HEADER LIGASE 11-MAR-21 7NUC TITLE CRYSTAL STRUCTURE OF NEISSERIA GONORRHOEAE LEURS L550G MUTANT IN TITLE 2 COMPLEX WITH ATP AND L-LEUCINOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LEUCYL-TRNA SYNTHETASE; COMPND 5 SYNONYM: LEUCYL-TRNA SYNTHETASE,LEURS; COMPND 6 EC: 6.1.1.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA GONORRHOEAE; SOURCE 3 ORGANISM_TAXID: 485; SOURCE 4 STRAIN: NCCP11945; SOURCE 5 GENE: LEUS, NGK_0009; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 (DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETRUK KEYWDS PROTEIN-LIGAND COMPLEX, ROSSMANN FOLD, LEUCYL-TRNA SYNTHETASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR L.PANG,S.V.STRELKOV,S.D.WEEKS REVDAT 4 31-JAN-24 7NUC 1 REMARK REVDAT 3 15-NOV-23 7NUC 1 ATOM REVDAT 2 14-SEP-22 7NUC 1 JRNL REVDAT 1 31-AUG-22 7NUC 0 JRNL AUTH L.PANG,V.ZANKI,S.V.STRELKOV,A.VAN AERSCHOT,I.GRUIC-SOVULJ, JRNL AUTH 2 S.D.WEEKS JRNL TITL PARTITIONING OF THE INITIAL CATALYTIC STEPS OF LEUCYL-TRNA JRNL TITL 2 SYNTHETASE IS DRIVEN BY AN ACTIVE SITE PEPTIDE-PLANE FLIP. JRNL REF COMMUN BIOL V. 5 883 2022 JRNL REFN ESSN 2399-3642 JRNL PMID 36038645 JRNL DOI 10.1038/S42003-022-03825-8 REMARK 2 REMARK 2 RESOLUTION. 2.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22948 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1137 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 76.3670 - 5.5394 1.00 2908 146 0.2083 0.2691 REMARK 3 2 5.5394 - 4.3969 1.00 2754 150 0.1599 0.2261 REMARK 3 3 4.3969 - 3.8411 1.00 2721 145 0.1496 0.2161 REMARK 3 4 3.8411 - 3.4899 1.00 2712 131 0.1658 0.2725 REMARK 3 5 3.4899 - 3.2398 1.00 2683 149 0.1868 0.2950 REMARK 3 6 3.2398 - 3.0488 1.00 2675 136 0.2175 0.2966 REMARK 3 7 3.0488 - 2.8961 1.00 2676 127 0.2222 0.2862 REMARK 3 8 2.8961 - 2.7700 1.00 2682 153 0.2398 0.3497 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.87 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 256 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.0515 -8.3224 -28.8850 REMARK 3 T TENSOR REMARK 3 T11: 0.1698 T22: 0.2870 REMARK 3 T33: 0.2384 T12: 0.0324 REMARK 3 T13: -0.0270 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 0.7415 L22: 0.8290 REMARK 3 L33: 1.0822 L12: 0.4656 REMARK 3 L13: 0.6786 L23: 0.6150 REMARK 3 S TENSOR REMARK 3 S11: -0.0097 S12: 0.0394 S13: 0.0041 REMARK 3 S21: 0.0079 S22: 0.0341 S23: -0.0398 REMARK 3 S31: -0.0168 S32: 0.0671 S33: -0.0288 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 257 THROUGH 403 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4887 30.2727 -13.3475 REMARK 3 T TENSOR REMARK 3 T11: 1.1881 T22: 0.4368 REMARK 3 T33: 0.4847 T12: -0.0271 REMARK 3 T13: -0.0885 T23: 0.1596 REMARK 3 L TENSOR REMARK 3 L11: 0.4601 L22: 0.9565 REMARK 3 L33: 2.3241 L12: -0.5638 REMARK 3 L13: 0.0082 L23: -0.7829 REMARK 3 S TENSOR REMARK 3 S11: -0.0535 S12: -0.4480 S13: -0.3535 REMARK 3 S21: 1.2683 S22: 0.2008 S23: 0.5171 REMARK 3 S31: 0.5381 S32: -0.4068 S33: -0.2889 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 404 THROUGH 780 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6007 -16.1591 -31.9671 REMARK 3 T TENSOR REMARK 3 T11: 0.2059 T22: 0.2491 REMARK 3 T33: 0.2133 T12: 0.0176 REMARK 3 T13: -0.0169 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 0.4788 L22: 0.5798 REMARK 3 L33: 0.5847 L12: -0.0378 REMARK 3 L13: 0.2827 L23: 0.2387 REMARK 3 S TENSOR REMARK 3 S11: -0.0153 S12: 0.0322 S13: 0.0328 REMARK 3 S21: 0.0887 S22: 0.0084 S23: 0.0193 REMARK 3 S31: 0.0550 S32: 0.0845 S33: -0.0038 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 781 THROUGH 876 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.7783 -22.6005 -62.4642 REMARK 3 T TENSOR REMARK 3 T11: 0.3804 T22: 0.5589 REMARK 3 T33: 0.6208 T12: 0.1252 REMARK 3 T13: -0.1053 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.1511 L22: 0.2726 REMARK 3 L33: 0.4663 L12: 0.1700 REMARK 3 L13: -0.1031 L23: 0.0897 REMARK 3 S TENSOR REMARK 3 S11: 0.1085 S12: 0.5697 S13: -0.0983 REMARK 3 S21: -0.0049 S22: 0.0013 S23: 0.5442 REMARK 3 S31: -0.1787 S32: -0.1294 S33: -0.0903 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 7NUC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292112266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978565 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23377 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 108.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.36800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 1.57600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6Q89 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HOLO PROTEIN AT 10 MG/ML IN 10 MM TRIS REMARK 280 PH 7, 100 MM NACL, 2.5 MM 2-MERCAPTOETHANOL WAS MIXED WITH 0.1 M REMARK 280 BIS-TRIS PROPANE PH 8.5, 0.1 M MGCL2, 20% W/V PEG 3350 AND A REMARK 280 CRYSTAL SEED STOCK IN A 0.75:1.0:0.25 (V/V) RATIO. THE SEED REMARK 280 STOCK WAS PREPARED IN THE SAME CRYSTALLIZATION BUFFER. SUITABLE REMARK 280 CRYSTALS WERE SOAKED WITH 5 MM ATP AND 5 MM L-LEUCINOL IN AN REMARK 280 EQUILVALENT PRECIPITANT SOLUTION SUPPLEMENTED WITH 22% V/V REMARK 280 ETHYLENE GLYCOL., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 24.45600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 108.48550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.79400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 108.48550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.45600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.79400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLY A 0 REMARK 465 ALA A 296 REMARK 465 GLY A 297 REMARK 465 SER A 298 REMARK 465 VAL A 299 REMARK 465 ALA A 300 REMARK 465 GLU A 301 REMARK 465 ALA A 302 REMARK 465 ASP A 303 REMARK 465 MET A 304 REMARK 465 ALA A 305 REMARK 465 THR A 306 REMARK 465 MET A 307 REMARK 465 GLU A 857 REMARK 465 GLY A 858 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 GLN A 2 CD OE1 NE2 REMARK 470 GLN A 6 CG CD OE1 NE2 REMARK 470 LYS A 92 CG CD CE NZ REMARK 470 ASP A 238 CG OD1 OD2 REMARK 470 LYS A 241 CG CD CE NZ REMARK 470 GLN A 242 CG CD OE1 NE2 REMARK 470 GLU A 245 CG CD OE1 OE2 REMARK 470 GLU A 273 CG CD OE1 OE2 REMARK 470 LEU A 276 CG CD1 CD2 REMARK 470 ASP A 283 CG OD1 OD2 REMARK 470 LYS A 284 CG CD CE NZ REMARK 470 LEU A 287 CG CD1 CD2 REMARK 470 GLN A 288 CG CD OE1 NE2 REMARK 470 ILE A 291 CG1 CG2 CD1 REMARK 470 GLU A 293 CG CD OE1 OE2 REMARK 470 LYS A 295 CG CD CE NZ REMARK 470 GLU A 308 CG CD OE1 OE2 REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 LYS A 310 CG CD CE NZ REMARK 470 LEU A 336 CG CD1 CD2 REMARK 470 GLU A 352 CG CD OE1 OE2 REMARK 470 ARG A 353 NE CZ NH1 NH2 REMARK 470 GLU A 356 CG CD OE1 OE2 REMARK 470 LYS A 366 CG CD CE NZ REMARK 470 ASP A 377 CG OD1 OD2 REMARK 470 ARG A 380 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 383 CG CD OE1 OE2 REMARK 470 GLN A 405 CG CD OE1 NE2 REMARK 470 GLU A 450 CG CD OE1 OE2 REMARK 470 LYS A 451 CG CD CE NZ REMARK 470 LYS A 498 CD CE NZ REMARK 470 GLU A 530 CD OE1 OE2 REMARK 470 LYS A 533 CD CE NZ REMARK 470 LYS A 594 CE NZ REMARK 470 ASP A 611 CG OD1 OD2 REMARK 470 LYS A 612 CG CD CE NZ REMARK 470 ARG A 614 NE CZ NH1 NH2 REMARK 470 VAL A 616 CG1 CG2 REMARK 470 SER A 617 OG REMARK 470 GLN A 698 CD OE1 NE2 REMARK 470 LYS A 703 CD CE NZ REMARK 470 LYS A 714 CD CE NZ REMARK 470 LYS A 756 CD CE NZ REMARK 470 GLU A 762 CD OE1 OE2 REMARK 470 VAL A 813 CG1 CG2 REMARK 470 LYS A 814 CG CD CE NZ REMARK 470 SER A 815 OG REMARK 470 ILE A 817 CG1 CG2 CD1 REMARK 470 GLU A 818 CD OE1 OE2 REMARK 470 VAL A 819 CG1 CG2 REMARK 470 VAL A 823 CG1 CG2 REMARK 470 ASN A 824 CG OD1 ND2 REMARK 470 LYS A 826 CG CD CE NZ REMARK 470 LEU A 827 CG CD1 CD2 REMARK 470 LYS A 830 CG CD CE NZ REMARK 470 VAL A 833 CG1 CG2 REMARK 470 SER A 838 OG REMARK 470 LYS A 839 CG CD CE NZ REMARK 470 ASP A 841 CG OD1 OD2 REMARK 470 GLU A 843 CG CD OE1 OE2 REMARK 470 LEU A 847 CG CD1 CD2 REMARK 470 ASN A 849 CG OD1 ND2 REMARK 470 GLU A 850 CG CD OE1 OE2 REMARK 470 VAL A 853 CG1 CG2 REMARK 470 LYS A 859 CG CD CE NZ REMARK 470 LYS A 862 CG CD CE NZ REMARK 470 LYS A 863 CG CD CE NZ REMARK 470 ARG A 870 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 871 CG CD1 CD2 REMARK 470 ASN A 873 CG OD1 ND2 REMARK 470 VAL A 875 CG1 CG2 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 28 69.15 -69.38 REMARK 500 TYR A 132 -66.19 -92.06 REMARK 500 ASP A 238 0.77 -64.49 REMARK 500 MET A 263 2.09 -66.75 REMARK 500 LYS A 309 110.78 -161.83 REMARK 500 ASN A 323 -5.63 -150.01 REMARK 500 TRP A 337 97.03 -56.60 REMARK 500 ASP A 373 61.99 -159.80 REMARK 500 ASN A 379 54.59 -109.80 REMARK 500 ARG A 380 86.81 -159.85 REMARK 500 ASP A 398 3.05 -63.67 REMARK 500 GLN A 437 47.41 -83.09 REMARK 500 TRP A 440 77.10 -69.65 REMARK 500 ASN A 469 36.14 -90.87 REMARK 500 SER A 519 73.33 -156.10 REMARK 500 GLN A 698 56.35 -102.35 REMARK 500 ARG A 736 -56.44 -143.76 REMARK 500 ALA A 848 25.18 -159.94 REMARK 500 ASN A 849 100.51 -162.00 REMARK 500 GLU A 850 -84.79 59.91 REMARK 500 PRO A 860 -179.10 -66.48 REMARK 500 PRO A 868 99.83 -58.57 REMARK 500 ARG A 870 -66.48 -137.66 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 A1006 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 449 SG REMARK 620 2 CYS A 452 SG 115.9 REMARK 620 3 CYS A 490 SG 98.2 117.0 REMARK 620 4 CYS A 493 SG 101.7 118.8 101.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1003 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A1002 O2G REMARK 620 2 ATP A1002 O2B 73.4 REMARK 620 3 ATP A1002 O2A 87.3 70.7 REMARK 620 4 HOH A1121 O 87.3 64.9 134.9 REMARK 620 5 HOH A1126 O 155.5 83.6 77.1 90.5 REMARK 620 6 HOH A1219 O 96.2 150.3 137.7 87.3 108.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1007 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1210 O REMARK 620 2 HOH A1236 O 72.4 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7NUA RELATED DB: PDB DBREF 7NUC A 1 876 UNP B4RNT1 SYL_NEIG2 1 876 SEQADV 7NUC GLY A 0 UNP B4RNT1 EXPRESSION TAG SEQADV 7NUC ASN A 454 UNP B4RNT1 ASP 454 CONFLICT SEQADV 7NUC ILE A 508 UNP B4RNT1 MET 508 CONFLICT SEQADV 7NUC GLY A 550 UNP B4RNT1 LEU 550 ENGINEERED MUTATION SEQRES 1 A 877 GLY MET GLN GLU HIS TYR GLN PRO ALA ALA ILE GLU PRO SEQRES 2 A 877 ALA ALA GLN LYS LYS TRP ASP ASP ALA ARG ILE SER ASN SEQRES 3 A 877 VAL SER GLU ASP ALA SER LYS PRO LYS TYR TYR CYS LEU SEQRES 4 A 877 SER MET PHE PRO TYR PRO SER GLY LYS LEU HIS MET GLY SEQRES 5 A 877 HIS VAL ARG ASN TYR THR ILE GLY ASP VAL LEU SER ARG SEQRES 6 A 877 PHE LYS LEU LEU ASN GLY PHE ASN VAL MET GLN PRO MET SEQRES 7 A 877 GLY TRP ASP ALA PHE GLY MET PRO ALA GLU ASN ALA ALA SEQRES 8 A 877 MET LYS ASN ASN VAL ALA PRO ALA ALA TRP THR TYR ASP SEQRES 9 A 877 ASN ILE GLU TYR MET LYS THR GLN LEU LYS SER LEU GLY SEQRES 10 A 877 PHE ALA VAL ASP TRP GLU ARG GLU VAL ALA THR CYS LYS SEQRES 11 A 877 PRO GLU TYR TYR ARG TRP GLU GLN TRP LEU PHE THR LYS SEQRES 12 A 877 LEU PHE GLU LYS GLY ILE VAL TYR ARG LYS ASN GLY THR SEQRES 13 A 877 VAL ASN TRP ASP PRO VAL ASP GLN THR VAL LEU ALA ASN SEQRES 14 A 877 GLU GLN VAL ILE ASP GLY ARG GLY TRP ARG SER GLY ALA SEQRES 15 A 877 LEU ILE GLU LYS ARG GLU ILE PRO MET TYR TYR PHE LYS SEQRES 16 A 877 ILE THR ASP TYR ALA GLU GLU LEU LEU ASN ASP LEU ASP SEQRES 17 A 877 LYS LEU GLU HIS TRP PRO GLU GLN VAL LYS THR MET GLN SEQRES 18 A 877 ARG ASN TRP ILE GLY LYS SER ARG GLY MET THR VAL ARG SEQRES 19 A 877 PHE ALA VAL SER ASP ASP SER LYS GLN GLY LEU GLU GLY SEQRES 20 A 877 ASP TYR ALA LYS PHE LEU GLN VAL TYR THR THR ARG PRO SEQRES 21 A 877 ASP THR LEU MET GLY ALA THR TYR VAL ALA VAL ALA ALA SEQRES 22 A 877 GLU HIS PRO LEU ALA THR ALA ALA ALA ALA ASP LYS PRO SEQRES 23 A 877 GLU LEU GLN ALA PHE ILE ALA GLU CYS LYS ALA GLY SER SEQRES 24 A 877 VAL ALA GLU ALA ASP MET ALA THR MET GLU LYS LYS GLY SEQRES 25 A 877 VAL PRO THR GLY ARG TYR VAL VAL ASN PRO LEU ASN GLY SEQRES 26 A 877 ASP LYS LEU GLU VAL TRP ILE ALA ASN TYR VAL LEU TRP SEQRES 27 A 877 GLY TYR GLY ASP GLY ALA VAL MET ALA VAL PRO ALA HIS SEQRES 28 A 877 ASP GLU ARG ASP PHE GLU PHE ALA ALA LYS TYR ASN LEU SEQRES 29 A 877 PRO LYS LYS GLN VAL ILE ALA VAL GLY ASP ASN ALA PHE SEQRES 30 A 877 ASP ALA ASN ARG TRP GLN GLU TRP TYR GLY ASP LYS GLU SEQRES 31 A 877 ASN GLY VAL LEU VAL ASN SER GLY ASP LEU ASP GLY LEU SEQRES 32 A 877 ASP PHE GLN THR ALA PHE ASP ALA VAL ALA ALA LYS LEU SEQRES 33 A 877 GLN SER GLN GLY ALA GLY GLU PRO LYS THR GLN TYR ARG SEQRES 34 A 877 LEU ARG ASP TRP GLY ILE SER ARG GLN ARG TYR TRP GLY SEQRES 35 A 877 CYS PRO ILE PRO ILE VAL HIS CYS GLU LYS CYS GLY ASN SEQRES 36 A 877 VAL PRO VAL PRO ALA ASP GLN LEU PRO VAL VAL LEU PRO SEQRES 37 A 877 GLU ASN VAL VAL PRO ASP GLY MET GLY SER PRO LEU ALA SEQRES 38 A 877 LYS MET PRO GLU PHE TYR GLU THR SER CYS PRO CYS CYS SEQRES 39 A 877 GLY GLY ALA ALA LYS ARG GLU THR ASP THR MET ASP THR SEQRES 40 A 877 PHE ILE GLU SER SER TRP TYR PHE PHE ARG TYR MET SER SEQRES 41 A 877 PRO LYS PHE SER ASP GLY MET VAL SER ALA GLU SER ALA SEQRES 42 A 877 LYS TYR TRP GLY ALA VAL ASP GLN TYR ILE GLY GLY ILE SEQRES 43 A 877 GLU HIS ALA ILE GLY HIS LEU LEU TYR ALA ARG PHE PHE SEQRES 44 A 877 THR LYS LEU MET ARG ASP GLU GLY LEU VAL ASN VAL ASP SEQRES 45 A 877 GLU PRO PHE GLU ARG LEU LEU THR GLN GLY MET VAL VAL SEQRES 46 A 877 CYS GLU THR TYR TYR ARG GLU ASN ASP LYS GLY GLY LYS SEQRES 47 A 877 ASP TRP ILE ASN PRO ALA ASP VAL GLU LEU THR PHE ASP SEQRES 48 A 877 ASP LYS GLY ARG PRO VAL SER ALA VAL LEU LYS ALA ASP SEQRES 49 A 877 GLY LEU PRO VAL VAL ILE SER GLY THR GLU LYS MET SER SEQRES 50 A 877 LYS SER LYS ASN ASN GLY VAL ASP PRO GLN GLU LEU ILE SEQRES 51 A 877 ASN ALA TYR GLY ALA ASP THR ALA ARG LEU PHE MET MET SEQRES 52 A 877 PHE ALA ALA PRO PRO GLU GLN SER LEU GLU TRP SER ASP SEQRES 53 A 877 SER GLY VAL GLU GLY ALA HIS ARG PHE LEU ARG ARG LEU SEQRES 54 A 877 TRP ARG THR VAL TYR GLU TYR LEU LYS GLN GLY GLY ALA SEQRES 55 A 877 VAL LYS ALA PHE ALA GLY ASN GLN ASP GLY LEU SER LYS SEQRES 56 A 877 GLU LEU LYS ASP LEU ARG HIS LYS LEU HIS SER THR THR SEQRES 57 A 877 ALA LYS VAL SER ASP ASP TYR GLY ARG ARG GLN GLN PHE SEQRES 58 A 877 ASN THR ALA ILE ALA ALA VAL MET GLU LEU LEU ASN GLN SEQRES 59 A 877 TYR ASP LYS THR ASP THR GLY SER GLU GLN GLY ARG ALA SEQRES 60 A 877 VAL ALA GLN GLU VAL LEU GLU ALA ALA VAL ARG LEU LEU SEQRES 61 A 877 TRP PRO ILE VAL PRO HIS ILE CYS GLU THR LEU TRP SER SEQRES 62 A 877 GLU LEU ASN GLY ALA LYS LEU TRP GLU ALA GLY TRP PRO SEQRES 63 A 877 THR VAL ASP GLU ALA ALA LEU VAL LYS SER GLU ILE GLU SEQRES 64 A 877 VAL MET VAL GLN VAL ASN GLY LYS LEU ARG GLY LYS ILE SEQRES 65 A 877 THR VAL ALA ALA ASP ALA SER LYS ALA ASP LEU GLU ALA SEQRES 66 A 877 ALA ALA LEU ALA ASN GLU GLY ALA VAL LYS PHE MET GLU SEQRES 67 A 877 GLY LYS PRO ALA LYS LYS ILE ILE VAL VAL PRO GLY ARG SEQRES 68 A 877 LEU VAL ASN ILE VAL VAL HET EDO A1001 4 HET ATP A1002 31 HET MG A1003 1 HET DCL A1004 8 HET EDO A1005 4 HET ZN A1006 1 HET MG A1007 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM DCL 2-AMINO-4-METHYL-PENTAN-1-OL HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL HETSYN DCL LEUCINOL FORMUL 2 EDO 2(C2 H6 O2) FORMUL 3 ATP C10 H16 N5 O13 P3 FORMUL 4 MG 2(MG 2+) FORMUL 5 DCL C6 H15 N O FORMUL 7 ZN ZN 2+ FORMUL 9 HOH *148(H2 O) HELIX 1 AA1 GLN A 6 ARG A 22 1 17 HELIX 2 AA2 HIS A 49 ASN A 69 1 21 HELIX 3 AA3 GLY A 83 ASN A 93 1 11 HELIX 4 AA4 ALA A 96 SER A 114 1 19 HELIX 5 AA5 ASP A 120 GLU A 124 5 5 HELIX 6 AA6 LYS A 129 LYS A 146 1 18 HELIX 7 AA7 ALA A 167 GLU A 169 5 3 HELIX 8 AA8 ILE A 195 ASP A 197 5 3 HELIX 9 AA9 TYR A 198 ASP A 205 1 8 HELIX 10 AB1 PRO A 213 GLY A 225 1 13 HELIX 11 AB2 GLY A 246 LYS A 250 1 5 HELIX 12 AB3 ARG A 258 ALA A 265 5 8 HELIX 13 AB4 HIS A 274 ALA A 282 1 9 HELIX 14 AB5 LYS A 284 CYS A 294 1 11 HELIX 15 AB6 ASP A 351 TYR A 361 1 11 HELIX 16 AB7 GLN A 382 ASP A 387 5 6 HELIX 17 AB8 SER A 396 ASP A 400 5 5 HELIX 18 AB9 ASP A 403 GLY A 419 1 17 HELIX 19 AC1 PRO A 458 LEU A 462 5 5 HELIX 20 AC2 SER A 477 LYS A 481 5 5 HELIX 21 AC3 MET A 482 TYR A 486 1 5 HELIX 22 AC4 ILE A 508 SER A 511 5 4 HELIX 23 AC5 TRP A 512 TYR A 517 1 6 HELIX 24 AC6 SER A 528 GLY A 536 1 9 HELIX 25 AC7 GLY A 544 ALA A 548 5 5 HELIX 26 AC8 GLY A 550 GLY A 566 1 17 HELIX 27 AC9 ASN A 601 ALA A 603 5 3 HELIX 28 AD1 ASP A 644 GLY A 653 1 10 HELIX 29 AD2 GLY A 653 ALA A 664 1 12 HELIX 30 AD3 ASP A 675 GLN A 698 1 24 HELIX 31 AD4 SER A 713 ARG A 736 1 24 HELIX 32 AD5 PHE A 740 LYS A 756 1 17 HELIX 33 AD6 SER A 761 TRP A 780 1 20 HELIX 34 AD7 VAL A 783 ASN A 795 1 13 HELIX 35 AD8 LYS A 798 GLY A 803 1 6 HELIX 36 AD9 ASP A 808 VAL A 813 5 6 HELIX 37 AE1 SER A 838 LEU A 847 1 10 SHEET 1 AA1 4 ASN A 72 MET A 74 0 SHEET 2 AA1 4 LYS A 34 SER A 39 1 N TYR A 35 O MET A 74 SHEET 3 AA1 4 VAL A 538 ILE A 542 1 O GLN A 540 N LEU A 38 SHEET 4 AA1 4 PHE A 574 LEU A 578 1 O GLU A 575 N VAL A 538 SHEET 1 AA2 3 VAL A 149 LYS A 152 0 SHEET 2 AA2 3 MET A 190 PHE A 193 -1 O TYR A 192 N TYR A 150 SHEET 3 AA2 3 TRP A 432 GLY A 433 -1 O TRP A 432 N PHE A 193 SHEET 1 AA3 3 THR A 164 LEU A 166 0 SHEET 2 AA3 3 THR A 155 ASP A 159 -1 N ASP A 159 O THR A 164 SHEET 3 AA3 3 GLU A 184 GLU A 187 -1 O ARG A 186 N VAL A 156 SHEET 1 AA4 2 VAL A 171 ILE A 172 0 SHEET 2 AA4 2 ARG A 175 GLY A 176 -1 O ARG A 175 N ILE A 172 SHEET 1 AA5 6 PHE A 251 THR A 256 0 SHEET 2 AA5 6 LYS A 226 VAL A 236 -1 N PHE A 234 O LEU A 252 SHEET 3 AA5 6 GLY A 311 VAL A 319 -1 O VAL A 319 N ALA A 235 SHEET 4 AA5 6 LYS A 326 ALA A 332 -1 O LEU A 327 N VAL A 318 SHEET 5 AA5 6 TYR A 267 VAL A 270 1 N VAL A 270 O TRP A 330 SHEET 6 AA5 6 ALA A 343 ALA A 346 -1 O VAL A 344 N ALA A 269 SHEET 1 AA6 3 PHE A 251 THR A 256 0 SHEET 2 AA6 3 LYS A 226 VAL A 236 -1 N PHE A 234 O LEU A 252 SHEET 3 AA6 3 GLY A 421 TYR A 427 -1 O GLU A 422 N THR A 231 SHEET 1 AA7 2 ILE A 369 ALA A 370 0 SHEET 2 AA7 2 VAL A 392 LEU A 393 -1 O VAL A 392 N ALA A 370 SHEET 1 AA8 2 SER A 435 ARG A 436 0 SHEET 2 AA8 2 THR A 503 MET A 504 -1 O THR A 503 N ARG A 436 SHEET 1 AA9 4 GLY A 453 PRO A 456 0 SHEET 2 AA9 4 ILE A 446 CYS A 449 -1 N CYS A 449 O GLY A 453 SHEET 3 AA9 4 ALA A 496 ARG A 499 -1 O LYS A 498 N HIS A 448 SHEET 4 AA9 4 GLU A 487 SER A 489 -1 N THR A 488 O ALA A 497 SHEET 1 AB1 3 GLU A 633 LYS A 634 0 SHEET 2 AB1 3 VAL A 583 CYS A 585 -1 N CYS A 585 O GLU A 633 SHEET 3 AB1 3 LEU A 671 GLU A 672 1 O LEU A 671 N VAL A 584 SHEET 1 AB2 3 LYS A 597 ILE A 600 0 SHEET 2 AB2 3 TYR A 588 GLU A 591 -1 N ARG A 590 O ASP A 598 SHEET 3 AB2 3 VAL A 628 ILE A 629 -1 O VAL A 628 N TYR A 589 SHEET 1 AB3 2 VAL A 605 PHE A 609 0 SHEET 2 AB3 2 PRO A 615 LEU A 620 -1 O VAL A 616 N THR A 608 SHEET 1 AB4 4 LYS A 826 ALA A 834 0 SHEET 2 AB4 4 GLU A 816 VAL A 823 -1 N VAL A 821 O GLY A 829 SHEET 3 AB4 4 LEU A 871 VAL A 875 1 O ILE A 874 N GLN A 822 SHEET 4 AB4 4 LYS A 863 VAL A 866 -1 N ILE A 865 O ASN A 873 LINK SG CYS A 449 ZN ZN A1006 1555 1555 2.33 LINK SG CYS A 452 ZN ZN A1006 1555 1555 2.66 LINK SG CYS A 490 ZN ZN A1006 1555 1555 2.37 LINK SG CYS A 493 ZN ZN A1006 1555 1555 2.59 LINK O2G ATP A1002 MG MG A1003 1555 1555 2.19 LINK O2B ATP A1002 MG MG A1003 1555 1555 2.59 LINK O2A ATP A1002 MG MG A1003 1555 1555 2.09 LINK MG MG A1003 O HOH A1121 1555 1555 2.13 LINK MG MG A1003 O HOH A1126 1555 1555 2.17 LINK MG MG A1003 O HOH A1219 1555 1555 2.75 LINK MG MG A1007 O HOH A1210 1555 1555 2.19 LINK MG MG A1007 O HOH A1236 1555 3554 2.02 CISPEP 1 LEU A 462 PRO A 463 0 9.03 CRYST1 48.912 81.588 216.971 90.00 90.00 90.00 P 21 21 21 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 0.020445 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012257 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004609 0.00000