HEADER HYDROLASE 26-JUN-18 6GX8 TITLE ALPHA-GALACTOSIDASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH TITLE 2 HYDROLYSED CYCLOHEXENE-BASED CARBASUGAR MIMIC OF GALACTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MELIBIASE; COMPND 5 EC: 3.2.1.22; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: THE ELECTRON DENSITY AT THE N- AND C-TERMINUS WAS TOO COMPND 8 DISORDERED TO MODEL THE STRUCTURE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA MSB8; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 GENE: GALA, TM_1192, TMARI_1199; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS GLYCOSIDE HYDROLASE, GALACTOSIDASE, CARBOHYDRATE PROCESSING ENZYME, KEYWDS 2 INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.M.GLOSTER,V.OEHLER REVDAT 2 17-JAN-24 6GX8 1 LINK REVDAT 1 22-AUG-18 6GX8 0 JRNL AUTH W.REN,R.PENGELLY,M.FARREN-DAI,S.SHAMSI KAZEM ABADI,V.OEHLER, JRNL AUTH 2 O.AKINTOLA,J.DRAPER,M.MEANWELL,S.CHAKLADAR,K.SWIDEREK, JRNL AUTH 3 V.MOLINER,R.BRITTON,T.M.GLOSTER,A.J.BENNET JRNL TITL REVEALING THE MECHANISM FOR COVALENT INHIBITION OF GLYCOSIDE JRNL TITL 2 HYDROLASES BY CARBASUGARS AT AN ATOMIC LEVEL. JRNL REF NAT COMMUN V. 9 3243 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30104598 JRNL DOI 10.1038/S41467-018-05702-7 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 111449 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5853 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) : 1.42 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7613 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.3750 REMARK 3 BIN FREE R VALUE SET COUNT : 406 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4304 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 538 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.79000 REMARK 3 B22 (A**2) : -0.77000 REMARK 3 B33 (A**2) : 1.56000 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): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.713 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4600 ; 0.010 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 4113 ; 0.000 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6280 ; 1.266 ; 1.658 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9671 ; 0.970 ; 1.639 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 580 ; 7.151 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 252 ;32.338 ;22.579 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 785 ;12.872 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;12.850 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 576 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5199 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 899 ; 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): 2186 ; 1.840 ; 1.902 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2185 ; 1.836 ; 1.900 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2744 ; 2.529 ; 2.847 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2745 ; 2.530 ; 2.849 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2414 ; 3.212 ; 2.261 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2414 ; 3.207 ; 2.261 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3514 ; 4.761 ; 3.249 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5300 ; 5.951 ;23.197 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5300 ; 5.952 ;23.194 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 : 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6GX8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010660. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-17 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 : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 117828 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 97.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.94800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: 5M0X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM SULFATE, 20% (W/V) PEG REMARK 280 3350, 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 47.90850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.70950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.75300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.70950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.90850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.75300 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: 720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 REMARK 465 GLY A -10 REMARK 465 LEU A -9 REMARK 465 GLY A 526 REMARK 465 LYS A 527 REMARK 465 SER A 528 REMARK 465 SER A 529 REMARK 465 LEU A 530 REMARK 465 LYS A 531 REMARK 465 LYS A 532 REMARK 465 ARG A 533 REMARK 465 VAL A 534 REMARK 465 VAL A 535 REMARK 465 LYS A 536 REMARK 465 ARG A 537 REMARK 465 GLU A 538 REMARK 465 ASP A 539 REMARK 465 GLY A 540 REMARK 465 ARG A 541 REMARK 465 ASN A 542 REMARK 465 PHE A 543 REMARK 465 TYR A 544 REMARK 465 PHE A 545 REMARK 465 TYR A 546 REMARK 465 GLU A 547 REMARK 465 GLU A 548 REMARK 465 GLY A 549 REMARK 465 GLU A 550 REMARK 465 ARG A 551 REMARK 465 GLU A 552 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 LYS A 77 CG CD CE NZ REMARK 470 GLU A 80 CB CG CD OE1 OE2 REMARK 470 ARG A 98 CD NE CZ NH1 NH2 REMARK 470 LYS A 181 CD CE NZ REMARK 470 LYS A 207 CD CE NZ REMARK 470 LYS A 245 CD CE NZ REMARK 470 GLU A 525 CB CG CD OE1 OE2 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 42 79.40 -117.23 REMARK 500 TRP A 85 32.48 -141.16 REMARK 500 SER A 90 143.54 -171.20 REMARK 500 TYR A 104 -50.15 76.41 REMARK 500 ILE A 120 -56.19 -121.50 REMARK 500 ASP A 157 142.20 -179.59 REMARK 500 PHE A 194 -141.21 51.22 REMARK 500 ALA A 222 -37.04 163.24 REMARK 500 ASP A 229 64.85 -103.80 REMARK 500 PRO A 238 -167.02 -79.63 REMARK 500 ALA A 259 75.27 -118.86 REMARK 500 PRO A 390 41.55 -75.80 REMARK 500 ALA A 403 128.55 -178.45 REMARK 500 ARG A 420 -52.94 -128.28 REMARK 500 TRP A 422 -175.66 169.56 REMARK 500 ASP A 427 169.21 77.47 REMARK 500 ARG A 467 -149.99 -119.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A -6 0.13 SIDE CHAIN REMARK 500 ARG A 12 0.12 SIDE CHAIN REMARK 500 ARG A 86 0.16 SIDE CHAIN REMARK 500 ARG A 234 0.10 SIDE CHAIN REMARK 500 ARG A 383 0.09 SIDE CHAIN 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 A1238 DISTANCE = 6.02 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 MG A 605 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 419 OD2 REMARK 620 2 ASP A 454 OD2 90.2 REMARK 620 3 HOH A 747 O 86.3 93.4 REMARK 620 4 HOH A 918 O 92.9 89.1 177.4 REMARK 620 5 HOH A 998 O 175.4 91.1 89.2 91.6 REMARK 620 6 HOH A1029 O 89.7 175.7 90.8 86.6 89.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FH2 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 606 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GTA RELATED DB: PDB REMARK 900 STRUCTURE OF MUTANT ENZYME D387A IN COMPLEX WITH INTACT COMPOUND REMARK 900 WITH OH GROUP AT C2 POSITION AND 3,5-DIFLUORO LEAVING GROUP REMARK 900 RELATED ID: 6GVD RELATED DB: PDB REMARK 900 STRUCTURE OF ENZYME WITH HYDROLYSED COMPOUND WITH OH GROUP AT C2 REMARK 900 POSITION REMARK 900 RELATED ID: 6GWF RELATED DB: PDB REMARK 900 STRUCTURE OF MUTANT ENZYME D387A IN COMPLEX WITH INTACT COMPOUND REMARK 900 WITH F GROUP AT C2 POSITION AND 2,4-DINITRO LEAVING GROUP REMARK 900 RELATED ID: 6GWG RELATED DB: PDB REMARK 900 STRUCTURE OF ENZYME WITH COVALENT COMPLEX WITH COMPOUND WITH F REMARK 900 GROUP AT THE C2 POSITION DBREF 6GX8 A 1 552 UNP G4FEF4 AGAL_THEMA 1 552 SEQADV 6GX8 MET A -22 UNP G4FEF4 INITIATING METHIONINE SEQADV 6GX8 GLY A -21 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 SER A -20 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 SER A -19 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 HIS A -18 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 HIS A -17 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 HIS A -16 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 HIS A -15 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 HIS A -14 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 HIS A -13 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 SER A -12 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 SER A -11 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 GLY A -10 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 LEU A -9 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 VAL A -8 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 PRO A -7 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 ARG A -6 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 GLY A -5 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 SER A -4 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 HIS A -3 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 MET A -2 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 ALA A -1 UNP G4FEF4 EXPRESSION TAG SEQADV 6GX8 SER A 0 UNP G4FEF4 EXPRESSION TAG SEQRES 1 A 575 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 575 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET GLU ILE SEQRES 3 A 575 PHE GLY LYS THR PHE ARG GLU GLY ARG PHE VAL LEU LYS SEQRES 4 A 575 GLU LYS ASN PHE THR VAL GLU PHE ALA VAL GLU LYS ILE SEQRES 5 A 575 HIS LEU GLY TRP LYS ILE SER GLY ARG VAL LYS GLY SER SEQRES 6 A 575 PRO GLY ARG LEU GLU VAL LEU ARG THR LYS ALA PRO GLU SEQRES 7 A 575 LYS VAL LEU VAL ASN ASN TRP GLN SER TRP GLY PRO CYS SEQRES 8 A 575 ARG VAL VAL ASP ALA PHE SER PHE LYS PRO PRO GLU ILE SEQRES 9 A 575 ASP PRO ASN TRP ARG TYR THR ALA SER VAL VAL PRO ASP SEQRES 10 A 575 VAL LEU GLU ARG ASN LEU GLN SER ASP TYR PHE VAL ALA SEQRES 11 A 575 GLU GLU GLY LYS VAL TYR GLY PHE LEU SER SER LYS ILE SEQRES 12 A 575 ALA HIS PRO PHE PHE ALA VAL GLU ASP GLY GLU LEU VAL SEQRES 13 A 575 ALA TYR LEU GLU TYR PHE ASP VAL GLU PHE ASP ASP PHE SEQRES 14 A 575 VAL PRO LEU GLU PRO LEU VAL VAL LEU GLU ASP PRO ASN SEQRES 15 A 575 THR PRO LEU LEU LEU GLU LYS TYR ALA GLU LEU VAL GLY SEQRES 16 A 575 MET GLU ASN ASN ALA ARG VAL PRO LYS HIS THR PRO THR SEQRES 17 A 575 GLY TRP CYS SER TRP TYR HIS TYR PHE LEU ASP LEU THR SEQRES 18 A 575 TRP GLU GLU THR LEU LYS ASN LEU LYS LEU ALA LYS ASN SEQRES 19 A 575 PHE PRO PHE GLU VAL PHE GLN ILE ASP ASP ALA TYR GLU SEQRES 20 A 575 LYS ASP ILE GLY ASP TRP LEU VAL THR ARG GLY ASP PHE SEQRES 21 A 575 PRO SER VAL GLU GLU MET ALA LYS VAL ILE ALA GLU ASN SEQRES 22 A 575 GLY PHE ILE PRO GLY ILE TRP THR ALA PRO PHE SER VAL SEQRES 23 A 575 SER GLU THR SER ASP VAL PHE ASN GLU HIS PRO ASP TRP SEQRES 24 A 575 VAL VAL LYS GLU ASN GLY GLU PRO LYS MET ALA TYR ARG SEQRES 25 A 575 ASN TRP ASN LYS LYS ILE TYR ALA LEU ASP LEU SER LYS SEQRES 26 A 575 ASP GLU VAL LEU ASN TRP LEU PHE ASP LEU PHE SER SER SEQRES 27 A 575 LEU ARG LYS MET GLY TYR ARG TYR PHE LYS ILE ASP PHE SEQRES 28 A 575 LEU PHE ALA GLY ALA VAL PRO GLY GLU ARG LYS LYS ASN SEQRES 29 A 575 ILE THR PRO ILE GLN ALA PHE ARG LYS GLY ILE GLU THR SEQRES 30 A 575 ILE ARG LYS ALA VAL GLY GLU ASP SER PHE ILE LEU GLY SEQRES 31 A 575 CYS GLY SER PRO LEU LEU PRO ALA VAL GLY CYS VAL ASP SEQRES 32 A 575 GLY MET ARG ILE GLY PRO ASP THR ALA PRO PHE TRP GLY SEQRES 33 A 575 GLU HIS ILE GLU ASP ASN GLY ALA PRO ALA ALA ARG TRP SEQRES 34 A 575 ALA LEU ARG ASN ALA ILE THR ARG TYR PHE MET HIS ASP SEQRES 35 A 575 ARG PHE TRP LEU ASN ASP PRO ASP CYS LEU ILE LEU ARG SEQRES 36 A 575 GLU GLU LYS THR ASP LEU THR GLN LYS GLU LYS GLU LEU SEQRES 37 A 575 TYR SER TYR THR CYS GLY VAL LEU ASP ASN MET ILE ILE SEQRES 38 A 575 GLU SER ASP ASP LEU SER LEU VAL ARG ASP HIS GLY LYS SEQRES 39 A 575 LYS VAL LEU LYS GLU THR LEU GLU LEU LEU GLY GLY ARG SEQRES 40 A 575 PRO ARG VAL GLN ASN ILE MET SER GLU ASP LEU ARG TYR SEQRES 41 A 575 GLU ILE VAL SER SER GLY THR LEU SER GLY ASN VAL LYS SEQRES 42 A 575 ILE VAL VAL ASP LEU ASN SER ARG GLU TYR HIS LEU GLU SEQRES 43 A 575 LYS GLU GLY LYS SER SER LEU LYS LYS ARG VAL VAL LYS SEQRES 44 A 575 ARG GLU ASP GLY ARG ASN PHE TYR PHE TYR GLU GLU GLY SEQRES 45 A 575 GLU ARG GLU HET SO4 A 601 5 HET SO4 A 602 5 HET SO4 A 603 5 HET FH2 A 604 12 HET MG A 605 1 HET GOL A 606 6 HETNAM SO4 SULFATE ION HETNAM FH2 (1~{S},2~{S},3~{S},4~{S})-3-FLUORANYL-6- HETNAM 2 FH2 (HYDROXYMETHYL)CYCLOHEX-5-ENE-1,2,4-TRIOL HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 FH2 C7 H11 F O4 FORMUL 6 MG MG 2+ FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *538(H2 O) HELIX 1 AA1 GLY A -5 SER A 0 1 6 HELIX 2 AA2 TRP A 85 SER A 90 1 6 HELIX 3 AA3 VAL A 92 GLU A 97 1 6 HELIX 4 AA4 ASN A 159 ASN A 176 1 18 HELIX 5 AA5 SER A 189 PHE A 194 1 6 HELIX 6 AA6 LEU A 195 LEU A 197 5 3 HELIX 7 AA7 THR A 198 ALA A 209 1 12 HELIX 8 AA8 LYS A 210 PHE A 212 5 3 HELIX 9 AA9 SER A 239 ASN A 250 1 12 HELIX 10 AB1 SER A 267 HIS A 273 1 7 HELIX 11 AB2 PRO A 274 VAL A 277 5 4 HELIX 12 AB3 LYS A 302 GLY A 320 1 19 HELIX 13 AB4 PHE A 328 VAL A 334 5 7 HELIX 14 AB5 THR A 343 GLY A 360 1 18 HELIX 15 AB6 LEU A 372 VAL A 376 5 5 HELIX 16 AB7 ALA A 403 ARG A 414 1 12 HELIX 17 AB8 TYR A 415 HIS A 418 5 4 HELIX 18 AB9 THR A 439 LEU A 453 1 15 HELIX 19 AC1 ASP A 462 VAL A 466 5 5 HELIX 20 AC2 ARG A 467 GLU A 479 1 13 SHEET 1 AA1 6 LYS A 6 THR A 7 0 SHEET 2 AA1 6 GLU A 2 ILE A 3 -1 N ILE A 3 O LYS A 6 SHEET 3 AA1 6 ARG A 45 LYS A 52 -1 O ARG A 50 N GLU A 2 SHEET 4 AA1 6 GLU A 131 GLU A 137 -1 O LEU A 132 N THR A 51 SHEET 5 AA1 6 HIS A 122 GLU A 128 -1 N PHE A 124 O TYR A 135 SHEET 6 AA1 6 LEU A 100 ASP A 103 -1 N SER A 102 O PHE A 125 SHEET 1 AA2 6 GLY A 11 LYS A 16 0 SHEET 2 AA2 6 PHE A 20 ILE A 29 -1 O PHE A 24 N PHE A 13 SHEET 3 AA2 6 GLY A 32 GLY A 41 -1 O ARG A 38 N GLU A 23 SHEET 4 AA2 6 LEU A 152 GLU A 156 -1 O LEU A 152 N ILE A 35 SHEET 5 AA2 6 LYS A 111 PHE A 115 -1 N GLY A 114 O VAL A 153 SHEET 6 AA2 6 PHE A 105 GLU A 108 -1 N VAL A 106 O TYR A 113 SHEET 1 AA3 4 GLY A 11 LYS A 16 0 SHEET 2 AA3 4 PHE A 20 ILE A 29 -1 O PHE A 24 N PHE A 13 SHEET 3 AA3 4 GLY A 32 GLY A 41 -1 O ARG A 38 N GLU A 23 SHEET 4 AA3 4 PHE A 143 PRO A 148 -1 O VAL A 147 N VAL A 39 SHEET 1 AA4 2 LYS A 56 ASN A 60 0 SHEET 2 AA4 2 CYS A 68 ASP A 72 -1 O ARG A 69 N VAL A 59 SHEET 1 AA5 8 LEU A 423 ASP A 425 0 SHEET 2 AA5 8 GLY A 381 ARG A 383 1 N MET A 382 O ASP A 425 SHEET 3 AA5 8 PHE A 364 GLY A 367 1 N GLY A 367 O ARG A 383 SHEET 4 AA5 8 TYR A 323 ILE A 326 1 N PHE A 324 O LEU A 366 SHEET 5 AA5 8 ILE A 253 THR A 258 1 N THR A 258 O LYS A 325 SHEET 6 AA5 8 VAL A 216 ILE A 219 1 N PHE A 217 O ILE A 253 SHEET 7 AA5 8 THR A 185 CYS A 188 1 N TRP A 187 O GLN A 218 SHEET 8 AA5 8 ILE A 457 GLU A 459 1 O GLU A 459 N GLY A 186 SHEET 1 AA6 3 SER A 262 SER A 264 0 SHEET 2 AA6 3 LYS A 293 ALA A 297 -1 O TYR A 296 N VAL A 263 SHEET 3 AA6 3 MET A 286 ASN A 290 -1 N ALA A 287 O ILE A 295 SHEET 1 AA7 2 LYS A 279 GLU A 280 0 SHEET 2 AA7 2 GLU A 283 PRO A 284 -1 O GLU A 283 N GLU A 280 SHEET 1 AA8 4 ARG A 484 VAL A 487 0 SHEET 2 AA8 4 ARG A 496 THR A 504 -1 O VAL A 500 N ARG A 486 SHEET 3 AA8 4 GLY A 507 ASP A 514 -1 O ILE A 511 N ILE A 499 SHEET 4 AA8 4 GLU A 519 LYS A 524 -1 O GLU A 523 N LYS A 510 LINK OD2 ASP A 419 MG MG A 605 1555 1555 2.11 LINK OD2 ASP A 454 MG MG A 605 1555 1555 2.03 LINK MG MG A 605 O HOH A 747 1555 1555 2.13 LINK MG MG A 605 O HOH A 918 1555 1555 2.11 LINK MG MG A 605 O HOH A 998 1555 1555 2.09 LINK MG MG A 605 O HOH A1029 1555 1555 2.14 SITE 1 AC1 9 ARG A 9 PHE A 391 GLY A 393 GLU A 394 SITE 2 AC1 9 HIS A 395 HOH A 730 HOH A 768 HOH A 852 SITE 3 AC1 9 HOH A 956 SITE 1 AC2 5 LYS A 302 ASP A 303 GLU A 304 LYS A 339 SITE 2 AC2 5 HOH A 911 SITE 1 AC3 3 GLU A 434 LYS A 435 THR A 436 SITE 1 AC4 14 SER A -4 TRP A 65 TRP A 190 TYR A 191 SITE 2 AC4 14 ASP A 220 ASP A 221 TRP A 257 LYS A 325 SITE 3 AC4 14 ASP A 327 PHE A 328 CYS A 368 ARG A 383 SITE 4 AC4 14 ASP A 387 HOH A 796 SITE 1 AC5 6 ASP A 419 ASP A 454 HOH A 747 HOH A 918 SITE 2 AC5 6 HOH A 998 HOH A1029 SITE 1 AC6 6 LEU A 195 ASP A 221 GLU A 224 LYS A 225 SITE 2 AC6 6 ASP A 226 TRP A 291 CRYST1 95.817 97.506 67.419 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 0.010437 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014833 0.00000