HEADER LIGASE 26-APR-17 5XIL TITLE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR PROLYL-TRNA SYNTHETASE (LMPRS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE PROLYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 223-731; COMPND 5 EC: 6.1.1.5,6.1.1.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 GENE: LMJF_18_1220; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETM41 KEYWDS PROTEIN TRANSLATION, PRS, SYNTHETASE, INHIBITOR, INFECTIOUS DISEASE, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR V.JAIN,Y.MANICKAM,A.SHARMA REVDAT 2 22-NOV-23 5XIL 1 REMARK LINK REVDAT 1 07-MAR-18 5XIL 0 JRNL AUTH V.JAIN,M.YOGAVEL,H.KIKUCHI,Y.OSHIMA,N.HARIGUCHI,M.MATSUMOTO, JRNL AUTH 2 P.GOEL,B.TOUQUET,R.S.JUMANI,F.TACCHINI-COTTIER,K.HARLOS, JRNL AUTH 3 C.D.HUSTON,M.A.HAKIMI,A.SHARMA JRNL TITL TARGETING PROLYL-TRNA SYNTHETASE TO ACCELERATE DRUG JRNL TITL 2 DISCOVERY AGAINST MALARIA, LEISHMANIASIS, TOXOPLASMOSIS, JRNL TITL 3 CRYPTOSPORIDIOSIS, AND COCCIDIOSIS JRNL REF STRUCTURE V. 25 1495 2017 JRNL REFN ISSN 1878-4186 JRNL PMID 28867614 JRNL DOI 10.1016/J.STR.2017.07.015 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 41101 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2203 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2947 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 180 REMARK 3 BIN FREE R VALUE : 0.2350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3530 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 358 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : 0.41000 REMARK 3 B33 (A**2) : -0.34000 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): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.784 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3879 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3613 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5291 ; 1.824 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8322 ; 0.907 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 495 ; 6.553 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;36.884 ;23.405 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 653 ;13.530 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.081 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 565 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4423 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 915 ; 0.001 ; 0.020 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 : NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5XIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-17. REMARK 100 THE DEPOSITION ID IS D_1300003570. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.289 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MXCUBE REMARK 200 DATA SCALING SOFTWARE : HKL-2000, HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43411 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.41400 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: SHELX, SHELXD REMARK 200 STARTING MODEL: 4TWA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM ACETATE AND 20%(W/V) REMARK 280 PEG 3,350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.16350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.16350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.64700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.43050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.64700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.43050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.16350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.64700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.43050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.16350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.64700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.43050 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 75.29400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -73.16350 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 C ACT A1004 LIES ON A SPECIAL POSITION. REMARK 375 OXT ACT A1004 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 GLY A 251 REMARK 465 ALA A 252 REMARK 465 TYR A 280 REMARK 465 ASP A 281 REMARK 465 VAL A 282 REMARK 465 SER A 283 REMARK 465 GLY A 284 REMARK 465 CYS A 285 REMARK 465 MET A 318A REMARK 465 PHE A 318B REMARK 465 VAL A 318C REMARK 465 SER A 318D REMARK 465 ARG A 318E REMARK 465 SER A 318F REMARK 465 CYS A 318G REMARK 465 LEU A 318H REMARK 465 GLU A 318I REMARK 465 ARG A 318J REMARK 465 GLU A 318K REMARK 465 LYS A 318L REMARK 465 ASP A 318M REMARK 465 HIS A 318N REMARK 465 ILE A 318O REMARK 465 GLU A 318P REMARK 465 GLY A 318Q REMARK 465 PHE A 318R REMARK 465 ALA A 318S REMARK 465 PRO A 318T REMARK 465 GLU A 318U REMARK 465 VAL A 318V REMARK 465 ALA A 318W REMARK 465 TRP A 318X REMARK 465 VAL A 318Y REMARK 465 THR A 318Z REMARK 465 ARG A 319A REMARK 465 ALA A 319B REMARK 465 GLY A 319C REMARK 465 ASP A 319D REMARK 465 THR A 319E REMARK 465 GLU A 319F REMARK 465 LEU A 319G REMARK 465 GLU A 319H REMARK 465 GLN A 319I REMARK 465 PRO A 319J REMARK 465 VAL A 319K REMARK 465 ALA A 319L REMARK 465 VAL A 319M REMARK 465 ARG A 319N REMARK 465 PRO A 319O REMARK 465 ARG A 390 REMARK 465 TRP A 391 REMARK 465 GLU A 392 REMARK 465 PHE A 393 REMARK 465 SER A 394 REMARK 465 HIS A 395 REMARK 465 VAL A 705A REMARK 465 ALA A 705B REMARK 465 GLN A 705C REMARK 465 ALA A 705D REMARK 465 GLN A 705E REMARK 465 GLU A 705F REMARK 465 THR A 705G REMARK 465 ARG A 705H REMARK 465 GLU A 705I REMARK 465 ASP A 705J REMARK 465 ALA A 705K REMARK 465 ARG A 705L 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 TYR A 286 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 403 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 498 CD OE1 OE2 REMARK 470 LYS A 551 CG CD CE NZ REMARK 470 GLU A 555 CG CD OE1 OE2 REMARK 470 GLU A 556 CG CD OE1 OE2 REMARK 470 GLN A 559 CG CD OE1 NE2 REMARK 470 TRP A 566 CE3 CZ2 CZ3 CH2 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 OD2 ASP A 646 NE2 GLN A 650 1.85 REMARK 500 NZ LYS A 453 O HOH A 1101 2.11 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 MG MG A 1006 O HOH A 1409 3554 1.68 REMARK 500 OE2 GLU A 450 NE2 GLN A 502 3554 1.89 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 ARG A 259 NE - CZ - NH1 ANGL. DEV. = 3.0 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 262 85.27 -151.99 REMARK 500 PHE A 399 6.03 59.78 REMARK 500 ALA A 477 161.81 179.24 REMARK 500 ASN A 499 98.95 -161.45 REMARK 500 ARG A 584 83.20 -68.82 REMARK 500 ASP A 633 -168.17 -165.11 REMARK 500 PRO A 728 150.09 -49.72 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 MG A1005 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 468 OE2 REMARK 620 2 HOH A1172 O 175.9 REMARK 620 3 HOH A1199 O 80.7 95.2 REMARK 620 4 HOH A1217 O 81.2 99.0 84.6 REMARK 620 5 HOH A1297 O 98.2 81.6 96.2 178.9 REMARK 620 N 1 2 3 4 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 687 SG REMARK 620 2 CYS A 692 SG 109.7 REMARK 620 3 CYS A 737 SG 110.8 115.1 REMARK 620 4 ACT A1002 O 109.8 108.2 103.0 REMARK 620 N 1 2 3 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 GLU A 736 OE1 REMARK 620 2 HOH A1192 O 176.5 REMARK 620 3 HOH A1228 O 89.5 89.4 REMARK 620 4 HOH A1275 O 90.5 92.9 92.2 REMARK 620 5 HOH A1319 O 94.1 82.4 75.9 167.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1006 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1101 O REMARK 620 2 HOH A1158 O 81.3 REMARK 620 3 HOH A1324 O 95.0 169.5 REMARK 620 4 HOH A1343 O 93.7 87.1 83.4 REMARK 620 5 HOH A1455 O 175.8 97.8 85.2 82.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1007 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XIF RELATED DB: PDB REMARK 900 RELATED ID: 5XIG RELATED DB: PDB REMARK 900 RELATED ID: 5XIH RELATED DB: PDB REMARK 900 RELATED ID: 5XII RELATED DB: PDB REMARK 900 RELATED ID: 5XIJ RELATED DB: PDB REMARK 900 RELATED ID: 5XIK RELATED DB: PDB REMARK 900 RELATED ID: 5XIO RELATED DB: PDB REMARK 900 RELATED ID: 5XIP RELATED DB: PDB REMARK 900 RELATED ID: 5XIR RELATED DB: PDB DBREF 5XIL A 254 756 UNP Q4QDS0 Q4QDS0_LEIMA 223 731 SEQADV 5XIL GLY A 251 UNP Q4QDS0 EXPRESSION TAG SEQADV 5XIL ALA A 252 UNP Q4QDS0 EXPRESSION TAG SEQADV 5XIL MET A 253 UNP Q4QDS0 EXPRESSION TAG SEQRES 1 A 512 GLY ALA MET GLY ILE ALA ALA LYS ARG GLU GLU ASN PHE SEQRES 2 A 512 SER ALA TRP TYR ILE ASP VAL ILE THR LYS ALA GLU MET SEQRES 3 A 512 ILE GLU TYR TYR ASP VAL SER GLY CYS TYR ILE ILE ARG SEQRES 4 A 512 PRO TRP ALA TYR TYR VAL TRP LYS CYS VAL GLN ARG PHE SEQRES 5 A 512 LEU GLY GLY LYS ILE GLU LYS LEU GLY VAL GLU ASP CYS SEQRES 6 A 512 TYR PHE PRO MET PHE VAL SER ARG SER CYS LEU GLU ARG SEQRES 7 A 512 GLU LYS ASP HIS ILE GLU GLY PHE ALA PRO GLU VAL ALA SEQRES 8 A 512 TRP VAL THR ARG ALA GLY ASP THR GLU LEU GLU GLN PRO SEQRES 9 A 512 VAL ALA VAL ARG PRO THR SER GLU THR VAL MET TYR PRO SEQRES 10 A 512 TYR TYR ALA LYS TRP ILE ARG SER HIS ARG ASP LEU PRO SEQRES 11 A 512 VAL ARG LEU ASN MET TRP ASN ASN VAL ILE ARG TRP GLU SEQRES 12 A 512 PHE SER HIS PRO THR PRO PHE ILE ARG THR ARG GLU PHE SEQRES 13 A 512 LEU TRP GLN GLU GLY HIS CYS ALA TRP ALA LYS ALA GLU SEQRES 14 A 512 GLU CYS ALA LYS GLU VAL LEU GLU ILE LEU GLU CYS TYR SEQRES 15 A 512 ALA SER VAL TYR GLU GLN LEU LEU ALA VAL PRO VAL VAL SEQRES 16 A 512 ARG GLY ARG LYS THR GLU LYS GLU LYS PHE ALA GLY GLY SEQRES 17 A 512 ASP TYR THR THR THR VAL GLU THR PHE ILE GLU ALA VAL SEQRES 18 A 512 GLY ARG GLY CYS GLN GLY ALA THR SER HIS ASN LEU GLY SEQRES 19 A 512 GLN ASN PHE GLY LYS MET PHE ASP ILE ARG PHE GLN ASP SEQRES 20 A 512 PRO GLU ASN ASN GLU GLN THR LEU ILE PRO TRP GLN ASN SEQRES 21 A 512 SER TRP GLY LEU SER THR ARG VAL ILE GLY VAL MET ILE SEQRES 22 A 512 MET VAL HIS GLY ASP ASN ARG GLY MET VAL MET PRO PRO SEQRES 23 A 512 ARG VAL ALA SER THR GLN VAL ILE ILE ILE PRO VAL GLY SEQRES 24 A 512 ILE THR LYS ASP THR THR GLU GLU ALA ARG GLN GLU LEU SEQRES 25 A 512 LEU ALA SER CYS TRP ARG LEU GLU SER GLU LEU CYS GLU SEQRES 26 A 512 GLY GLY VAL ARG ALA ARG CYS ASP LEU ARG ASP ASN TYR SEQRES 27 A 512 SER PRO GLY TRP ARG PHE ASN HIS TRP GLU VAL LYS GLY SEQRES 28 A 512 VAL PRO LEU ARG VAL GLU LEU GLY PRO ARG GLU LEU ALA SEQRES 29 A 512 GLU ARG SER LEU ALA VAL ALA VAL ARG HIS SER GLY ALA SEQRES 30 A 512 ARG HIS SER VAL ALA TRP ASP ALA GLN THR PRO ALA ALA SEQRES 31 A 512 VAL ALA ALA LEU LEU GLU ASP VAL HIS ALA GLN MET TYR SEQRES 32 A 512 ALA ARG ALA LYS GLU THR MET GLU THR HIS ARG VAL ARG SEQRES 33 A 512 VAL THR GLU TRP THR GLU PHE VAL PRO THR LEU ASN ARG SEQRES 34 A 512 LYS CYS LEU ILE LEU ALA PRO TRP CYS GLY ALA MET GLU SEQRES 35 A 512 CYS GLU ASN GLN VAL LYS LYS ASP SER ALA GLU GLU SER SEQRES 36 A 512 LYS VAL ALA GLN ALA GLN GLU THR ARG GLU ASP ALA ARG SEQRES 37 A 512 ALA PRO SER MET GLY ALA LYS THR LEU CYS ILE PRO PHE SEQRES 38 A 512 GLU GLN PRO GLU GLU PRO ALA GLU GLY HIS GLU CYS ILE SEQRES 39 A 512 CYS LYS GLY CYS THR LYS PRO ALA THR THR TRP VAL LEU SEQRES 40 A 512 PHE GLY ARG SER TYR HET ZN A1001 1 HET ACT A1002 4 HET ACT A1003 4 HET ACT A1004 4 HET MG A1005 1 HET MG A1006 1 HET MG A1007 1 HETNAM ZN ZINC ION HETNAM ACT ACETATE ION HETNAM MG MAGNESIUM ION FORMUL 2 ZN ZN 2+ FORMUL 3 ACT 3(C2 H3 O2 1-) FORMUL 6 MG 3(MG 2+) FORMUL 9 HOH *358(H2 O) HELIX 1 AA1 ASN A 262 ALA A 274 1 13 HELIX 2 AA2 ARG A 289 GLY A 311 1 23 HELIX 3 AA3 SER A 360 ILE A 372 1 13 HELIX 4 AA4 SER A 374 LEU A 378 5 5 HELIX 5 AA5 LYS A 416 LEU A 438 1 23 HELIX 6 AA6 GLN A 484 ASP A 491 1 8 HELIX 7 AA7 THR A 515 GLY A 526 1 12 HELIX 8 AA8 PRO A 534 ALA A 538 5 5 HELIX 9 AA9 THR A 554 GLY A 575 1 22 HELIX 10 AB1 SER A 588 GLY A 600 1 13 HELIX 11 AB2 GLY A 608 ARG A 615 1 8 HELIX 12 AB3 GLN A 635 HIS A 662 1 28 HELIX 13 AB4 GLU A 668 THR A 670 5 3 HELIX 14 AB5 GLU A 671 ARG A 678 1 8 HELIX 15 AB6 ALA A 689 LYS A 705 1 17 HELIX 16 AB7 PRO A 731 HIS A 735 5 5 SHEET 1 AA1 2 ILE A 277 GLU A 278 0 SHEET 2 AA1 2 ILE A 287 ILE A 288 -1 O ILE A 287 N GLU A 278 SHEET 1 AA211 GLU A 313 ASP A 314 0 SHEET 2 AA211 VAL A 380 VAL A 388 1 O ARG A 381 N GLU A 313 SHEET 3 AA211 PHE A 405 TRP A 414 -1 O HIS A 411 N LEU A 382 SHEET 4 AA211 TRP A 507 SER A 514 -1 O TRP A 507 N TRP A 414 SHEET 5 AA211 ARG A 472 GLY A 483 -1 N HIS A 480 O SER A 510 SHEET 6 AA211 TYR A 459 ILE A 467 -1 N ILE A 467 O ARG A 472 SHEET 7 AA211 VAL A 444 ARG A 447 -1 N VAL A 444 O GLU A 464 SHEET 8 AA211 LYS A 719 PRO A 724 -1 O ILE A 723 N ARG A 447 SHEET 9 AA211 THR A 748 GLY A 753 -1 O LEU A 751 N LEU A 721 SHEET 10 AA211 LEU A 681 TRP A 686 -1 N ILE A 682 O PHE A 752 SHEET 11 AA211 ARG A 663 ARG A 665 1 N VAL A 664 O LEU A 681 SHEET 1 AA3 2 PHE A 494 ASP A 496 0 SHEET 2 AA3 2 ASN A 499 LEU A 504 -1 O LEU A 504 N PHE A 494 SHEET 1 AA4 5 ALA A 579 CYS A 581 0 SHEET 2 AA4 5 VAL A 542 PRO A 546 1 N ILE A 544 O ARG A 580 SHEET 3 AA4 5 LEU A 603 LEU A 607 1 O VAL A 605 N ILE A 545 SHEET 4 AA4 5 SER A 616 VAL A 621 -1 O ALA A 620 N ARG A 604 SHEET 5 AA4 5 ARG A 627 ALA A 631 -1 O VAL A 630 N LEU A 617 SSBOND 1 CYS A 739 CYS A 742 1555 1555 2.06 LINK OE2 GLU A 468 MG MG A1005 1555 1555 2.22 LINK SG CYS A 687 ZN ZN A1001 1555 1555 2.31 LINK SG CYS A 692 ZN ZN A1001 1555 1555 2.20 LINK OE1 GLU A 736 MG MG A1007 1555 1555 2.16 LINK SG CYS A 737 ZN ZN A1001 1555 1555 2.37 LINK ZN ZN A1001 O ACT A1002 1555 1555 2.12 LINK MG MG A1005 O HOH A1172 1555 1555 2.20 LINK MG MG A1005 O HOH A1199 1555 1555 1.90 LINK MG MG A1005 O HOH A1217 1555 1555 2.22 LINK MG MG A1005 O HOH A1297 1555 1555 2.02 LINK MG MG A1006 O HOH A1101 1555 1555 2.02 LINK MG MG A1006 O HOH A1158 1555 3554 1.81 LINK MG MG A1006 O HOH A1324 1555 1555 1.90 LINK MG MG A1006 O HOH A1343 1555 1555 1.91 LINK MG MG A1006 O HOH A1455 1555 1555 2.15 LINK MG MG A1007 O HOH A1192 1555 1555 2.11 LINK MG MG A1007 O HOH A1228 1555 1555 1.86 LINK MG MG A1007 O HOH A1275 1555 1555 1.77 LINK MG MG A1007 O HOH A1319 1555 1555 1.77 CISPEP 1 LEU A 378 PRO A 379 0 -5.78 SITE 1 AC1 4 CYS A 687 CYS A 692 CYS A 737 ACT A1002 SITE 1 AC2 7 CYS A 687 CYS A 692 CYS A 737 CYS A 742 SITE 2 AC2 7 THR A 743 LYS A 744 ZN A1001 SITE 1 AC3 7 PHE A 263 SER A 264 TYR A 267 MET A 523 SITE 2 AC3 7 TYR A 756 HOH A1157 HOH A1257 SITE 1 AC4 3 ARG A 665 THR A 667 GLU A 730 SITE 1 AC5 6 GLU A 468 HIS A 662 HOH A1172 HOH A1199 SITE 2 AC5 6 HOH A1217 HOH A1297 SITE 1 AC6 7 LYS A 453 HOH A1101 HOH A1158 HOH A1324 SITE 2 AC6 7 HOH A1343 HOH A1409 HOH A1455 SITE 1 AC7 5 GLU A 736 HOH A1192 HOH A1228 HOH A1275 SITE 2 AC7 5 HOH A1319 CRYST1 75.294 98.861 146.327 90.00 90.00 90.00 C 2 2 21 8 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 0.013281 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010115 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006834 0.00000