HEADER TRANSFERASE 26-SEP-15 5DZT TITLE CRYSTAL STRUCTURE OF CLASS II LANTHIPEPTIDE SYNTHETASE CYLM IN COMPLEX TITLE 2 WITH AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYLM; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EF0046; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_TAXID: 1351; SOURCE 4 GENE: EF0046, CYLM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYTOLYSIN, LANTHIPEPTIDE SYNTHETASE, KINASE, CYLM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.H.DONG,T.LUKK,S.K.NAIR REVDAT 4 06-MAR-24 5DZT 1 REMARK REVDAT 3 25-DEC-19 5DZT 1 REMARK REVDAT 2 27-SEP-17 5DZT 1 REMARK REVDAT 1 14-OCT-15 5DZT 0 JRNL AUTH S.H.DONG,W.TANG,T.LUKK,Y.YU,S.K.NAIR,W.A.VAN DER DONK JRNL TITL THE ENTEROCOCCAL CYTOLYSIN SYNTHETASE HAS AN UNANTICIPATED JRNL TITL 2 LIPID KINASE FOLD. JRNL REF ELIFE V. 4 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26226635 JRNL DOI 10.7554/ELIFE.07607 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 3 NUMBER OF REFLECTIONS : 49239 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2636 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1742 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 42.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7251 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.50000 REMARK 3 B22 (A**2) : -0.13000 REMARK 3 B33 (A**2) : -0.37000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.353 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.250 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.169 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.744 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7423 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10032 ; 1.308 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 880 ; 5.780 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 362 ;38.163 ;25.304 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1367 ;17.388 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.214 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1117 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5524 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5DZT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000214086. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51875 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: SHELXD, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CACL, 0.1 M HEPES, PH 7.5, 10 MM REMARK 280 BETAINE HYDROCHLORIDE, AND 28% PEG 400; 0.2 M KCL, 0.05 M HEPES REMARK 280 PH7.5, 10 MM BARIUM CHLORIDE, AND 33% 5/4 PO/OH, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 25.59550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 123.18050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.34950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 123.18050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.59550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.34950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 0 REMARK 465 GLU A 1 REMARK 465 ASP A 2 REMARK 465 THR A 163 REMARK 465 PHE A 164 REMARK 465 LYS A 165 REMARK 465 LYS A 166 REMARK 465 ASN A 167 REMARK 465 GLU A 168 REMARK 465 PRO A 169 REMARK 465 LEU A 170 REMARK 465 LYS A 171 REMARK 465 GLY A 172 REMARK 465 ASN A 173 REMARK 465 ASP A 174 REMARK 465 SER A 175 REMARK 465 SER A 176 REMARK 465 LYS A 177 REMARK 465 TYR A 401 REMARK 465 LEU A 402 REMARK 465 ALA A 403 REMARK 465 MET A 404 REMARK 465 LYS A 405 REMARK 465 ASP A 406 REMARK 465 LYS A 407 REMARK 465 SER A 408 REMARK 465 ASP A 409 REMARK 465 SER A 410 REMARK 465 LYS A 411 REMARK 465 ASP A 412 REMARK 465 GLU A 413 REMARK 465 GLY A 414 REMARK 465 VAL A 415 REMARK 465 ASN A 416 REMARK 465 LEU A 417 REMARK 465 SER A 418 REMARK 465 ALA A 419 REMARK 465 LEU A 420 REMARK 465 ASN A 421 REMARK 465 PHE A 422 REMARK 465 LYS A 423 REMARK 465 GLU A 424 REMARK 465 GLN A 425 REMARK 465 SER A 426 REMARK 465 VAL A 427 REMARK 465 PRO A 428 REMARK 465 PHE A 429 REMARK 465 LYS A 430 REMARK 465 ILE A 431 REMARK 465 LEU A 432 REMARK 465 LYS A 433 REMARK 465 ILE A 434 REMARK 465 LYS A 435 REMARK 465 ASN A 436 REMARK 465 THR A 437 REMARK 465 PHE A 438 REMARK 465 THR A 439 REMARK 465 ASP A 440 REMARK 465 GLU A 441 REMARK 465 MET A 442 REMARK 465 ARG A 443 REMARK 465 PHE A 444 REMARK 465 GLU A 445 REMARK 465 TYR A 446 REMARK 465 GLN A 447 REMARK 465 THR A 448 REMARK 465 HIS A 449 REMARK 465 ILE A 450 REMARK 465 MET A 451 REMARK 465 ASP A 452 REMARK 465 THR A 453 REMARK 465 ALA A 454 REMARK 465 LEU A 773 REMARK 465 ILE A 774 REMARK 465 GLU A 775 REMARK 465 LYS A 776 REMARK 465 LYS A 777 REMARK 465 PRO A 778 REMARK 465 ILE A 779 REMARK 465 ASN A 780 REMARK 465 ASN A 781 REMARK 465 GLY A 782 REMARK 465 GLU A 783 REMARK 465 LEU A 784 REMARK 465 LYS A 785 REMARK 465 ASN A 786 REMARK 465 GLU A 862 REMARK 465 SER A 863 REMARK 465 TYR A 864 REMARK 465 PHE A 865 REMARK 465 GLU A 866 REMARK 465 GLU A 867 REMARK 465 GLU A 868 REMARK 465 PRO A 869 REMARK 465 LYS A 870 REMARK 465 ILE A 886 REMARK 465 GLU A 887 REMARK 465 LEU A 888 REMARK 465 TYR A 889 REMARK 465 ASP A 890 REMARK 465 ASP A 891 REMARK 465 ASN A 892 REMARK 465 ILE A 893 REMARK 465 SER A 894 REMARK 465 ASN A 895 REMARK 465 ILE A 896 REMARK 465 LEU A 993 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 ASP A 159 CG OD1 OD2 REMARK 470 ARG A 178 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 179 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE A 180 CG1 CG2 CD1 REMARK 470 TYR A 181 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR A 182 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 183 CG CD1 CD2 REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 LYS A 185 CG CD CE NZ REMARK 470 LYS A 716 CG CD CE NZ REMARK 470 TYR A 719 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR A 827 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 PHE A 847 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 848 CG OD1 ND2 REMARK 470 ARG A 849 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 851 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1124 O HOH A 1175 1.77 REMARK 500 N ILE A 459 O HOH A 1101 1.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1124 O HOH A 1209 4456 1.96 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 ASP A 561 CB ASP A 561 CG 0.179 REMARK 500 ASP A 561 CG ASP A 561 OD2 0.154 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 PRO A 458 C - N - CA ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP A 561 CB - CG - OD1 ANGL. DEV. = -16.7 DEGREES REMARK 500 ASP A 561 CB - CG - OD2 ANGL. DEV. = 11.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 4 -39.16 -36.11 REMARK 500 GLU A 23 -33.65 -163.99 REMARK 500 ASP A 26 -31.99 -38.95 REMARK 500 ILE A 27 -36.09 72.38 REMARK 500 LYS A 37 109.51 -59.63 REMARK 500 PRO A 65 -158.65 -69.84 REMARK 500 ILE A 66 -88.83 -64.11 REMARK 500 ASN A 68 7.80 -66.66 REMARK 500 SER A 98 -64.37 -165.35 REMARK 500 GLU A 99 68.93 65.28 REMARK 500 GLU A 100 -2.75 -164.55 REMARK 500 VAL A 105 95.11 -65.18 REMARK 500 ALA A 107 -11.32 107.51 REMARK 500 ARG A 256 51.88 74.36 REMARK 500 HIS A 349 102.88 73.08 REMARK 500 ASN A 352 -19.52 118.13 REMARK 500 ASN A 379 67.26 -116.51 REMARK 500 ILE A 459 115.32 60.18 REMARK 500 ASN A 462 7.92 54.69 REMARK 500 GLN A 634 -164.79 61.29 REMARK 500 ASN A 635 -80.66 -117.99 REMARK 500 LYS A 638 150.18 74.08 REMARK 500 GLN A 683 -40.49 70.61 REMARK 500 ASN A 691 -169.95 -114.81 REMARK 500 ILE A 711 -96.68 -73.34 REMARK 500 LYS A 716 -51.77 74.86 REMARK 500 PRO A 732 95.62 -43.87 REMARK 500 ILE A 736 141.85 -30.95 REMARK 500 PHE A 741 126.07 75.11 REMARK 500 ASN A 758 -74.49 -61.61 REMARK 500 ASP A 759 82.31 25.04 REMARK 500 HIS A 790 -21.77 73.07 REMARK 500 GLU A 807 -13.93 62.94 REMARK 500 GLU A 809 6.47 -68.83 REMARK 500 ARG A 831 72.09 -116.27 REMARK 500 PHE A 847 36.97 -84.44 REMARK 500 ASN A 848 -36.25 57.44 REMARK 500 ARG A 849 67.57 -68.45 REMARK 500 ASP A 851 -55.66 72.65 REMARK 500 ILE A 860 -32.42 -142.45 REMARK 500 ASN A 872 -25.82 56.14 REMARK 500 LYS A 876 -138.35 -109.53 REMARK 500 HIS A 912 50.26 -158.93 REMARK 500 ASP A 928 80.16 -150.87 REMARK 500 ASP A 982 108.06 -165.55 REMARK 500 PHE A 991 89.83 62.13 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 875 SG REMARK 620 2 CYS A 911 SG 116.9 REMARK 620 3 HIS A 912 ND1 117.9 112.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP A 1002 DBREF 5DZT A 0 993 UNP Q8KUA3 Q8KUA3_ENTFL 1 993 SEQRES 1 A 993 MET GLU ASP ASN LEU ILE ASN VAL LEU SER ILE ASN GLU SEQRES 2 A 993 ARG CYS PHE LEU LEU LYS GLN SER GLY ASN GLU LYS TYR SEQRES 3 A 993 ASP ILE LYS ASN LEU GLN ALA TRP LYS GLU ARG LYS SER SEQRES 4 A 993 VAL LEU LYS GLN ASP ASP LEU ASP TYR LEU ILE LYS TYR SEQRES 5 A 993 LYS TYR GLU SER LEU ASP ASN PHE GLY LEU GLY ILE THR SEQRES 6 A 993 PRO ILE GLU ASN PHE PRO ASP LYS GLU VAL ALA ILE GLN SEQRES 7 A 993 TYR ILE LYS ASP GLN SER TRP TYR ILE PHE PHE GLU SER SEQRES 8 A 993 ILE LEU ASP SER TYR ASN ASP SER GLU GLU GLN LEU LEU SEQRES 9 A 993 GLU VAL ASP ALA SER TYR PRO PHE ARG TYR PHE LEU GLN SEQRES 10 A 993 TYR ALA ARG LEU PHE LEU LEU ASP LEU ASN SER GLU LEU SEQRES 11 A 993 ASN ILE CYS THR LYS GLU PHE ILE ILE ASN LEU LEU GLU SEQRES 12 A 993 ILE LEU THR GLN GLU LEU ILE HIS LEU THR SER LYS THR SEQRES 13 A 993 LEU VAL LEU ASP LEU HIS THR PHE LYS LYS ASN GLU PRO SEQRES 14 A 993 LEU LYS GLY ASN ASP SER SER LYS ARG PHE ILE TYR TYR SEQRES 15 A 993 LEU LYS LYS ARG PHE ASN SER LYS LYS ASP ILE ILE ALA SEQRES 16 A 993 PHE TYR THR CYS TYR PRO GLU LEU MET ARG ILE THR VAL SEQRES 17 A 993 VAL ARG MET ARG TYR PHE LEU ASP ASN THR LYS GLN MET SEQRES 18 A 993 LEU ILE ARG VAL THR GLU ASP LEU PRO SER ILE GLN ASN SEQRES 19 A 993 CYS PHE ASN ILE GLN SER SER GLU LEU ASN SER ILE SER SEQRES 20 A 993 GLU SER GLN GLY ASP SER HIS SER ARG GLY LYS THR VAL SEQRES 21 A 993 SER THR LEU THR PHE SER ASP GLY LYS LYS ILE VAL TYR SEQRES 22 A 993 LYS PRO LYS ILE ASN SER GLU ASN LYS LEU ARG ASP PHE SEQRES 23 A 993 PHE GLU PHE LEU ASN LYS GLU LEU GLU ALA ASP ILE TYR SEQRES 24 A 993 ILE VAL LYS LYS VAL THR ARG ASN THR TYR PHE TYR GLU SEQRES 25 A 993 GLU TYR ILE ASP ASN ILE GLU ILE ASN ASN ILE GLU GLU SEQRES 26 A 993 VAL LYS LYS TYR TYR GLU ARG TYR GLY LYS LEU ILE GLY SEQRES 27 A 993 ILE ALA PHE LEU PHE ASN VAL THR ASP LEU HIS TYR GLU SEQRES 28 A 993 ASN ILE ILE ALA HIS GLY GLU TYR PRO VAL ILE ILE ASP SEQRES 29 A 993 ASN GLU THR PHE PHE GLN GLN ASN ILE PRO ILE GLU PHE SEQRES 30 A 993 GLY ASN SER ALA THR VAL ASP ALA LYS TYR LYS TYR LEU SEQRES 31 A 993 ASP SER ILE MET VAL THR GLY LEU VAL PRO TYR LEU ALA SEQRES 32 A 993 MET LYS ASP LYS SER ASP SER LYS ASP GLU GLY VAL ASN SEQRES 33 A 993 LEU SER ALA LEU ASN PHE LYS GLU GLN SER VAL PRO PHE SEQRES 34 A 993 LYS ILE LEU LYS ILE LYS ASN THR PHE THR ASP GLU MET SEQRES 35 A 993 ARG PHE GLU TYR GLN THR HIS ILE MET ASP THR ALA LYS SEQRES 36 A 993 ASN THR PRO ILE MET ASN ASN GLU LYS ILE SER PHE ILE SEQRES 37 A 993 SER TYR GLU LYS TYR ILE VAL THR GLY MET LYS SER ILE SEQRES 38 A 993 LEU MET LYS ALA LYS ASP SER LYS LYS LYS ILE LEU ALA SEQRES 39 A 993 TYR ILE ASN ASN ASN LEU GLN ASN LEU ILE VAL ARG ASN SEQRES 40 A 993 VAL ILE ARG PRO THR GLN ARG TYR ALA ASP MET LEU GLU SEQRES 41 A 993 PHE SER TYR HIS PRO ASN CYS PHE SER ASN ALA ILE GLU SEQRES 42 A 993 ARG GLU LYS VAL LEU HIS ASN MET TRP ALA TYR PRO TYR SEQRES 43 A 993 LYS ASN LYS LYS VAL VAL HIS TYR GLU PHE SER ASP LEU SEQRES 44 A 993 ILE ASP GLY ASP ILE PRO ILE PHE TYR ASN ASN ILE SER SEQRES 45 A 993 LYS THR SER LEU ILE ALA SER ASP GLY CYS LEU VAL GLU SEQRES 46 A 993 ASP PHE TYR GLN GLU SER ALA LEU ASN ARG CYS LEU ASN SEQRES 47 A 993 LYS ILE ASN ASP LEU CYS ASP GLU ASP ILE SER ILE GLN SEQRES 48 A 993 THR VAL TRP LEU GLU ILE ALA LEU ASN ILE TYR ASN PRO SEQRES 49 A 993 TYR LYS TYR ILE ASN ASP LEU LYS ASN GLN ASN SER ASN SEQRES 50 A 993 LYS TYR ILE TYR THR GLY LEU GLU LEU ASN GLY LYS ILE SEQRES 51 A 993 ILE GLN ALA CYS GLN LYS ILE GLU LYS LYS ILE PHE LYS SEQRES 52 A 993 ARG ALA ILE PHE ASN LYS LYS THR ASN THR VAL ASN TRP SEQRES 53 A 993 ILE ASP ILE LYS LEU ASP GLN ASP TRP ASN VAL GLY ILE SEQRES 54 A 993 LEU ASN ASN ASN MET TYR ASP GLY LEU PRO GLY ILE PHE SEQRES 55 A 993 ILE PHE TYR VAL ALA LEU LYS TYR ILE THR LYS ASN HIS SEQRES 56 A 993 LYS TYR ASP TYR VAL ILE GLU CYS ILE LYS ASN SER ILE SEQRES 57 A 993 TYR THR ILE PRO SER GLU ASP ILE LEU SER ALA PHE PHE SEQRES 58 A 993 GLY LYS GLY SER LEU ILE TYR PRO LEU LEU VAL ASP TYR SEQRES 59 A 993 ARG LEU ASN ASN ASP ILE ASN SER LEU ASN VAL ALA VAL SEQRES 60 A 993 GLU ILE ALA ASP MET LEU ILE GLU LYS LYS PRO ILE ASN SEQRES 61 A 993 ASN GLY GLU LEU LYS ASN ASP TRP ILE HIS GLY HIS ASN SEQRES 62 A 993 SER ILE ILE LYS VAL LEU LEU LEU LEU SER GLU ILE THR SEQRES 63 A 993 GLU ASP GLU LYS TYR ARG LYS PHE SER LEU GLU ILE PHE SEQRES 64 A 993 GLU LYS LEU SER GLU GLU PRO TYR PHE ASN PHE ARG GLY SEQRES 65 A 993 PHE GLY HIS GLY ILE TYR SER TYR VAL HIS LEU LEU SER SEQRES 66 A 993 LYS PHE ASN ARG ILE ASP LYS ALA ASN SER LEU LEU HIS SEQRES 67 A 993 LYS ILE LYS GLU SER TYR PHE GLU GLU GLU PRO LYS ASN SEQRES 68 A 993 ASN SER TRP CYS LYS GLY THR VAL GLY GLU LEU LEU ALA SEQRES 69 A 993 THR ILE GLU LEU TYR ASP ASP ASN ILE SER ASN ILE ASP SEQRES 70 A 993 ILE ASN LYS THR ILE GLU TYR LYS ASN LYS ASP CYS LEU SEQRES 71 A 993 CYS HIS GLY ASN ALA GLY THR LEU GLU GLY LEU ILE GLN SEQRES 72 A 993 LEU ALA LYS LYS ASP PRO GLU THR TYR GLN TYR LYS LYS SEQRES 73 A 993 ASN LYS LEU ILE SER TYR MET LEU LYS TYR PHE GLU LYS SEQRES 74 A 993 ASN ASN THR LEU LYS VAL ALA GLY SER GLU TYR LEU GLU SEQRES 75 A 993 SER LEU GLY PHE PHE VAL GLY ILE SER GLY VAL GLY TYR SEQRES 76 A 993 GLU LEU LEU ARG ASN LEU ASP SER GLU ILE PRO ASN ALA SEQRES 77 A 993 LEU LEU PHE GLU LEU HET ZN A1001 1 HET AMP A1002 23 HETNAM ZN ZINC ION HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 ZN ZN 2+ FORMUL 3 AMP C10 H14 N5 O7 P FORMUL 4 HOH *160(H2 O) HELIX 1 AA1 ASN A 3 LEU A 8 5 6 HELIX 2 AA2 SER A 9 SER A 20 1 12 HELIX 3 AA3 ILE A 27 GLU A 35 1 9 HELIX 4 AA4 LYS A 41 TYR A 53 1 13 HELIX 5 AA5 SER A 55 ILE A 63 1 9 HELIX 6 AA6 ASP A 71 ASP A 81 1 11 HELIX 7 AA7 GLN A 82 TYR A 95 1 14 HELIX 8 AA8 SER A 108 PRO A 110 5 3 HELIX 9 AA9 PHE A 111 ASN A 130 1 20 HELIX 10 AB1 THR A 133 ASP A 159 1 27 HELIX 11 AB2 LEU A 160 HIS A 161 5 2 HELIX 12 AB3 ARG A 178 ARG A 178 5 1 HELIX 13 AB4 PHE A 179 PHE A 187 1 9 HELIX 14 AB5 SER A 189 TYR A 200 1 12 HELIX 15 AB6 TYR A 200 ASN A 237 1 38 HELIX 16 AB7 SER A 279 LEU A 294 1 16 HELIX 17 AB8 ASN A 322 PHE A 343 1 22 HELIX 18 AB9 SER A 380 LYS A 388 1 9 HELIX 19 AC1 SER A 392 GLY A 397 5 6 HELIX 20 AC2 TYR A 470 ASP A 487 1 18 HELIX 21 AC3 SER A 488 LEU A 500 1 13 HELIX 22 AC4 PRO A 511 SER A 522 1 12 HELIX 23 AC5 HIS A 524 ASN A 530 1 7 HELIX 24 AC6 ASN A 530 ASN A 540 1 11 HELIX 25 AC7 MET A 541 TYR A 544 5 4 HELIX 26 AC8 ASN A 548 LYS A 550 5 3 HELIX 27 AC9 VAL A 551 ASP A 561 1 11 HELIX 28 AD1 SER A 591 ASP A 602 1 12 HELIX 29 AD2 CYS A 604 LEU A 619 1 16 HELIX 30 AD3 TYR A 625 ASP A 630 1 6 HELIX 31 AD4 THR A 642 ARG A 664 1 23 HELIX 32 AD5 GLY A 697 THR A 712 1 16 HELIX 33 AD6 TYR A 717 THR A 730 1 14 HELIX 34 AD7 GLY A 742 SER A 745 5 4 HELIX 35 AD8 LEU A 746 ASN A 757 1 12 HELIX 36 AD9 ASP A 759 MET A 772 1 14 HELIX 37 AE1 HIS A 792 GLU A 807 1 16 HELIX 38 AE2 GLU A 809 LEU A 822 1 14 HELIX 39 AE3 ILE A 837 SER A 845 1 9 HELIX 40 AE4 ASP A 851 LYS A 859 1 9 HELIX 41 AE5 LYS A 876 THR A 885 1 10 HELIX 42 AE6 ILE A 898 ILE A 902 1 5 HELIX 43 AE7 GLY A 913 ASP A 928 1 16 HELIX 44 AE8 ASP A 928 ASN A 951 1 24 HELIX 45 AE9 GLY A 969 ASP A 982 1 14 HELIX 46 AF1 ASN A 987 PHE A 991 5 5 SHEET 1 AA1 5 LEU A 243 SER A 247 0 SHEET 2 AA1 5 SER A 261 PHE A 265 -1 O THR A 264 N ASN A 244 SHEET 3 AA1 5 LYS A 270 LYS A 274 -1 O TYR A 273 N SER A 261 SHEET 4 AA1 5 PHE A 310 GLU A 313 -1 O PHE A 310 N LYS A 274 SHEET 5 AA1 5 LYS A 303 THR A 305 -1 N VAL A 304 O TYR A 311 SHEET 1 AA2 2 ILE A 354 HIS A 356 0 SHEET 2 AA2 2 TYR A 359 VAL A 361 -1 O TYR A 359 N HIS A 356 SHEET 1 AA3 2 ILE A 504 ARG A 506 0 SHEET 2 AA3 2 TYR A 568 ASN A 570 -1 O ASN A 569 N VAL A 505 SHEET 1 AA4 2 LEU A 576 ILE A 577 0 SHEET 2 AA4 2 LEU A 583 VAL A 584 -1 O VAL A 584 N LEU A 576 SHEET 1 AA5 2 ILE A 666 ASN A 668 0 SHEET 2 AA5 2 THR A 673 ASN A 675 -1 O THR A 673 N ASN A 668 SHEET 1 AA6 2 ILE A 677 LEU A 681 0 SHEET 2 AA6 2 TRP A 685 ILE A 689 -1 O ASN A 686 N LYS A 680 SHEET 1 AA7 2 GLY A 957 SER A 958 0 SHEET 2 AA7 2 LEU A 961 GLU A 962 -1 O LEU A 961 N SER A 958 LINK SG CYS A 875 ZN ZN A1001 1555 1555 2.40 LINK SG CYS A 911 ZN ZN A1001 1555 1555 2.18 LINK ND1 HIS A 912 ZN ZN A1001 1555 1555 2.09 CISPEP 1 THR A 712 LYS A 713 0 4.94 SITE 1 AC1 3 CYS A 875 CYS A 911 HIS A 912 SITE 1 AC2 11 GLN A 250 VAL A 260 VAL A 272 LYS A 274 SITE 2 AC2 11 LYS A 276 GLU A 312 GLU A 313 TYR A 314 SITE 3 AC2 11 ILE A 315 ASP A 364 HOH A1103 CRYST1 51.191 90.699 246.361 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 0.019535 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004059 0.00000