10 20 30 40 50 60 70 80 2J47 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER INHIBITOR 25-AUG-06 2J47
TITLE BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX TITLE 2 WITH A IMIDAZOLE-PUGNAC HYBRID INHIBITOR
COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSAMINIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 22-737; COMPND 5 SYNONYM: O-GLCNACASE; COMPND 6 EC: 3.2.1.52; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: PUGNAC-IMIDAZOLE HYBRID INHIBITOR
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON; SOURCE 3 ORGANISM_TAXID: 226186; SOURCE 4 STRAIN: VPI-5482; SOURCE 5 ATCC: 29148; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A
KEYWDS INHIBITOR, O-GLCNACASE, IMIDAZOLE, GH84, PUGNAC, ENZYME, KEYWDS 2 INHIBITION
EXPDTA X-RAY DIFFRACTION
AUTHOR R.J.DENNIS,G.J.DAVIES
REVDAT 4 24-FEB-09 2J47 1 VERSN REVDAT 3 05-JUN-07 2J47 1 REMARK REVDAT 2 25-OCT-06 2J47 1 JRNL REVDAT 1 03-OCT-06 2J47 0
JRNL AUTH B.SHANMUGASUNDARAM,A.W.DEBOWSKI,R.J.DENNIS, JRNL AUTH 2 G.J.DAVIES,D.J.VOCADLO,A.VASELLA JRNL TITL INHIBITION OF O-GLCNACASE BY A GLUCO-CONFIGURED JRNL TITL 2 NAGSTATIN AND A PUGNAC-IMIDAZOLE HYBRID INHIBITOR JRNL REF CHEM. COMMUN. V. 42 4372 2006 JRNL REFN ISSN 1359-7345 JRNL PMID 17057847 JRNL DOI 10.1039/B612154C
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.J.DENNIS,E.J.TAYLOR,M.S.MACAULEY,K.A.STUBBS, REMARK 1 AUTH 2 J.P.TURKENBURG,S.J.HART,G.N.BLACK,D.J.VOCADLO, REMARK 1 AUTH 3 G.J.DAVIES REMARK 1 TITL STRUCTURE AND MECHANISM OF A BACTERIAL BETA- REMARK 1 TITL 2 GLUCOSAMINIDASE HAVING O-GLCNACSAE ACTIVITY REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 13 365 2006 REMARK 1 REFN ISSN 1545-9993 REMARK 1 PMID 16565725 REMARK 1 DOI 10.1038/NSMB1079
REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 92.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 53713 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2870 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3874 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4668 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 319 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.37000 REMARK 3 B33 (A**2) : -0.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.38000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.149 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.089 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.060 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4812 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6530 ; 1.482 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 572 ; 8.587 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 243 ;34.937 ;24.691 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 815 ;13.941 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;16.969 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 686 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3722 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2277 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3312 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 325 ; 0.149 ; 0.200 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): 47 ; 0.192 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.138 ; 0.200 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): 2953 ; 1.030 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4630 ; 1.608 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2181 ; 2.632 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1898 ; 3.955 ; 4.500 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 : 1.40 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 REMARK 3 RIDING POSITIONS.
REMARK 4 REMARK 4 2J47 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-AUG-06. REMARK 100 THE PDBE ID CODE IS EBI-29827.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53713 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2CHO REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.4 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6M SODIUM ACETATE,13% (V/V) REMARK 280 PEG3500, 0.1M MES PH6.0, 10% (V/V) GLYCEROL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 94.21300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.67000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 94.21300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.67000 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 GENERATING THE BIOMOLECULE 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: PQS 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 375 REMARK 375 SPECIAL POSITION REMARK 375 HOH A2164 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2284 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 GLN A 1 REMARK 465 ASN A 2 REMARK 465 VAL A 3 REMARK 465 LEU A 21 REMARK 465 PRO A 22 REMARK 465 ALA A 23 REMARK 465 VAL A 24 REMARK 465 LYS A 48 REMARK 465 GLN A 49 REMARK 465 SER A 50 REMARK 465 SER A 51 REMARK 465 LYS A 52 REMARK 465 LYS A 53 REMARK 465 GLU A 456 REMARK 465 GLY A 457 REMARK 465 LYS A 458 REMARK 465 ASN A 459 REMARK 465 TYR A 590 REMARK 465 MET A 591 REMARK 465 PRO A 592 REMARK 465 HIS A 593 REMARK 465 LYS A 594 REMARK 465 MET A 595 REMARK 465 ILE A 596 REMARK 465 SER A 597 REMARK 465 ASN A 598 REMARK 465 VAL A 599 REMARK 465 GLU A 600 REMARK 465 GLN A 601 REMARK 465 ILE A 602 REMARK 465 LYS A 603 REMARK 465 ASN A 604 REMARK 465 LEU A 605 REMARK 465 PRO A 606 REMARK 465 LEU A 607 REMARK 465 GLN A 608 REMARK 465 VAL A 609 REMARK 465 LYS A 610 REMARK 465 ALA A 611 REMARK 465 ASN A 612 REMARK 465 ARG A 613 REMARK 465 VAL A 614 REMARK 465 LEU A 615 REMARK 465 ILE A 616 REMARK 465 SER A 617 REMARK 465 PRO A 618 REMARK 465 ALA A 619 REMARK 465 ASN A 620 REMARK 465 GLU A 621 REMARK 465 VAL A 622 REMARK 465 VAL A 623 REMARK 465 LYS A 624 REMARK 465 TRP A 625 REMARK 465 ALA A 626 REMARK 465 ALA A 627 REMARK 465 GLY A 628 REMARK 465 ASN A 629 REMARK 465 SER A 630 REMARK 465 VAL A 631 REMARK 465 GLU A 632 REMARK 465 ILE A 633 REMARK 465 GLU A 634 REMARK 465 LEU A 635 REMARK 465 ASP A 636 REMARK 465 ALA A 637 REMARK 465 ILE A 638 REMARK 465 TYR A 639 REMARK 465 PRO A 640 REMARK 465 GLY A 641 REMARK 465 GLU A 642 REMARK 465 ASN A 643 REMARK 465 ILE A 644 REMARK 465 GLN A 645 REMARK 465 ILE A 646 REMARK 465 ASN A 647 REMARK 465 PHE A 648 REMARK 465 GLY A 649 REMARK 465 LYS A 650 REMARK 465 ASP A 651 REMARK 465 ALA A 652 REMARK 465 PRO A 653 REMARK 465 CYS A 654 REMARK 465 THR A 655 REMARK 465 TRP A 656 REMARK 465 GLY A 657 REMARK 465 ARG A 658 REMARK 465 LEU A 659 REMARK 465 GLU A 660 REMARK 465 ILE A 661 REMARK 465 SER A 662 REMARK 465 THR A 663 REMARK 465 ASP A 664 REMARK 465 GLY A 665 REMARK 465 LYS A 666 REMARK 465 GLU A 667 REMARK 465 TRP A 668 REMARK 465 LYS A 669 REMARK 465 THR A 670 REMARK 465 VAL A 671 REMARK 465 ASP A 672 REMARK 465 LEU A 673 REMARK 465 LYS A 674 REMARK 465 GLN A 675 REMARK 465 LYS A 676 REMARK 465 GLU A 677 REMARK 465 SER A 678 REMARK 465 ARG A 679 REMARK 465 LEU A 680 REMARK 465 SER A 681 REMARK 465 ALA A 682 REMARK 465 GLY A 683 REMARK 465 LEU A 684 REMARK 465 GLN A 685 REMARK 465 LYS A 686 REMARK 465 ALA A 687 REMARK 465 PRO A 688 REMARK 465 VAL A 689 REMARK 465 LYS A 690 REMARK 465 PHE A 691 REMARK 465 VAL A 692 REMARK 465 ARG A 693 REMARK 465 PHE A 694 REMARK 465 THR A 695 REMARK 465 ASN A 696 REMARK 465 VAL A 697 REMARK 465 SER A 698 REMARK 465 ASP A 699 REMARK 465 GLU A 700 REMARK 465 GLU A 701 REMARK 465 GLN A 702 REMARK 465 GLN A 703 REMARK 465 VAL A 704 REMARK 465 TYR A 705 REMARK 465 LEU A 706 REMARK 465 ARG A 707 REMARK 465 GLN A 708 REMARK 465 PHE A 709 REMARK 465 VAL A 710 REMARK 465 LEU A 711 REMARK 465 THR A 712 REMARK 465 ILE A 713 REMARK 465 GLU A 714 REMARK 465 LYS A 715 REMARK 465 LYS A 716
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 112 CG CD CE NZ
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; REMARK 480 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 480 I=INSERTION CODE): REMARK 480 M RES CSSEQI ATOMS REMARK 480 LYS A 17 CG CD CE NZ REMARK 480 GLU A 31 CD OE1 OE2 REMARK 480 LYS A 88 CG CD CE NZ
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 GLU A 31 CG GLU A 31 CD -0.181 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 GLU A 31 CB - CG - CD ANGL. DEV. = 17.8 DEGREES REMARK 500 GLU A 31 CG - CD - OE1 ANGL. DEV. = 14.4 DEGREES REMARK 500 GLU A 31 CG - CD - OE2 ANGL. DEV. = -14.1 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 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 16 33.33 -93.62 REMARK 500 SER A 172 -142.42 -124.97 REMARK 500 PHE A 265 -61.73 -141.51 REMARK 500 ASP A 271 29.89 -146.81 REMARK 500 ASN A 273 -84.95 -90.84 REMARK 500 VAL A 346 57.42 -142.10 REMARK 500 ALA A 414 42.56 -148.99 REMARK 500 VAL A 560 -50.33 -121.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 5 GLN A 6 -146.77 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 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL.
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDV A1590 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1719
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CHN RELATED DB: PDB REMARK 900 BACTEROIDES THETAIOTAOMICRON HEXOSAMINIDASE WITH REMARK 900 O-GLCNACASE ACTIVITY REMARK 900 RELATED ID: 2CHO RELATED DB: PDB REMARK 900 BACTEROIDES THETAIOTAOMICRON HEXOSAMINIDASE WITH REMARK 900 O-GLCNACASE ACTIVITY
REMARK 999 REMARK 999 SEQUENCE REMARK 999 SIGNAL PETIDE FROM RESIDUE 1-22. SEQUENCE CLONED FROM N23. REMARK 999 NUMBERED IN PDB AS IN MATURE PROTEIN, GLN 1, ASN 2, ETC.
DBREF 2J47 A 1 716 UNP Q89ZI2 Q89ZI2_BACTN 22 737
SEQRES 1 A 716 GLN ASN VAL SER LEU GLN PRO PRO PRO GLN GLN LEU ILE SEQRES 2 A 716 VAL GLN ASN LYS THR ILE ASP LEU PRO ALA VAL TYR GLN SEQRES 3 A 716 LEU ASN GLY GLY GLU GLU ALA ASN PRO HIS ALA VAL LYS SEQRES 4 A 716 VAL LEU LYS GLU LEU LEU SER GLY LYS GLN SER SER LYS SEQRES 5 A 716 LYS GLY MET LEU ILE SER ILE GLY GLU LYS GLY ASP LYS SEQRES 6 A 716 SER VAL ARG LYS TYR SER ARG GLN ILE PRO ASP HIS LYS SEQRES 7 A 716 GLU GLY TYR TYR LEU SER VAL ASN GLU LYS GLU ILE VAL SEQRES 8 A 716 LEU ALA GLY ASN ASP GLU ARG GLY THR TYR TYR ALA LEU SEQRES 9 A 716 GLN THR PHE ALA GLN LEU LEU LYS ASP GLY LYS LEU PRO SEQRES 10 A 716 GLU VAL GLU ILE LYS ASP TYR PRO SER VAL ARG TYR ARG SEQRES 11 A 716 GLY VAL VAL GLU GLY PHE TYR GLY THR PRO TRP SER HIS SEQRES 12 A 716 GLN ALA ARG LEU SER GLN LEU LYS PHE TYR GLY LYS ASN SEQRES 13 A 716 LYS MET ASN THR TYR ILE TYR GLY PRO LYS ASP ASP PRO SEQRES 14 A 716 TYR HIS SER ALA PRO ASN TRP ARG LEU PRO TYR PRO ASP SEQRES 15 A 716 LYS GLU ALA ALA GLN LEU GLN GLU LEU VAL ALA VAL ALA SEQRES 16 A 716 ASN GLU ASN GLU VAL ASP PHE VAL TRP ALA ILE HIS PRO SEQRES 17 A 716 GLY GLN ASP ILE LYS TRP ASN LYS GLU ASP ARG ASP LEU SEQRES 18 A 716 LEU LEU ALA LYS PHE GLU LYS MET TYR GLN LEU GLY VAL SEQRES 19 A 716 ARG SER PHE ALA VAL PHE PHE ASP ASP ILE SER GLY GLU SEQRES 20 A 716 GLY THR ASN PRO GLN LYS GLN ALA GLU LEU LEU ASN TYR SEQRES 21 A 716 ILE ASP GLU LYS PHE ALA GLN VAL LYS PRO ASP ILE ASN SEQRES 22 A 716 GLN LEU VAL MET CYS PRO THR GLU TYR ASN LYS SER TRP SEQRES 23 A 716 SER ASN PRO ASN GLY ASN TYR LEU THR THR LEU GLY ASP SEQRES 24 A 716 LYS LEU ASN PRO SER ILE GLN ILE MET TRP THR GLY ASP SEQRES 25 A 716 ARG VAL ILE SER ASP ILE THR ARG ASP GLY ILE SER TRP SEQRES 26 A 716 ILE ASN GLU ARG ILE LYS ARG PRO ALA TYR ILE TRP TRP SEQRES 27 A 716 ASN PHE PRO VAL SER ASP TYR VAL ARG ASP HIS LEU LEU SEQRES 28 A 716 LEU GLY PRO VAL TYR GLY ASN ASP THR THR ILE ALA LYS SEQRES 29 A 716 GLU MET SER GLY PHE VAL THR ASN PRO MET GLU HIS ALA SEQRES 30 A 716 GLU SER SER LYS ILE ALA ILE TYR SER VAL ALA SER TYR SEQRES 31 A 716 ALA TRP ASN PRO ALA LYS TYR ASP THR TRP GLN THR TRP SEQRES 32 A 716 LYS ASP ALA ILE ARG THR ILE LEU PRO SER ALA ALA GLU SEQRES 33 A 716 GLU LEU GLU CYS PHE ALA MET HIS ASN SER ASP LEU GLY SEQRES 34 A 716 PRO ASN GLY HIS GLY TYR ARG ARG GLU GLU SER MET ASP SEQRES 35 A 716 ILE GLN PRO ALA ALA GLU ARG PHE LEU LYS ALA PHE LYS SEQRES 36 A 716 GLU GLY LYS ASN TYR ASP LYS ALA ASP PHE GLU THR LEU SEQRES 37 A 716 GLN TYR THR PHE GLU ARG MET LYS GLU SER ALA ASP ILE SEQRES 38 A 716 LEU LEU MET ASN THR GLU ASN LYS PRO LEU ILE VAL GLU SEQRES 39 A 716 ILE THR PRO TRP VAL HIS GLN PHE LYS LEU THR ALA GLU SEQRES 40 A 716 MET GLY GLU GLU VAL LEU LYS MET VAL GLU GLY ARG ASN SEQRES 41 A 716 GLU SER TYR PHE LEU ARG LYS TYR ASN HIS VAL LYS ALA SEQRES 42 A 716 LEU GLN GLN GLN MET PHE TYR ILE ASP GLN THR SER ASN SEQRES 43 A 716 GLN ASN PRO TYR GLN PRO GLY VAL LYS THR ALA THR ARG SEQRES 44 A 716 VAL ILE LYS PRO LEU ILE ASP ARG THR PHE ALA THR VAL SEQRES 45 A 716 VAL LYS PHE PHE ASN GLN LYS PHE ASN ALA HIS LEU ASP SEQRES 46 A 716 ALA THR THR ASP TYR MET PRO HIS LYS MET ILE SER ASN SEQRES 47 A 716 VAL GLU GLN ILE LYS ASN LEU PRO LEU GLN VAL LYS ALA SEQRES 48 A 716 ASN ARG VAL LEU ILE SER PRO ALA ASN GLU VAL VAL LYS SEQRES 49 A 716 TRP ALA ALA GLY ASN SER VAL GLU ILE GLU LEU ASP ALA SEQRES 50 A 716 ILE TYR PRO GLY GLU ASN ILE GLN ILE ASN PHE GLY LYS SEQRES 51 A 716 ASP ALA PRO CYS THR TRP GLY ARG LEU GLU ILE SER THR SEQRES 52 A 716 ASP GLY LYS GLU TRP LYS THR VAL ASP LEU LYS GLN LYS SEQRES 53 A 716 GLU SER ARG LEU SER ALA GLY LEU GLN LYS ALA PRO VAL SEQRES 54 A 716 LYS PHE VAL ARG PHE THR ASN VAL SER ASP GLU GLU GLN SEQRES 55 A 716 GLN VAL TYR LEU ARG GLN PHE VAL LEU THR ILE GLU LYS SEQRES 56 A 716 LYS
HET GDV A1590 26 HET GOL A1719 6
HETNAM GDV (5R,6R,7R,8S)-8-(ACETYLAMINO)-6,7-DIHYDROXY- HETNAM 2 GDV 5-(HYDROXYMETHYL)-N-PHENYL-1,5,6,7,8,8A- HETNAM 3 GDV HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-2- HETNAM 4 GDV CARBOXAMIDE HETNAM GOL GLYCEROL
FORMUL 2 GDV C17 H21 N4 O5 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *319(H2 O1)
HELIX 1 1 ASN A 34 LEU A 45 1 12 HELIX 2 2 ASP A 64 SER A 71 5 8 HELIX 3 3 ASP A 96 LEU A 111 1 16 HELIX 4 4 SER A 142 ASN A 156 1 15 HELIX 5 5 PRO A 181 ASN A 198 1 18 HELIX 6 6 ASN A 215 LEU A 232 1 18 HELIX 7 7 GLY A 246 THR A 249 5 4 HELIX 8 8 ASN A 250 PHE A 265 1 16 HELIX 9 9 ASN A 283 SER A 287 5 5 HELIX 10 10 ASN A 292 LEU A 301 1 10 HELIX 11 11 THR A 319 LYS A 331 1 13 HELIX 12 12 ILE A 362 LYS A 364 5 3 HELIX 13 13 HIS A 376 ASN A 393 1 18 HELIX 14 14 PRO A 394 TYR A 397 5 4 HELIX 15 15 ASP A 398 LEU A 411 1 14 HELIX 16 16 ALA A 414 HIS A 424 1 11 HELIX 17 17 ILE A 443 LYS A 455 1 13 HELIX 18 18 ASP A 461 MET A 484 1 24 HELIX 19 19 ASN A 488 GLU A 517 1 30 HELIX 20 20 ASN A 520 SER A 545 1 26 HELIX 21 21 VAL A 560 PHE A 580 1 21
SHEET 1 AA 6 GLN A 11 ILE A 19 0 SHEET 2 AA 6 LEU A 116 ASP A 123 -1 O LEU A 116 N ILE A 19 SHEET 3 AA 6 TYR A 81 VAL A 85 -1 O TYR A 81 N ASP A 123 SHEET 4 AA 6 GLU A 89 GLY A 94 -1 O VAL A 91 N SER A 84 SHEET 5 AA 6 LEU A 56 GLU A 61 1 O LEU A 56 N ILE A 90 SHEET 6 AA 6 GLN A 26 ASN A 28 1 O GLN A 26 N ILE A 57 SHEET 1 AB 9 TYR A 129 GLU A 134 0 SHEET 2 AB 9 MET A 366 THR A 371 1 O SER A 367 N TYR A 129 SHEET 3 AB 9 ALA A 334 TRP A 338 1 O ALA A 334 N SER A 367 SHEET 4 AB 9 GLN A 306 TRP A 309 1 O ILE A 307 N TYR A 335 SHEET 5 AB 9 LEU A 275 CYS A 278 1 O LEU A 275 N GLN A 306 SHEET 6 AB 9 SER A 236 PHE A 240 1 O PHE A 237 N VAL A 276 SHEET 7 AB 9 ASP A 201 ILE A 206 1 O PHE A 202 N SER A 236 SHEET 8 AB 9 THR A 160 TYR A 163 1 O TYR A 161 N VAL A 203 SHEET 9 AB 9 TYR A 129 GLU A 134 1 O ARG A 130 N THR A 160
CISPEP 1 GLN A 6 PRO A 7 0 -0.82 CISPEP 2 ALA A 173 PRO A 174 0 -6.13 CISPEP 3 PHE A 340 PRO A 341 0 4.48
SITE 1 AC1 17 GLY A 135 PHE A 136 LYS A 166 ASP A 242 SITE 2 AC1 17 ASP A 243 TYR A 282 TRP A 286 ASN A 288 SITE 3 AC1 17 VAL A 314 TRP A 337 ASN A 339 ASP A 344 SITE 4 AC1 17 TYR A 345 ASN A 372 HIS A 433 HOH A2167 SITE 5 AC1 17 HOH A2318 SITE 1 AC2 7 TYR A 137 ASP A 344 TYR A 345 ARG A 347 SITE 2 AC2 7 TYR A 550 GLN A 551 HOH A2319
CRYST1 188.426 51.340 85.474 90.00 100.22 90.00 C 1 2 1 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 0.005307 0.000000 0.000957 0.00000
SCALE2 0.000000 0.019478 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011888 0.00000