HEADER LIGASE 11-MAR-21 7NU0 TITLE CRYSTAL STRUCTURE OF NEISSERIA GONORRHOEAE LEURS L550A 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2 PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETRUK KEYWDS PROTEIN-LIGAND COMPLEX, ROSSMANN FOLD, TRNA SYNTHETASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR L.PANG,S.V.STRELKOV,S.D.WEEKS REVDAT 3 31-JAN-24 7NU0 1 REMARK REVDAT 2 15-NOV-23 7NU0 1 ATOM REVDAT 1 28-SEP-22 7NU0 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. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 69540 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2149 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 53.9300 - 4.6600 1.00 4801 167 0.1785 0.1879 REMARK 3 2 4.6600 - 3.7000 1.00 4571 148 0.1524 0.2153 REMARK 3 3 3.7000 - 3.2300 1.00 4545 141 0.1802 0.2288 REMARK 3 4 3.2300 - 2.9400 1.00 4536 147 0.1902 0.2016 REMARK 3 5 2.9400 - 2.7300 1.00 4489 125 0.1891 0.1973 REMARK 3 6 2.7300 - 2.5700 1.00 4462 149 0.1778 0.1943 REMARK 3 7 2.5700 - 2.4400 1.00 4489 125 0.1775 0.2007 REMARK 3 8 2.4400 - 2.3300 1.00 4468 140 0.1805 0.2300 REMARK 3 9 2.3300 - 2.2400 1.00 4462 163 0.1831 0.2417 REMARK 3 10 2.2400 - 2.1600 1.00 4437 134 0.1878 0.2707 REMARK 3 11 2.1600 - 2.1000 1.00 4442 130 0.1915 0.2188 REMARK 3 12 2.1000 - 2.0400 1.00 4425 143 0.1925 0.2670 REMARK 3 13 2.0400 - 1.9800 1.00 4426 151 0.1921 0.2246 REMARK 3 14 1.9800 - 1.9300 1.00 4408 141 0.2111 0.2432 REMARK 3 15 1.9300 - 1.8900 1.00 4430 145 0.2332 0.2719 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.93 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 : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 274 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5543 -5.9128 -27.9878 REMARK 3 T TENSOR REMARK 3 T11: 0.1817 T22: 0.2282 REMARK 3 T33: 0.2104 T12: 0.0142 REMARK 3 T13: -0.0191 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.5002 L22: 0.9156 REMARK 3 L33: 0.7360 L12: 0.1598 REMARK 3 L13: 0.3337 L23: 0.2694 REMARK 3 S TENSOR REMARK 3 S11: -0.0456 S12: 0.0135 S13: 0.0130 REMARK 3 S21: 0.1031 S22: 0.0212 S23: -0.0173 REMARK 3 S31: -0.0547 S32: 0.0225 S33: 0.0127 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 275 THROUGH 449 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.2075 24.6891 -16.0921 REMARK 3 T TENSOR REMARK 3 T11: 0.5971 T22: 0.2919 REMARK 3 T33: 0.3479 T12: 0.0549 REMARK 3 T13: -0.0014 T23: 0.0397 REMARK 3 L TENSOR REMARK 3 L11: 0.3089 L22: 1.5590 REMARK 3 L33: 0.0889 L12: -0.6849 REMARK 3 L13: 0.1158 L23: -0.3164 REMARK 3 S TENSOR REMARK 3 S11: -0.2348 S12: -0.0746 S13: 0.0069 REMARK 3 S21: 0.6124 S22: 0.2338 S23: 0.1622 REMARK 3 S31: -0.2642 S32: 0.0310 S33: 0.0004 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 450 THROUGH 876 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4969 -20.5022 -39.0542 REMARK 3 T TENSOR REMARK 3 T11: 0.1502 T22: 0.1716 REMARK 3 T33: 0.1834 T12: 0.0208 REMARK 3 T13: -0.0046 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.7957 L22: 0.6551 REMARK 3 L33: 0.5723 L12: 0.2259 REMARK 3 L13: 0.2306 L23: 0.2615 REMARK 3 S TENSOR REMARK 3 S11: 0.0346 S12: 0.0618 S13: -0.0001 REMARK 3 S21: 0.0527 S22: -0.0170 S23: 0.1139 REMARK 3 S31: 0.0611 S32: -0.0290 S33: -0.0534 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 7NU0 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_1292110353. 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 : 8.0 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 : 72099 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 107.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.89000 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 (%): 43.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 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 8.0, 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 24.25550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 107.85650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.72050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 107.85650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.25550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.72050 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 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 LYS A 92 CG CD CE NZ 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 ASP A 283 CG OD1 OD2 REMARK 470 LYS A 284 CG CD CE NZ REMARK 470 LYS A 295 CG CD CE NZ REMARK 470 MET A 307 CG SD CE 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 ARG A 353 NE CZ NH1 NH2 REMARK 470 PHE A 357 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 366 CG CD CE NZ REMARK 470 ASP A 377 CG OD1 OD2 REMARK 470 ASN A 379 CG OD1 ND2 REMARK 470 ARG A 380 CG CD NE CZ NH1 NH2 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 LYS A 714 CD CE NZ REMARK 470 LYS A 756 CD CE NZ REMARK 470 GLU A 762 CD OE1 OE2 REMARK 470 LYS A 814 CG CD CE NZ REMARK 470 ILE A 817 CG1 CG2 CD1 REMARK 470 GLU A 818 CD OE1 OE2 REMARK 470 LYS A 826 CG CD CE NZ REMARK 470 LEU A 827 CG CD1 CD2 REMARK 470 VAL A 833 CG1 CG2 REMARK 470 LYS A 839 CG CD CE NZ REMARK 470 GLU A 850 CG CD OE1 OE2 REMARK 470 VAL A 853 CG1 CG2 REMARK 470 LYS A 854 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 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 ASP A 373 52.45 -111.96 REMARK 500 ALA A 378 0.52 -69.81 REMARK 500 ASP A 398 0.27 -69.14 REMARK 500 ASN A 469 38.93 -97.97 REMARK 500 SER A 519 72.63 -154.12 REMARK 500 ALA A 550 -88.55 -95.00 REMARK 500 ARG A 870 -54.37 -141.01 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 115.0 REMARK 620 3 CYS A 490 SG 105.0 110.2 REMARK 620 4 CYS A 493 SG 105.5 110.7 110.1 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 89.2 REMARK 620 3 ATP A1002 O2A 96.1 86.1 REMARK 620 4 HOH A1309 O 179.5 91.0 83.4 REMARK 620 5 HOH A1381 O 91.1 178.4 92.3 88.7 REMARK 620 6 HOH A1396 O 94.4 87.7 167.7 86.1 93.9 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 A1131 O REMARK 620 2 HOH A1250 O 79.2 REMARK 620 3 HOH A1350 O 91.7 91.8 REMARK 620 4 HOH A1483 O 157.4 79.8 80.8 REMARK 620 5 HOH A1521 O 106.5 169.0 78.8 92.9 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7NTY RELATED DB: PDB REMARK 900 RELATED ID: 7NU2 RELATED DB: PDB REMARK 900 RELATED ID: 7NU3 RELATED DB: PDB DBREF 7NU0 A 1 876 UNP B4RNT1 SYL_NEIG2 1 876 SEQADV 7NU0 GLY A 0 UNP B4RNT1 EXPRESSION TAG SEQADV 7NU0 ASN A 454 UNP B4RNT1 ASP 454 CONFLICT SEQADV 7NU0 ILE A 508 UNP B4RNT1 MET 508 CONFLICT SEQADV 7NU0 ALA 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 ALA 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 *423(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 LEU A 115 1 20 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 LEU A 206 LEU A 209 5 4 HELIX 11 AB2 PRO A 213 GLY A 225 1 13 HELIX 12 AB3 GLY A 246 LYS A 250 1 5 HELIX 13 AB4 ARG A 258 ALA A 265 5 8 HELIX 14 AB5 HIS A 274 ALA A 282 1 9 HELIX 15 AB6 LYS A 284 LYS A 295 1 12 HELIX 16 AB7 ASP A 351 TYR A 361 1 11 HELIX 17 AB8 GLN A 382 ASP A 387 5 6 HELIX 18 AB9 SER A 396 ASP A 400 5 5 HELIX 19 AC1 ASP A 403 GLN A 418 1 16 HELIX 20 AC2 PRO A 458 LEU A 462 5 5 HELIX 21 AC3 PRO A 478 LYS A 481 5 4 HELIX 22 AC4 MET A 482 TYR A 486 1 5 HELIX 23 AC5 THR A 506 SER A 511 1 6 HELIX 24 AC6 TRP A 512 TYR A 517 1 6 HELIX 25 AC7 SER A 528 GLY A 536 1 9 HELIX 26 AC8 GLY A 544 ALA A 548 5 5 HELIX 27 AC9 ALA A 550 GLU A 565 1 16 HELIX 28 AD1 ASN A 601 ALA A 603 5 3 HELIX 29 AD2 SER A 636 ASN A 640 5 5 HELIX 30 AD3 ASP A 644 GLY A 653 1 10 HELIX 31 AD4 GLY A 653 ALA A 664 1 12 HELIX 32 AD5 SER A 674 GLN A 698 1 25 HELIX 33 AD6 SER A 713 ARG A 736 1 24 HELIX 34 AD7 PHE A 740 LYS A 756 1 17 HELIX 35 AD8 SER A 761 TRP A 780 1 20 HELIX 36 AD9 VAL A 783 ASN A 795 1 13 HELIX 37 AE1 LYS A 798 GLY A 803 1 6 HELIX 38 AE2 ASP A 808 VAL A 813 5 6 HELIX 39 AE3 SER A 838 LEU A 847 1 10 HELIX 40 AE4 ASN A 849 GLU A 857 1 9 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 2 GLY A 78 TRP A 79 0 SHEET 2 AA2 2 VAL A 125 ALA A 126 1 O VAL A 125 N TRP A 79 SHEET 1 AA3 3 VAL A 149 LYS A 152 0 SHEET 2 AA3 3 MET A 190 PHE A 193 -1 O TYR A 192 N TYR A 150 SHEET 3 AA3 3 TRP A 432 GLY A 433 -1 O TRP A 432 N PHE A 193 SHEET 1 AA4 3 THR A 164 LEU A 166 0 SHEET 2 AA4 3 THR A 155 ASP A 159 -1 N ASP A 159 O THR A 164 SHEET 3 AA4 3 GLU A 184 GLU A 187 -1 O GLU A 184 N TRP A 158 SHEET 1 AA5 2 VAL A 171 ILE A 172 0 SHEET 2 AA5 2 ARG A 175 GLY A 176 -1 O ARG A 175 N ILE A 172 SHEET 1 AA6 6 PHE A 251 THR A 256 0 SHEET 2 AA6 6 LYS A 226 VAL A 236 -1 N PHE A 234 O LEU A 252 SHEET 3 AA6 6 GLY A 311 VAL A 319 -1 O VAL A 319 N ALA A 235 SHEET 4 AA6 6 LYS A 326 ALA A 332 -1 O LEU A 327 N VAL A 318 SHEET 5 AA6 6 TYR A 267 VAL A 270 1 N VAL A 270 O TRP A 330 SHEET 6 AA6 6 ALA A 343 ALA A 346 -1 O VAL A 344 N ALA A 269 SHEET 1 AA7 3 PHE A 251 THR A 256 0 SHEET 2 AA7 3 LYS A 226 VAL A 236 -1 N PHE A 234 O LEU A 252 SHEET 3 AA7 3 GLY A 421 TYR A 427 -1 O GLN A 426 N SER A 227 SHEET 1 AA8 2 ILE A 369 ALA A 370 0 SHEET 2 AA8 2 VAL A 392 LEU A 393 -1 O VAL A 392 N ALA A 370 SHEET 1 AA9 2 SER A 435 ARG A 436 0 SHEET 2 AA9 2 THR A 503 MET A 504 -1 O THR A 503 N ARG A 436 SHEET 1 AB1 4 GLY A 453 PRO A 456 0 SHEET 2 AB1 4 ILE A 446 CYS A 449 -1 N VAL A 447 O VAL A 455 SHEET 3 AB1 4 ALA A 496 ARG A 499 -1 O LYS A 498 N HIS A 448 SHEET 4 AB1 4 GLU A 487 SER A 489 -1 N THR A 488 O ALA A 497 SHEET 1 AB2 3 GLU A 633 LYS A 634 0 SHEET 2 AB2 3 VAL A 583 CYS A 585 -1 N CYS A 585 O GLU A 633 SHEET 3 AB2 3 LEU A 671 GLU A 672 1 O LEU A 671 N VAL A 584 SHEET 1 AB3 3 LYS A 597 ILE A 600 0 SHEET 2 AB3 3 TYR A 588 GLU A 591 -1 N ARG A 590 O ASP A 598 SHEET 3 AB3 3 VAL A 628 ILE A 629 -1 O VAL A 628 N TYR A 589 SHEET 1 AB4 2 VAL A 605 THR A 608 0 SHEET 2 AB4 2 SER A 617 LEU A 620 -1 O SER A 617 N THR A 608 SHEET 1 AB5 4 LYS A 826 ALA A 834 0 SHEET 2 AB5 4 GLU A 816 VAL A 823 -1 N ILE A 817 O VAL A 833 SHEET 3 AB5 4 LEU A 871 VAL A 875 1 O ILE A 874 N GLN A 822 SHEET 4 AB5 4 LYS A 863 VAL A 867 -1 N ILE A 865 O ASN A 873 LINK SG CYS A 449 ZN ZN A1006 1555 1555 2.23 LINK SG CYS A 452 ZN ZN A1006 1555 1555 2.37 LINK SG CYS A 490 ZN ZN A1006 1555 1555 2.34 LINK SG CYS A 493 ZN ZN A1006 1555 1555 2.42 LINK O2G ATP A1002 MG MG A1003 1555 1555 2.06 LINK O2B ATP A1002 MG MG A1003 1555 1555 2.22 LINK O2A ATP A1002 MG MG A1003 1555 1555 2.08 LINK MG MG A1003 O HOH A1309 1555 1555 2.15 LINK MG MG A1003 O HOH A1381 1555 1555 2.07 LINK MG MG A1003 O HOH A1396 1555 1555 2.10 LINK MG MG A1007 O HOH A1131 1555 1555 2.11 LINK MG MG A1007 O HOH A1250 1555 1555 2.13 LINK MG MG A1007 O HOH A1350 1555 3554 2.19 LINK MG MG A1007 O HOH A1483 1555 3554 2.27 LINK MG MG A1007 O HOH A1521 1555 3554 2.03 CISPEP 1 LEU A 462 PRO A 463 0 1.30 CRYST1 48.511 81.441 215.713 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 0.020614 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012279 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004636 0.00000