HEADER HYDROLASE 16-MAY-17 5O0S TITLE CRYSTAL STRUCTURE OF TXGH116 (BETA-GLUCOSIDASE FROM TITLE 2 THERMOANAEROBACTERIUM XYLOLYTICUM) IN COMPLEX WITH UNREACTED BETA TITLE 3 CYCLOPHELLITOL CYCLOSULFATE PROBE ME711 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSYLCERAMIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.45; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOANAEROBACTERIUM XYLANOLYTICUM LX-11; SOURCE 3 ORGANISM_TAXID: 858215; SOURCE 4 GENE: THEXY_2211; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.WU,W.A.OFFEN,I.Z.BREEN,G.J.DAVIES REVDAT 3 17-JAN-24 5O0S 1 REMARK REVDAT 2 23-AUG-17 5O0S 1 JRNL REVDAT 1 09-AUG-17 5O0S 0 JRNL AUTH M.ARTOLA,L.WU,M.J.FERRAZ,C.L.KUO,L.RAICH,I.Z.BREEN, JRNL AUTH 2 W.A.OFFEN,J.D.C.CODEE,G.A.VAN DER MAREL,C.ROVIRA, JRNL AUTH 3 J.M.F.G.AERTS,G.J.DAVIES,H.S.OVERKLEEFT JRNL TITL 1,6-CYCLOPHELLITOL CYCLOSULFATES: A NEW CLASS OF JRNL TITL 2 IRREVERSIBLE GLYCOSIDASE INHIBITOR. JRNL REF ACS CENT SCI V. 3 784 2017 JRNL REFN ESSN 2374-7943 JRNL PMID 28776021 JRNL DOI 10.1021/ACSCENTSCI.7B00214 REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 261588 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : SAME AS 5NPF REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 13813 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) : 1.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 19142 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 1065 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6225 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 567 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.36000 REMARK 3 B22 (A**2) : -1.65000 REMARK 3 B33 (A**2) : 2.02000 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): 0.031 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.032 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.030 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.620 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.977 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6704 ; 0.016 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5962 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9098 ; 1.785 ; 1.939 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13937 ; 1.031 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 820 ; 6.543 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 319 ;36.982 ;25.298 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1139 ;12.050 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;19.592 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 916 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7553 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1412 ; 0.002 ; 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): 3202 ; 1.778 ; 1.605 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3199 ; 1.758 ; 1.604 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4040 ; 2.246 ; 2.425 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4041 ; 2.248 ; 2.425 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3502 ; 2.301 ; 1.829 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3499 ; 2.301 ; 1.828 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5057 ; 2.703 ; 2.641 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8103 ; 6.575 ;19.794 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8104 ; 6.575 ;19.794 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 12666 ; 2.853 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 363 ;30.854 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 12662 ;17.621 ; 5.000 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 REMARK 4 REMARK 4 5O0S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200005002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-17 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 275502 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 59.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 2.09000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5FJS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.5 0.2 M AMMONIUM REMARK 280 SULFATE 16% PEG 3350, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 89.08500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.86550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 89.08500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.86550 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 TOTAL BURIED SURFACE AREA: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 16.0 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 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 20 REMARK 465 GLY A 21 REMARK 465 CYS A 22 REMARK 465 SER A 23 REMARK 465 GLU A 24 REMARK 465 LYS A 25 REMARK 465 ILE A 26 REMARK 465 ASN A 27 REMARK 465 ILE A 28 REMARK 465 ASN A 29 REMARK 465 GLU A 30 REMARK 465 LYS A 429 REMARK 465 ASP A 430 REMARK 465 LYS A 431 REMARK 465 ASN A 802 REMARK 465 TYR A 803 REMARK 465 ASN A 804 REMARK 465 GLU A 805 REMARK 465 VAL A 806 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 1422 O HOH A 1473 1.93 REMARK 500 O HOH A 1448 O HOH A 1497 2.03 REMARK 500 O HOH A 1117 O HOH A 1502 2.03 REMARK 500 OE2 GLU A 333 O HOH A 1003 2.06 REMARK 500 O HOH A 1254 O HOH A 1499 2.11 REMARK 500 O LEU A 96 O1 EDO A 909 2.14 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 1473 O HOH A 1473 2675 1.87 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 SER A 68 CB SER A 68 OG 0.090 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 85 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 288 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 432 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 432 NE - CZ - NH2 ANGL. DEV. = -3.7 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 SER A 68 172.50 76.51 REMARK 500 LYS A 186 -81.20 -111.01 REMARK 500 LYS A 240 33.95 -98.52 REMARK 500 SER A 244 49.32 -143.82 REMARK 500 THR A 286 46.01 -94.67 REMARK 500 ASN A 299 11.59 -142.05 REMARK 500 ASP A 307 105.06 -163.59 REMARK 500 ASP A 307 105.06 -174.16 REMARK 500 LYS A 312 -86.12 -109.73 REMARK 500 LYS A 312 -81.19 -109.73 REMARK 500 CYS A 442 -174.11 -176.40 REMARK 500 ALA A 514 -118.82 -128.62 REMARK 500 TRP A 517 -19.77 73.37 REMARK 500 PRO A 588 105.83 -57.69 REMARK 500 ASP A 589 30.99 -145.20 REMARK 500 GLN A 590 -179.93 -174.43 REMARK 500 PHE A 699 -76.77 -101.77 REMARK 500 ARG A 774 40.59 -159.28 REMARK 500 ALA A 787 76.04 64.72 REMARK 500 MET A 789 65.05 60.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1566 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A1567 DISTANCE = 7.01 ANGSTROMS 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 CA A 910 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 575 OD1 REMARK 620 2 ASP A 577 OD1 80.6 REMARK 620 3 ASP A 579 OD1 86.4 89.8 REMARK 620 4 ILE A 581 O 80.9 161.5 89.7 REMARK 620 5 ASP A 583 OD1 94.9 80.5 169.8 100.5 REMARK 620 6 ASP A 583 OD1 94.9 96.3 173.9 84.6 16.0 REMARK 620 7 HOH A1012 O 162.9 116.5 93.2 82.1 88.5 83.7 REMARK 620 8 HOH A1085 O 143.5 63.2 88.8 135.4 84.1 93.6 53.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 910 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9FQ A 911 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5NPF RELATED DB: PDB REMARK 900 SAME ENZYME WITH UNREACTED VERSION OF SAME LIGAND DBREF 5O0S A 21 806 UNP F6BL85 F6BL85_THEXL 21 806 SEQADV 5O0S MET A 20 UNP F6BL85 INITIATING METHIONINE SEQRES 1 A 787 MET GLY CYS SER GLU LYS ILE ASN ILE ASN GLU ASP LYS SEQRES 2 A 787 ILE SER HIS LYS ILE ASP ILE PRO ASP SER ALA TRP THR SEQRES 3 A 787 ILE GLY ILE GLY GLU LYS PHE LYS ASN ALA GLY HIS PRO SEQRES 4 A 787 ASN VAL LYS TYR PRO MET ILE ASP ASP SER TYR VAL GLN SEQRES 5 A 787 GLY ALA PRO LEU GLY GLY PHE GLY ALA GLY THR ILE GLY SEQRES 6 A 787 ARG THR TYR ASN GLY GLY PHE SER ARG TRP HIS LEU GLU SEQRES 7 A 787 ILE GLY LYS ASN LYS TYR THR THR VAL TYR ALA ASN GLN SEQRES 8 A 787 PHE SER VAL PHE GLN LYS VAL GLU GLY ASN LYS ASP GLY SEQRES 9 A 787 VAL ALA GLN VAL LEU TYR ALA GLY GLU PRO GLU ASN GLY SEQRES 10 A 787 TYR LEU SER SER TRP LYS TRP ASP TYR PRO LYS GLU SER SEQRES 11 A 787 GLY MET TYR TYR ALA LEU TYR PRO ASN SER TRP TYR THR SEQRES 12 A 787 TYR THR ASN LYS ASP LEU PRO VAL GLN LEU ALA VAL LYS SEQRES 13 A 787 GLN PHE SER PRO ILE ILE PRO TYR ASN TYR LYS GLU THR SEQRES 14 A 787 SER TYR PRO VAL ALA VAL PHE LYS TRP THR ALA TYR ASN SEQRES 15 A 787 PRO THR ASN LYS ASN VAL ASP VAL SER ILE MET PHE THR SEQRES 16 A 787 TRP GLN ASN MET ILE GLY PHE PHE GLY LYS GLN VAL ASN SEQRES 17 A 787 VAL ASN SER GLY ASN PHE ASN LYS ILE ILE LYS ASP LYS SEQRES 18 A 787 SER LYS ASP SER GLU ILE VAL ALA ALA VAL MET GLY ASN SEQRES 19 A 787 ILE SER ASN ASP ASN GLU GLU TRP ASN GLY GLU TYR SER SEQRES 20 A 787 ILE GLY VAL LYS LYS VAL PRO GLY VAL ASP ILE SER TYR SEQRES 21 A 787 LYS ALA LYS PHE VAL THR THR GLY ASP GLY SER ASP LEU SEQRES 22 A 787 TRP HIS GLU PHE SER LYS ASN GLY ILE LEU ASP ASN LYS SEQRES 23 A 787 ASP ASP GLU THR PRO THR LYS GLN ASP GLY ILE GLY SER SEQRES 24 A 787 ALA ILE ALA VAL ASN PHE LYS LEU GLN PRO GLY GLN THR SEQRES 25 A 787 ILE GLU VAL PRO PHE ALA LEU SER TRP ASP LEU PRO ILE SEQRES 26 A 787 MET LYS PHE GLY GLY GLY ASP LYS TRP TYR LYS MET TYR SEQRES 27 A 787 THR LYS TYR PHE GLY LYS ASN GLY LYS ASN SER PHE ALA SEQRES 28 A 787 ILE LEU LYS GLU ALA LEU ASN ASN TYR GLN LYS TRP GLU SEQRES 29 A 787 LYS MET ILE ASP ASP TRP GLN LYS PRO ILE LEU SER ASN SEQRES 30 A 787 LYS SER LYS PRO ASP TRP TYR LYS THR ALA LEU PHE ASN SEQRES 31 A 787 GLU LEU TYR TYR LEU ALA ASP GLY GLY THR ALA TRP GLU SEQRES 32 A 787 ASN GLY LYS VAL GLY GLU LYS ASP LYS ARG THR ASN ASN SEQRES 33 A 787 MET PHE GLY LEU LEU GLU CYS PHE ASP TYR ASN TYR TYR SEQRES 34 A 787 GLU THR LEU ASP VAL ARG PHE TYR GLY SER PHE PRO LEU SEQRES 35 A 787 VAL MET LEU TRP PRO ASP ILE GLU LYS GLN VAL MET ARG SEQRES 36 A 787 GLN PHE ALA ASP THR ILE ASN VAL GLN ASP SER SER GLU SEQRES 37 A 787 PHE LYS VAL GLY SER ASN GLY ALA MET ALA VAL LYS LYS SEQRES 38 A 787 VAL GLN GLY MET ILE PRO HIS ASP LEU GLY SER SER TYR SEQRES 39 A 787 ALA LEU PRO TRP ILE LYS ILE ASN ALA TYR ASP TRP GLN SEQRES 40 A 787 ASN PRO ASN ILE TRP LYS ASP LEU ASN SER LYS TYR VAL SEQRES 41 A 787 LEU LEU VAL TYR ARG ASP TYR VAL LEU THR GLY LYS THR SEQRES 42 A 787 ASP LYS GLU PHE LEU LYS TYR THR TRP LYS SER VAL LYS SEQRES 43 A 787 THR ALA LEU ASP LYS LEU LYS GLU MET ASP LYS ASP ASN SEQRES 44 A 787 ASP GLY ILE PRO ASP ASN GLU GLY ILE PRO ASP GLN THR SEQRES 45 A 787 TYR ASP THR TRP SER MET LYS GLY THR SER ALA TYR CYS SEQRES 46 A 787 GLY SER LEU TRP LEU ALA ALA LEU LYS ALA ALA GLN GLU SEQRES 47 A 787 ILE GLY LYS VAL LEU LYS ASP ASN GLU ALA TYR ILE LYS SEQRES 48 A 787 TYR ASN GLU TRP TYR LYS ILE ALA GLN GLN ASN PHE GLU SEQRES 49 A 787 LYS GLU LEU TRP ASN GLY GLU TYR TYR ASN PHE ASP THR SEQRES 50 A 787 GLU SER ASP HIS LYS ASP SER ILE MET ALA ASP GLN LEU SEQRES 51 A 787 ALA GLY GLN TRP TYR ALA ASP ILE LEU ARG LEU GLY ASP SEQRES 52 A 787 ILE LEU PRO LYS ASP HIS VAL GLN LYS ALA LEU LYS LYS SEQRES 53 A 787 ILE TYR GLU PHE ASN VAL MET LYS PHE GLU ASN GLY LYS SEQRES 54 A 787 MET GLY ALA VAL ASN GLY MET ARG PRO ASP GLY ILE VAL SEQRES 55 A 787 ASP GLU SER ASP ILE GLN ALA GLN GLU VAL TRP THR GLY SEQRES 56 A 787 VAL THR TYR ALA LEU ALA SER PHE MET LYS TYR ARG GLY SEQRES 57 A 787 MET THR GLU GLU ALA TYR ASN THR ALA TYR GLY VAL TYR SEQRES 58 A 787 LYS MET THR TYR ASP LYS SER GLY LYS GLY TYR TRP PHE SEQRES 59 A 787 ARG THR PRO GLU ALA TRP THR LYS ASP GLY ASN TYR ARG SEQRES 60 A 787 ALA SER MET TYR MET ARG PRO LEU SER ILE TRP SER MET SEQRES 61 A 787 GLU VAL ASN TYR ASN GLU VAL HET EDO A 901 4 HET EDO A 902 4 HET EDO A 903 4 HET EDO A 904 4 HET EDO A 905 4 HET EDO A 906 4 HET EDO A 907 4 HET EDO A 908 4 HET EDO A 909 4 HET CA A 910 1 HET 9FQ A 911 16 HETNAM EDO 1,2-ETHANEDIOL HETNAM CA CALCIUM ION HETNAM 9FQ (3~{A}~{S},4~{R},5~{S},6~{R},7~{R},7~{A}~{R})-7- HETNAM 2 9FQ (HYDROXYMETHYL)-2,2-BIS(OXIDANYLIDENE)-3~{A},4,5,6,7, HETNAM 3 9FQ 7~{A}-HEXAHYDROBENZO[D][1,3,2]DIOXATHIOLE-4,5,6-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 9(C2 H6 O2) FORMUL 11 CA CA 2+ FORMUL 12 9FQ C7 H12 O8 S FORMUL 13 HOH *567(H2 O) HELIX 1 AA1 LYS A 186 TYR A 190 5 5 HELIX 2 AA2 GLY A 289 GLY A 300 1 12 HELIX 3 AA3 TYR A 357 GLY A 362 1 6 HELIX 4 AA4 ASN A 367 SER A 395 1 29 HELIX 5 AA5 PRO A 400 LEU A 411 1 12 HELIX 6 AA6 LEU A 411 GLY A 417 1 7 HELIX 7 AA7 THR A 450 SER A 458 1 9 HELIX 8 AA8 SER A 458 TRP A 465 1 8 HELIX 9 AA9 TRP A 465 ILE A 480 1 16 HELIX 10 AB1 ASN A 527 TRP A 531 5 5 HELIX 11 AB2 ASP A 533 LEU A 548 1 16 HELIX 12 AB3 ASP A 553 GLU A 573 1 21 HELIX 13 AB4 SER A 601 LEU A 622 1 22 HELIX 14 AB5 ASP A 624 TRP A 647 1 24 HELIX 15 AB6 LEU A 669 LEU A 678 1 10 HELIX 16 AB7 PRO A 685 PHE A 699 1 15 HELIX 17 AB8 PHE A 704 LYS A 708 5 5 HELIX 18 AB9 ASP A 725 GLU A 730 5 6 HELIX 19 AC1 THR A 733 ARG A 746 1 14 HELIX 20 AC2 MET A 748 ASP A 765 1 18 HELIX 21 AC3 MET A 791 VAL A 801 5 11 SHEET 1 AA1 9 TRP A 44 GLY A 47 0 SHEET 2 AA1 9 GLY A 150 LEU A 155 -1 O TYR A 152 N ILE A 46 SHEET 3 AA1 9 ASN A 158 TYR A 163 -1 O ASN A 158 N LEU A 155 SHEET 4 AA1 9 GLN A 171 PHE A 177 -1 O GLN A 176 N SER A 159 SHEET 5 AA1 9 VAL A 192 TYR A 200 -1 O LYS A 196 N LYS A 175 SHEET 6 AA1 9 THR A 331 ASP A 341 -1 O PHE A 336 N PHE A 195 SHEET 7 AA1 9 GLU A 264 LYS A 270 -1 N GLU A 264 O ASP A 341 SHEET 8 AA1 9 ILE A 246 ASN A 253 -1 N MET A 251 O TYR A 265 SHEET 9 AA1 9 ASN A 232 ASP A 239 -1 N LYS A 235 O VAL A 250 SHEET 1 AA2 4 PRO A 74 LEU A 75 0 SHEET 2 AA2 4 THR A 82 ARG A 85 -1 O ILE A 83 N LEU A 75 SHEET 3 AA2 4 PHE A 91 HIS A 95 -1 O HIS A 95 N THR A 82 SHEET 4 AA2 4 LYS A 102 TYR A 103 -1 O LYS A 102 N TRP A 94 SHEET 1 AA3 5 VAL A 124 VAL A 127 0 SHEET 2 AA3 5 GLN A 110 VAL A 117 -1 N VAL A 113 O GLN A 126 SHEET 3 AA3 5 VAL A 207 GLN A 216 -1 O ASP A 208 N LYS A 116 SHEET 4 AA3 5 ILE A 316 LEU A 326 -1 O ILE A 320 N PHE A 213 SHEET 5 AA3 5 VAL A 275 VAL A 284 -1 N SER A 278 O ALA A 321 SHEET 1 AA4 4 ILE A 344 LYS A 346 0 SHEET 2 AA4 4 LYS A 352 LYS A 355 -1 O TRP A 353 N MET A 345 SHEET 3 AA4 4 ALA A 420 LYS A 425 -1 O GLY A 424 N TYR A 354 SHEET 4 AA4 4 PHE A 437 GLY A 438 -1 O GLY A 438 N ALA A 420 SHEET 1 AA5 2 ASP A 484 LYS A 489 0 SHEET 2 AA5 2 MET A 496 LYS A 500 -1 O LYS A 500 N ASP A 484 SHEET 1 AA6 2 ASN A 584 GLU A 585 0 SHEET 2 AA6 2 LYS A 598 GLY A 599 -1 O GLY A 599 N ASN A 584 SHEET 1 AA7 2 ILE A 664 MET A 665 0 SHEET 2 AA7 2 GLY A 714 MET A 715 -1 O MET A 715 N ILE A 664 SHEET 1 AA8 3 VAL A 731 TRP A 732 0 SHEET 2 AA8 3 ALA A 778 TRP A 779 -1 O TRP A 779 N VAL A 731 SHEET 3 AA8 3 TYR A 785 ARG A 786 -1 O ARG A 786 N ALA A 778 LINK OD1 ASP A 575 CA CA A 910 1555 1555 2.36 LINK OD1 ASP A 577 CA CA A 910 1555 1555 2.39 LINK OD1 ASP A 579 CA CA A 910 1555 1555 2.31 LINK O ILE A 581 CA CA A 910 1555 1555 2.29 LINK OD1AASP A 583 CA CA A 910 1555 1555 2.37 LINK OD1BASP A 583 CA CA A 910 1555 1555 2.38 LINK CA CA A 910 O HOH A1012 1555 1555 2.56 LINK CA CA A 910 O HOH A1085 1555 1555 2.69 CISPEP 1 TYR A 156 PRO A 157 0 11.07 SITE 1 AC1 6 THR A 45 ILE A 46 GLU A 50 TYR A 764 SITE 2 AC1 6 LYS A 766 HOH A1108 SITE 1 AC2 8 GLN A 225 LYS A 235 GLU A 264 LYS A 366 SITE 2 AC2 8 SER A 368 PHE A 369 HOH A1368 HOH A1398 SITE 1 AC3 6 VAL A 124 GLN A 126 LYS A 142 PRO A 146 SITE 2 AC3 6 ASN A 165 ASP A 167 SITE 1 AC4 4 GLY A 362 LYS A 363 ASN A 364 HOH A1175 SITE 1 AC5 6 PHE A 443 ASP A 444 TYR A 513 EDO A 906 SITE 2 AC5 6 HOH A1046 HOH A1365 SITE 1 AC6 7 LYS A 312 ASP A 444 ASN A 446 TYR A 447 SITE 2 AC6 7 EDO A 905 HOH A1101 HOH A1167 SITE 1 AC7 10 MET A 218 ILE A 219 GLY A 220 PHE A 221 SITE 2 AC7 10 PHE A 222 TRP A 261 TYR A 265 LEU A 342 SITE 3 AC7 10 HOH A1001 HOH A1002 SITE 1 AC8 5 LYS A 644 GLU A 645 TRP A 647 ASN A 648 SITE 2 AC8 5 ASN A 653 SITE 1 AC9 8 LEU A 96 GLU A 97 ILE A 98 GLU A 260 SITE 2 AC9 8 MET A 345 LYS A 346 LYS A 355 HOH A1138 SITE 1 AD1 7 ASP A 575 ASP A 577 ASP A 579 ILE A 581 SITE 2 AD1 7 ASP A 583 HOH A1012 HOH A1085 SITE 1 AD2 13 GLU A 441 TYR A 445 ASP A 452 HIS A 507 SITE 2 AD2 13 TYR A 523 TRP A 531 THR A 591 ASP A 593 SITE 3 AD2 13 TRP A 732 GLU A 777 ARG A 786 TYR A 790 SITE 4 AD2 13 ARG A 792 CRYST1 178.170 53.731 83.138 90.00 90.00 90.00 P 21 21 2 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 0.005613 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018611 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012028 0.00000