HEADER HYDROLASE/DNA 18-SEP-14 4RD5 TITLE CRYSTAL STRUCTURE OF R.NGOAVII RESTRICTION ENDONUCLEASE B3 DOMAIN WITH TITLE 2 COGNATE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESTRICTION ENDONUCLEASE R.NGOVII; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.21.4; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)- COMPND 8 3'); COMPND 9 CHAIN: C, E; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)- COMPND 13 3'); COMPND 14 CHAIN: D, F; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA GONORRHOEAE; SOURCE 3 ORGANISM_TAXID: 242231; SOURCE 4 STRAIN: ATCC 700825 / FA 1090; SOURCE 5 GENE: NGO0364; 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: PLATE31; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC CONSTRUCT; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: SYNTHETIC CONSTRUCT KEYWDS RESTRICTION ENDONUCLEASE, B3 DNA BINDING DOMAIN, PROTEIN-DNA COMPLEX, KEYWDS 2 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.TAMULAITIENE,A.SILANSKAS,S.GRAZULIS,M.ZAREMBA,V.SIKSNYS REVDAT 4 28-FEB-24 4RD5 1 SEQADV REVDAT 3 07-MAR-18 4RD5 1 REMARK REVDAT 2 31-DEC-14 4RD5 1 JRNL REVDAT 1 24-DEC-14 4RD5 0 JRNL AUTH G.TAMULAITIENE,A.SILANSKAS,S.GRAZULIS,M.ZAREMBA,V.SIKSNYS JRNL TITL CRYSTAL STRUCTURE OF THE R-PROTEIN OF THE MULTISUBUNIT JRNL TITL 2 ATP-DEPENDENT RESTRICTION ENDONUCLEASE NGOAVII. JRNL REF NUCLEIC ACIDS RES. V. 42 14022 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 25429979 JRNL DOI 10.1093/NAR/GKU1237 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.3_1479 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.670 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17265 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.230 REMARK 3 FREE R VALUE TEST SET COUNT : 3242 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 48.3451 - 7.6687 0.99 1230 139 0.1946 0.2262 REMARK 3 2 7.6687 - 6.0907 1.00 1258 130 0.2460 0.2501 REMARK 3 3 6.0907 - 5.3219 1.00 1225 148 0.2063 0.2344 REMARK 3 4 5.3219 - 4.8358 1.00 1232 152 0.1863 0.2210 REMARK 3 5 4.8358 - 4.4895 1.00 1223 144 0.1932 0.2107 REMARK 3 6 4.4895 - 4.2249 1.00 1253 130 0.1780 0.2131 REMARK 3 7 4.2249 - 4.0135 1.00 1197 159 0.1840 0.2364 REMARK 3 8 4.0135 - 3.8388 1.00 1267 122 0.2002 0.2040 REMARK 3 9 3.8388 - 3.6911 1.00 1264 132 0.2015 0.2660 REMARK 3 10 3.6911 - 3.5638 1.00 1233 139 0.2081 0.3168 REMARK 3 11 3.5638 - 3.4524 1.00 1255 135 0.2010 0.2186 REMARK 3 12 3.4524 - 3.3537 1.00 1234 150 0.2140 0.2586 REMARK 3 13 3.3537 - 3.2654 1.00 1223 139 0.2015 0.2412 REMARK 3 14 3.2654 - 3.1858 1.00 1230 125 0.2294 0.2130 REMARK 3 15 3.1858 - 3.1134 1.00 1284 129 0.2356 0.2788 REMARK 3 16 3.1134 - 3.0471 1.00 1185 160 0.2492 0.3272 REMARK 3 17 3.0471 - 2.9862 1.00 1261 130 0.2604 0.3274 REMARK 3 18 2.9862 - 2.9298 1.00 1255 126 0.2493 0.2779 REMARK 3 19 2.9298 - 2.8775 1.00 1243 158 0.2644 0.2378 REMARK 3 20 2.8775 - 2.8288 1.00 1226 140 0.2488 0.3205 REMARK 3 21 2.8288 - 2.7831 1.00 1193 164 0.2627 0.3466 REMARK 3 22 2.7831 - 2.7403 1.00 1251 133 0.2624 0.3048 REMARK 3 23 2.7403 - 2.7000 1.00 1233 158 0.2495 0.2534 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.006 3923 REMARK 3 ANGLE : 0.794 5566 REMARK 3 CHIRALITY : 0.041 606 REMARK 3 PLANARITY : 0.005 512 REMARK 3 DIHEDRAL : 24.050 1496 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 4RD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087197. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976300 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17327 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 152.437 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09700 REMARK 200 FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 18.60 REMARK 200 R MERGE FOR SHELL (I) : 0.34500 REMARK 200 R SYM FOR SHELL (I) : 0.34500 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 6.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION BUFFER WAS 0.1 M MES REMARK 280 -IMIDAZOLE PH 6.5, 12.5% W/V PEG1000, 12.5% W/V PEG3350, 12.5% REMARK 280 MPD, 0.02 M OF EACH GLU, ALA, GLY, LYS, SER, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 76.21850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.20700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.20700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.10925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.20700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.20700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 114.32775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.20700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.20700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 38.10925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.20700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.20700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 114.32775 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 76.21850 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 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 455 LIES ON A SPECIAL POSITION. 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 178 REMARK 465 SER A 179 REMARK 465 HIS A 180 REMARK 465 LEU A 181 REMARK 465 GLU A 182 REMARK 465 ASN A 183 REMARK 465 CYS A 184 REMARK 465 ASN A 345 REMARK 465 SER A 346 REMARK 465 GLY A 347 REMARK 465 GLY A 348 REMARK 465 HIS A 349 REMARK 465 HIS A 350 REMARK 465 HIS A 351 REMARK 465 HIS A 352 REMARK 465 HIS A 353 REMARK 465 HIS A 354 REMARK 465 GLY A 355 REMARK 465 MET B 178 REMARK 465 SER B 179 REMARK 465 HIS B 180 REMARK 465 LEU B 181 REMARK 465 GLU B 182 REMARK 465 ASN B 183 REMARK 465 CYS B 184 REMARK 465 LYS B 344 REMARK 465 ASN B 345 REMARK 465 SER B 346 REMARK 465 GLY B 347 REMARK 465 GLY B 348 REMARK 465 HIS B 349 REMARK 465 HIS B 350 REMARK 465 HIS B 351 REMARK 465 HIS B 352 REMARK 465 HIS B 353 REMARK 465 HIS B 354 REMARK 465 GLY B 355 REMARK 465 DC C 1 REMARK 465 DG D 32 REMARK 465 DC E 1 REMARK 465 DG F 32 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 ARG A 196 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 344 CG CD CE NZ REMARK 470 LEU B 185 CG CD1 CD2 REMARK 470 GLU B 193 CG CD OE1 OE2 REMARK 470 GLN B 194 CG CD OE1 NE2 REMARK 470 ILE B 195 CG1 CG2 CD1 REMARK 470 ARG B 196 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 197 CG CD OE1 NE2 REMARK 470 LEU B 198 CG CD1 CD2 REMARK 470 PHE B 199 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 201 CG CD OE1 NE2 REMARK 470 THR B 202 OG1 CG2 REMARK 470 GLU B 204 CD OE1 OE2 REMARK 470 HIS B 206 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 225 CG CD OE1 OE2 REMARK 470 ARG B 228 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 231 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 233 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 248 CG CD CE NZ REMARK 470 GLU B 254 CG CD OE1 OE2 REMARK 470 GLN B 308 CG CD OE1 NE2 REMARK 470 ASN B 309 CG OD1 ND2 REMARK 470 GLU B 311 CG CD OE1 OE2 REMARK 470 LYS B 312 CG CD CE NZ REMARK 470 ILE B 313 CG1 CG2 CD1 REMARK 470 HIS B 315 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 316 CG CD OE1 OE2 REMARK 470 LEU B 318 CG CD1 CD2 REMARK 470 ARG B 319 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 320 CG CD OE1 OE2 REMARK 470 ASP B 332 CG OD1 OD2 REMARK 470 LYS B 342 CG CD CE NZ 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 OH TYR A 256 O HOH A 420 2.14 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 D 28 O3' DT D 28 C3' -0.044 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 DC C 8 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG C 10 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT D 28 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT D 29 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC E 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG E 10 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DG E 10 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 218 -123.51 61.23 REMARK 500 TYR A 280 14.05 59.83 REMARK 500 ASN A 288 -12.94 83.31 REMARK 500 PHE A 341 67.79 -159.30 REMARK 500 ASN B 218 -123.69 61.83 REMARK 500 ASN B 220 42.88 -108.45 REMARK 500 ASN B 288 -8.72 79.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 4RD5 A 179 345 UNP Q5F9M9 Q5F9M9_NEIG1 179 345 DBREF 4RD5 B 179 345 UNP Q5F9M9 Q5F9M9_NEIG1 179 345 DBREF 4RD5 C 1 16 PDB 4RD5 4RD5 1 16 DBREF 4RD5 E 1 16 PDB 4RD5 4RD5 1 16 DBREF 4RD5 D 17 32 PDB 4RD5 4RD5 17 32 DBREF 4RD5 F 17 32 PDB 4RD5 4RD5 17 32 SEQADV 4RD5 MET A 178 UNP Q5F9M9 INITIATING METHIONINE SEQADV 4RD5 SER A 346 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 GLY A 347 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 GLY A 348 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS A 349 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS A 350 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS A 351 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS A 352 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS A 353 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS A 354 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 GLY A 355 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 MET B 178 UNP Q5F9M9 INITIATING METHIONINE SEQADV 4RD5 SER B 346 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 GLY B 347 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 GLY B 348 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS B 349 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS B 350 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS B 351 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS B 352 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS B 353 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 HIS B 354 UNP Q5F9M9 EXPRESSION TAG SEQADV 4RD5 GLY B 355 UNP Q5F9M9 EXPRESSION TAG SEQRES 1 A 178 MET SER HIS LEU GLU ASN CYS LEU GLY VAL GLN LYS ILE SEQRES 2 A 178 ALA PRO GLU GLN ILE ARG GLN LEU PHE ALA GLN THR SER SEQRES 3 A 178 GLU TYR HIS PHE SER ILE PRO ALA LYS THR GLU GLU LYS SEQRES 4 A 178 SER ASN LEU ASN VAL PHE PHE GLY GLU GLY ARG ARG ASP SEQRES 5 A 178 LYS ARG GLY PHE VAL LYS PRO ARG PRO TRP TYR GLU VAL SEQRES 6 A 178 GLU LEU ILE VAL SER LYS ASP ILE THR SER GLN GLU GLY SEQRES 7 A 178 TYR PRO VAL LEU LYS SER PHE THR VAL ILE THR ASP ASP SEQRES 8 A 178 GLY TRP GLN PHE GLN CYS LYS THR SER GLY ASP TYR SER SEQRES 9 A 178 LYS ASN PHE ARG SER GLU ASN ASP LEU LYS THR LEU GLY SEQRES 10 A 178 LYS TRP ILE LYS GLY ARG LEU GLU SER HIS GLY CYS LEU SEQRES 11 A 178 GLN ASN ASN GLU LYS ILE THR HIS GLU THR LEU ARG GLU SEQRES 12 A 178 TYR GLY ASN ASP HIS PHE GLU LEU ARG SER THR ASP ASN SEQRES 13 A 178 PRO ASP VAL TRP LEU LEU SER PHE LYS GLY LYS ASN SER SEQRES 14 A 178 GLY GLY HIS HIS HIS HIS HIS HIS GLY SEQRES 1 B 178 MET SER HIS LEU GLU ASN CYS LEU GLY VAL GLN LYS ILE SEQRES 2 B 178 ALA PRO GLU GLN ILE ARG GLN LEU PHE ALA GLN THR SER SEQRES 3 B 178 GLU TYR HIS PHE SER ILE PRO ALA LYS THR GLU GLU LYS SEQRES 4 B 178 SER ASN LEU ASN VAL PHE PHE GLY GLU GLY ARG ARG ASP SEQRES 5 B 178 LYS ARG GLY PHE VAL LYS PRO ARG PRO TRP TYR GLU VAL SEQRES 6 B 178 GLU LEU ILE VAL SER LYS ASP ILE THR SER GLN GLU GLY SEQRES 7 B 178 TYR PRO VAL LEU LYS SER PHE THR VAL ILE THR ASP ASP SEQRES 8 B 178 GLY TRP GLN PHE GLN CYS LYS THR SER GLY ASP TYR SER SEQRES 9 B 178 LYS ASN PHE ARG SER GLU ASN ASP LEU LYS THR LEU GLY SEQRES 10 B 178 LYS TRP ILE LYS GLY ARG LEU GLU SER HIS GLY CYS LEU SEQRES 11 B 178 GLN ASN ASN GLU LYS ILE THR HIS GLU THR LEU ARG GLU SEQRES 12 B 178 TYR GLY ASN ASP HIS PHE GLU LEU ARG SER THR ASP ASN SEQRES 13 B 178 PRO ASP VAL TRP LEU LEU SER PHE LYS GLY LYS ASN SER SEQRES 14 B 178 GLY GLY HIS HIS HIS HIS HIS HIS GLY SEQRES 1 C 16 DC DC DC DT DA DA DG DC DG DG DC DA DA SEQRES 2 C 16 DT DC DC SEQRES 1 D 16 DG DG DG DA DT DT DG DC DC DG DC DT DT SEQRES 2 D 16 DA DG DG SEQRES 1 E 16 DC DC DC DT DA DA DG DC DG DG DC DA DA SEQRES 2 E 16 DT DC DC SEQRES 1 F 16 DG DG DG DA DT DT DG DC DC DG DC DT DT SEQRES 2 F 16 DA DG DG FORMUL 7 HOH *86(H2 O) HELIX 1 1 ALA A 191 GLN A 201 1 11 HELIX 2 2 SER A 217 GLY A 224 5 8 HELIX 3 3 SER A 247 SER A 252 1 6 HELIX 4 4 GLY A 278 SER A 281 5 4 HELIX 5 5 LEU A 290 HIS A 304 1 15 HELIX 6 6 THR A 314 GLY A 322 1 9 HELIX 7 7 ALA B 191 GLN B 201 1 11 HELIX 8 8 SER B 217 GLY B 224 5 8 HELIX 9 9 SER B 247 SER B 252 1 6 HELIX 10 10 GLY B 278 SER B 281 5 4 HELIX 11 11 LEU B 290 HIS B 304 1 15 HELIX 12 12 THR B 314 GLY B 322 1 9 SHEET 1 A 6 GLN A 188 LYS A 189 0 SHEET 2 A 6 TRP A 270 SER A 277 -1 O GLN A 271 N GLN A 188 SHEET 3 A 6 SER A 261 THR A 266 -1 N THR A 266 O TRP A 270 SHEET 4 A 6 VAL A 336 SER A 340 1 O TRP A 337 N THR A 263 SHEET 5 A 6 HIS A 325 SER A 330 -1 N ARG A 329 O LEU A 338 SHEET 6 A 6 HIS A 206 PRO A 210 -1 N ILE A 209 O PHE A 326 SHEET 1 B 4 GLN A 188 LYS A 189 0 SHEET 2 B 4 TRP A 270 SER A 277 -1 O GLN A 271 N GLN A 188 SHEET 3 B 4 ASN A 283 SER A 286 -1 O ARG A 285 N LYS A 275 SHEET 4 B 4 LEU A 244 ILE A 245 -1 N LEU A 244 O PHE A 284 SHEET 1 C 2 ARG A 227 ARG A 228 0 SHEET 2 C 2 VAL A 234 LYS A 235 -1 O LYS A 235 N ARG A 227 SHEET 1 D 6 GLN B 188 LYS B 189 0 SHEET 2 D 6 TRP B 270 SER B 277 -1 O GLN B 271 N GLN B 188 SHEET 3 D 6 SER B 261 THR B 266 -1 N PHE B 262 O CYS B 274 SHEET 4 D 6 VAL B 336 SER B 340 1 O TRP B 337 N THR B 263 SHEET 5 D 6 HIS B 325 SER B 330 -1 N GLU B 327 O SER B 340 SHEET 6 D 6 HIS B 206 PRO B 210 -1 N ILE B 209 O PHE B 326 SHEET 1 E 4 GLN B 188 LYS B 189 0 SHEET 2 E 4 TRP B 270 SER B 277 -1 O GLN B 271 N GLN B 188 SHEET 3 E 4 ASN B 283 SER B 286 -1 O ARG B 285 N LYS B 275 SHEET 4 E 4 LEU B 244 ILE B 245 -1 N LEU B 244 O PHE B 284 SHEET 1 F 2 ARG B 227 ARG B 228 0 SHEET 2 F 2 VAL B 234 LYS B 235 -1 O LYS B 235 N ARG B 227 CRYST1 88.414 88.414 152.437 90.00 90.00 90.00 P 41 21 2 16 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 0.011310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011310 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006560 0.00000