HEADER INHIBITOR 25-AUG-06 2J47
TITLE BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX WITH A
TITLE 2 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, INHIBITION
EXPDTA X-RAY DIFFRACTION
AUTHOR R.J.DENNIS,G.J.DAVIES
REVDAT 5 13-DEC-23 2J47 1 REMARK
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,G.J.DAVIES,
JRNL AUTH 2 D.J.VOCADLO,A.VASELLA
JRNL TITL INHIBITION OF O-GLCNACASE BY A GLUCO-CONFIGURED NAGSTATIN
JRNL TITL 2 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,G.J.DAVIES
REMARK 1 TITL STRUCTURE AND MECHANISM OF A BACTERIAL BETA-GLUCOSAMINIDASE
REMARK 1 TITL 2 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,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) : 1.98
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 : 4652
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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2181 ; 2.632 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1898 ; 3.955 ; 4.500
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 : 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 RIDING
REMARK 3 POSITIONS.
REMARK 4
REMARK 4 2J47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-AUG-06.
REMARK 100 THE DEPOSITION ID IS D_1290029827.
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 CCD
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 (%): 49.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6M SODIUM ACETATE,13% (V/V) PEG3500,
REMARK 280 0.1M MES PH6.0, 10% (V/V) GLYCEROL, PH 6.00
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 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 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 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; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI 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
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 46 87.55 -58.17
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 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 O-GLCNACASE
REMARK 900 ACTIVITY
REMARK 900 RELATED ID: 2CHO RELATED DB: PDB
REMARK 900 BACTEROIDES THETAIOTAOMICRON HEXOSAMINIDASE WITH O-GLCNACASE
REMARK 900 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-5-
HETNAM 2 GDV (HYDROXYMETHYL)-N-PHENYL-1,5,6,7,8,8A-
HETNAM 3 GDV HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-2-CARBOXAMIDE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 GDV C17 H21 N4 O5 1+
FORMUL 3 GOL C3 H8 O3
FORMUL 4 HOH *319(H2 O)
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
(ATOM LINES ARE NOT SHOWN.)
END
