET 3 B 3 TYR A 199 ASN A 201 -1 N ASN A 201 O GLN A 207 SHEET 1 C 6 LYS B 19 VAL B 20 0 SHEET 2 C 6 ASP B 179 GLU B 189 -1 O LEU B 180 N VAL B 20 SHEET 3 C 6 PHE B 164 ASN B 176 -1 N TYR B 168 O ALA B 188 SHEET 4 C 6 PHE B 122 ASN B 132 1 N LEU B 125 O ASP B 165 SHEET 5 C 6 ILE B 115 LYS B 119 -1 N ILE B 115 O LEU B 126 SHEET 6 C 6 THR B 53 LYS B 55 -1 N PHE B 54 O LEU B 116 SHEET 1 D 3 ASN B 141 SER B 144 0 SHEET 2 D 3 GLN B 207 GLN B 209 -1 O ILE B 208 N ILE B 142 SHEET 3 D 3 ILE B 200 ASN B 201 -1 N ASN B 201 O GLN B 207 LINK OD1 ASP A 114 CA CA A 259 1555 1555 2.43 LINK OD2 ASP A 114 NA NA F 15 1555 1555 2.68 LINK OD2 ASP A 127 CA CA A 259 1555 1555 2.54 LINK OD1 ASP A 127 NA NA A 260 1555 1555 2.61 LINK O VAL A 128 CA CA A 259 1555 1555 2.48 LINK O ILE A 142 NA NA A 260 1555 1555 2.53 LINK CA CA A 259 O HOH A 410 1555 1555 2.63 LINK CA CA A 259 OP1 DA F 8 1555 1555 2.36 LINK CA CA A 259 OP2 DA F 9 1555 1555 2.55 LINK CA CA A 259 O HOH F 391 1555 1555 2.99 LINK NA NA A 260 O HOH A 297 1555 1555 2.82 LINK NA NA A 260 O HOH A 459 1555 1555 2.71 LINK NA NA A 260 OP2 DA F 8 1555 1555 2.64 LINK O HOH A 309 NA NA F 15 1555 1555 2.72 LINK O HOH A 366 NA NA F 15 1555 1555 2.38 LINK O HOH A 367 NA NA F 15 1555 1555 2.90 LINK OD2 ASP B 114 CA CA B 259 1555 1555 2.44 LINK OD1 ASP B 127 CA CA B 259 1555 1555 2.59 LINK OD2 ASP B 127 NA NA B 260 1555 1555 2.70 LINK O VAL B 128 CA CA B 259 1555 1555 2.43 LINK O ILE B 142 NA NA B 260 1555 1555 2.64 LINK CA CA B 259 O HOH B 389 1555 1555 2.64 LINK CA CA B 259 OP1 DA E 8 1555 1555 2.47 LINK CA CA B 259 OP2 DA E 9 1555 1555 2.62 LINK CA CA B 259 O HOH E 34 1555 1555 2.98 LINK NA NA B 260 O HOH B 302 1555 1555 2.76 LINK NA NA B 260 OP2 DA E 8 1555 1555 2.66 LINK NA NA B 260 O HOH E 17 1555 1555 2.67 LINK O3' DT F 7 NA NA F 15 1555 1555 2.99 LINK OP1 DA F 8 NA NA F 15 1555 1555 2.62 SITE 1 AC1 7 ASP A 114 ASP A 127 VAL A 128 HOH A 410 SITE 2 AC1 7 DA F 8 DA F 9 HOH F 391 SITE 1 AC2 6 ASP A 127 ILE A 142 HOH A 297 HOH A 459 SITE 2 AC2 6 DT F 7 DA F 8 SITE 1 AC3 7 ASP B 114 ASP B 127 VAL B 128 HOH B 389 SITE 2 AC3 7 DA E 8 DA E 9 HOH E 34 SITE 1 AC4 6 ASP B 127 ILE B 142 HOH B 302 DT E 7 SITE 2 AC4 6 DA E 8 HOH E 17 SITE 1 AC5 6 ASP A 114 HOH A 309 HOH A 366 HOH A 367 SITE 2 AC5 6 DT F 7 DA F 8 CRYST1 50.480 91.640 65.780 90.00 104.92 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 0.019810 0.000000 0.005278 0.00000 SCALE2 0.000000 0.010912 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015733 0.00000