HEADER HYDROLASE 02-OCT-08 2V5D TITLE STRUCTURE OF A FAMILY 84 GLYCOSIDE HYDROLASE AND A FAMILY TITLE 2 32 CARBOHYDRATE-BINDING MODULE IN TANDEM FROM CLOSTRIDIUM TITLE 3 PERFRINGENS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: O-GLCNACASE NAGJ; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 31-767; COMPND 5 SYNONYM: BETA-HEXOSAMINIDASE, HEXOSAMINIDASE B, GH84, COMPND 6 N-ACETYL-BETA-GLUCOSAMINIDASE, COMPND 7 BETA-N-ACETYLHEXOSAMINIDASE, FAMILY 84 GLYCOSIDE COMPND 8 HYDROLASE, FAMILY 32 CARBOHYDRATE BINDING MODULE; COMPND 9 EC: 3.2.1.52; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS; SOURCE 3 ORGANISM_TAXID: 1502; SOURCE 4 ATCC: 13124; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS FAMILY 32 CARBOHYDRATE BINDING MODULE, GLYCOSIDASE, KEYWDS 2 CLOSTRIDIUM PERFRINGENS, GH84, GH84C, CBM32, HYDROLASE, KEYWDS 3 COILED COIL, FAMILY 84 GLYCOSIDE HYDROLASE, CARBOHYDRATE KEYWDS 4 BINDING MODULE EXPDTA X-RAY DIFFRACTION AUTHOR E.FICKO-BLEAN,K.J.GREGG,J.J.ADAMS,J.H.HEHEMANN,S.J.SMITH, AUTHOR 2 M.CZJZEK,A.B.BORASTON REVDAT 3 14-APR-09 2V5D 1 JRNL REMARK REVDAT 2 17-FEB-09 2V5D 1 JRNL REMARK REVDAT 1 27-JAN-09 2V5D 0 JRNL AUTH E.FICKO-BLEAN,K.J.GREGG,J.J.ADAMS,J.H.HEHEMANN, JRNL AUTH 2 S.J.SMITH,M.CZJZEK,A.B.BORASTON JRNL TITL PORTRAIT OF AN ENZYME: A COMPLETE STRUCTURAL JRNL TITL 2 ANALYSIS OF A MULTI-MODULAR BETA-N- JRNL TITL 3 ACETYLGLUCOSAMINIDASE FROM CLOSTRIDIUM PERFRINGENS JRNL REF J.BIOL.CHEM. V. 284 9876 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19193644 JRNL DOI 10.1074/JBC.M808954200 REMARK 2 REMARK 2 RESOLUTION. 3.30 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 141.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.75 REMARK 3 NUMBER OF REFLECTIONS : 11825 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) : 0.32479 REMARK 3 R VALUE (WORKING SET) : 0.32249 REMARK 3 FREE R VALUE : 0.36981 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 594 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) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 884 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.374 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.364 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5677 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.808 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.05000 REMARK 3 B22 (A**2) : -0.68000 REMARK 3 B33 (A**2) : -0.78000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.884 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.845 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 113.607 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.834 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.780 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5792 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3804 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7863 ; 0.904 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9320 ; 0.925 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 720 ; 4.553 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;37.260 ;25.859 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 971 ;12.136 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;12.566 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 860 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6567 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1111 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1286 ; 0.159 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3980 ; 0.164 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2860 ; 0.163 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3010 ; 0.079 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 123 ; 0.098 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.122 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 6 ; 0.058 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 26 ; 0.125 ; 0.200 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): 3753 ; 0.117 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1460 ; 0.013 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5787 ; 0.212 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2397 ; 0.121 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2076 ; 0.168 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 10784 ; 0.201 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 31 ; 0.562 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 9480 ; 0.085 ; 3.000 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 : 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 2V5D COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JAN-09. REMARK 100 THE PDBE ID CODE IS EBI-37731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 113.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12400 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.30 REMARK 200 RESOLUTION RANGE LOW (A) : 141.42 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 2.54 REMARK 200 R MERGE (I) : 0.11 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.40 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.77300 REMARK 290 SMTRY3 2 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 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 VAL A 31 REMARK 465 GLY A 32 REMARK 465 PRO A 33 REMARK 465 LYS A 34 REMARK 465 THR A 35 REMARK 465 GLY A 36 REMARK 465 GLU A 37 REMARK 465 GLU A 38 REMARK 465 ASN A 39 REMARK 465 GLN A 40 REMARK 465 ARG A 228 REMARK 465 GLU A 229 REMARK 465 PRO A 230 REMARK 465 TYR A 231 REMARK 465 PRO A 232 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 694 NZ 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 GLU A 186 - O ALA A 216 1.68 REMARK 500 O ARG A 224 - CD1 TRP A 227 1.62 REMARK 500 O GLY A 260 - CD1 ILE A 299 2.05 REMARK 500 CG1 VAL A 629 - O GLU A 675 2.09 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 HIS A 223 O - C - N ANGL. DEV. = 11.8 DEGREES REMARK 500 ASP A 268 N - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 ALA A 269 N - CA - C ANGL. DEV. = 28.7 DEGREES REMARK 500 ASP A 268 CA - C - N ANGL. DEV. = 13.5 DEGREES REMARK 500 ASP A 268 O - C - N ANGL. DEV. = -12.0 DEGREES REMARK 500 ALA A 269 C - N - CA ANGL. DEV. = 31.4 DEGREES REMARK 500 GLY A 270 N - CA - C ANGL. DEV. = -19.3 DEGREES REMARK 500 ALA A 269 CA - C - N ANGL. DEV. = 14.3 DEGREES REMARK 500 ILE A 278 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 GLN A 345 C - N - CA ANGL. DEV. = 20.8 DEGREES REMARK 500 PRO A 346 C - N - CA ANGL. DEV. = 14.7 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 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 ALA A 216 152.98 90.15 REMARK 500 LYS A 218 -121.63 -125.43 REMARK 500 HIS A 223 -41.12 -174.95 REMARK 500 ARG A 224 -85.16 -122.99 REMARK 500 GLU A 225 -118.53 -27.31 REMARK 500 ASP A 262 28.45 -140.65 REMARK 500 ALA A 269 -0.67 85.31 REMARK 500 LEU A 277 -67.23 -142.13 REMARK 500 GLN A 300 -56.89 72.99 REMARK 500 PHE A 318 -71.24 -132.71 REMARK 500 SER A 342 103.03 -165.31 REMARK 500 ASN A 343 70.59 -153.31 REMARK 500 PHE A 425 108.77 -162.35 REMARK 500 THR A 489 -106.86 -148.44 REMARK 500 SER A 514 23.51 -150.90 REMARK 500 LYS A 515 -15.67 77.28 REMARK 500 VAL A 608 -75.15 -99.82 REMARK 500 LEU A 623 -71.75 -135.58 REMARK 500 ASN A 625 4.92 86.01 REMARK 500 PRO A 626 -162.38 73.23 REMARK 500 THR A 628 80.54 84.23 REMARK 500 THR A 638 -45.14 -131.76 REMARK 500 GLU A 667 47.97 -96.79 REMARK 500 ASN A 695 109.10 -52.86 REMARK 500 THR A 713 -164.36 -121.65 REMARK 500 VAL A 715 -37.59 -136.27 REMARK 500 GLN A 750 39.08 -142.33 REMARK 500 ALA A 751 -75.27 63.27 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 GLY A 344 GLN A 345 86.83 REMARK 500 ASP A 620 LEU A 621 -76.25 REMARK 500 ILE A 624 ASN A 625 35.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 620 -10.24 REMARK 500 LEU A 676 14.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN A 121 22.3 L L OUTSIDE RANGE REMARK 500 ASP A 268 22.9 L L OUTSIDE RANGE REMARK 500 ALA A 269 15.5 L L OUTSIDE RANGE REMARK 500 ILE A 299 21.5 L L OUTSIDE RANGE REMARK 500 THR A 628 24.1 L L OUTSIDE RANGE 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 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 A1768 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 557 OE1 REMARK 620 2 ALA A 597 O 60.4 REMARK 620 3 SER A 600 O 97.4 80.1 REMARK 620 4 ALA A 602 O 63.3 114.7 76.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1769 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 73 O REMARK 620 2 GLU A 108 OE2 73.6 REMARK 620 3 ASP A 111 OD1 68.8 94.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1770 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 652 O REMARK 620 2 THR A 655 O 84.2 REMARK 620 3 THR A 655 OG1 67.6 67.9 REMARK 620 4 GLU A 762 OE1 87.0 149.5 134.0 REMARK 620 5 PHE A 647 O 162.1 103.1 99.6 94.1 REMARK 620 6 ALA A 761 O 115.4 70.5 137.7 87.4 82.5 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AC" 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 700 REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1768 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1769 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1770 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2J62 RELATED DB: PDB REMARK 900 STRUCTURE OF A BACTERIAL O-GLCNACASE IN REMARK 900 COMPLEX WITH GLCNACSTATIN REMARK 900 RELATED ID: 2JH2 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF A COHESIN-LIKE REMARK 900 MODULE FROM CLOSTRIDIUM PERFRINGENS REMARK 900 RELATED ID: 2V5C RELATED DB: PDB REMARK 900 FAMILY 84 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM REMARK 900 PERFRINGENS, 2.1 ANGSTROM STRUCTURE REMARK 900 RELATED ID: 2VUR RELATED DB: PDB REMARK 900 CHEMICAL DISSECTION OF THE LINK BETWEEN REMARK 900 STREPTOZOTOCIN, O-GLCNAC AND PANCREATIC CELL REMARK 900 DEATH DBREF 2V5D A 31 767 UNP Q0TR53 OGA_CLOP1 31 767 SEQRES 1 A 737 VAL GLY PRO LYS THR GLY GLU GLU ASN GLN VAL LEU VAL SEQRES 2 A 737 PRO ASN LEU ASN PRO THR PRO GLU ASN LEU GLU VAL VAL SEQRES 3 A 737 GLY ASP GLY PHE LYS ILE THR SER SER ILE ASN LEU VAL SEQRES 4 A 737 GLY GLU GLU GLU ALA ASP GLU ASN ALA VAL ASN ALA LEU SEQRES 5 A 737 ARG GLU PHE LEU THR ALA ASN ASN ILE GLU ILE ASN SER SEQRES 6 A 737 GLU ASN ASP PRO ASN SER THR THR LEU ILE ILE GLY GLU SEQRES 7 A 737 VAL ASP ASP ASP ILE PRO GLU LEU ASP GLU ALA LEU ASN SEQRES 8 A 737 GLY THR THR ALA GLU ASN LEU LYS GLU GLU GLY TYR ALA SEQRES 9 A 737 LEU VAL SER ASN ASP GLY LYS ILE ALA ILE GLU GLY LYS SEQRES 10 A 737 ASP GLY ASP GLY THR PHE TYR GLY VAL GLN THR PHE LYS SEQRES 11 A 737 GLN LEU VAL LYS GLU SER ASN ILE PRO GLU VAL ASN ILE SEQRES 12 A 737 THR ASP TYR PRO THR VAL SER ALA ARG GLY ILE VAL GLU SEQRES 13 A 737 GLY PHE TYR GLY THR PRO TRP THR HIS GLN ASP ARG LEU SEQRES 14 A 737 ASP GLN ILE LYS PHE TYR GLY GLU ASN LYS LEU ASN THR SEQRES 15 A 737 TYR ILE TYR ALA PRO LYS ASP ASP PRO TYR HIS ARG GLU SEQRES 16 A 737 LYS TRP ARG GLU PRO TYR PRO GLU SER GLU MET GLN ARG SEQRES 17 A 737 MET GLN GLU LEU ILE ASN ALA SER ALA GLU ASN LYS VAL SEQRES 18 A 737 ASP PHE VAL PHE GLY ILE SER PRO GLY ILE ASP ILE ARG SEQRES 19 A 737 PHE ASP GLY ASP ALA GLY GLU GLU ASP PHE ASN HIS LEU SEQRES 20 A 737 ILE THR LYS ALA GLU SER LEU TYR ASP MET GLY VAL ARG SEQRES 21 A 737 SER PHE ALA ILE TYR TRP ASP ASP ILE GLN ASP LYS SER SEQRES 22 A 737 ALA ALA LYS HIS ALA GLN VAL LEU ASN ARG PHE ASN GLU SEQRES 23 A 737 GLU PHE VAL LYS ALA LYS GLY ASP VAL LYS PRO LEU ILE SEQRES 24 A 737 THR VAL PRO THR GLU TYR ASP THR GLY ALA MET VAL SER SEQRES 25 A 737 ASN GLY GLN PRO ARG ALA TYR THR ARG ILE PHE ALA GLU SEQRES 26 A 737 THR VAL ASP PRO SER ILE GLU VAL MET TRP THR GLY PRO SEQRES 27 A 737 GLY VAL VAL THR ASN GLU ILE PRO LEU SER ASP ALA GLN SEQRES 28 A 737 LEU ILE SER GLY ILE TYR ASN ARG ASN MET ALA VAL TRP SEQRES 29 A 737 TRP ASN TYR PRO VAL THR ASP TYR PHE LYS GLY LYS LEU SEQRES 30 A 737 ALA LEU GLY PRO MET HIS GLY LEU ASP LYS GLY LEU ASN SEQRES 31 A 737 GLN TYR VAL ASP PHE PHE THR VAL ASN PRO MET GLU HIS SEQRES 32 A 737 ALA GLU LEU SER LYS ILE SER ILE HIS THR ALA ALA ASP SEQRES 33 A 737 TYR SER TRP ASN MET ASP ASN TYR ASP TYR ASP LYS ALA SEQRES 34 A 737 TRP ASN ARG ALA ILE ASP MET LEU TYR GLY ASP LEU ALA SEQRES 35 A 737 GLU ASP MET LYS VAL PHE ALA ASN HIS SER THR ARG MET SEQRES 36 A 737 ASP ASN LYS THR TRP ALA LYS SER GLY ARG GLU ASP ALA SEQRES 37 A 737 PRO GLU LEU ARG ALA LYS MET ASP GLU LEU TRP ASN LYS SEQRES 38 A 737 LEU SER SER LYS GLU ASP ALA SER ALA LEU ILE GLU GLU SEQRES 39 A 737 LEU TYR GLY GLU PHE ALA ARG MET GLU GLU ALA CYS ASN SEQRES 40 A 737 ASN LEU LYS ALA ASN LEU PRO GLU VAL ALA LEU GLU GLU SEQRES 41 A 737 CYS SER ARG GLN LEU ASP GLU LEU ILE THR LEU ALA GLN SEQRES 42 A 737 GLY ASP LYS ALA SER LEU ASP MET ILE VAL ALA GLN LEU SEQRES 43 A 737 ASN GLU ASP THR GLU ALA TYR GLU SER ALA LYS GLU ILE SEQRES 44 A 737 ALA GLN ASN LYS LEU ASN THR ALA LEU SER SER PHE ALA SEQRES 45 A 737 VAL ILE SER GLU LYS VAL ALA GLN SER PHE ILE GLN GLU SEQRES 46 A 737 ALA LEU SER PHE ASP LEU THR LEU ILE ASN PRO ARG THR SEQRES 47 A 737 VAL LYS ILE THR ALA SER SER GLU GLU THR SER GLY GLU SEQRES 48 A 737 ASN ALA PRO ALA SER PHE ALA SER ASP GLY ASP MET ASN SEQRES 49 A 737 THR PHE TRP HIS SER LYS TRP SER SER PRO ALA HIS GLU SEQRES 50 A 737 GLY PRO HIS HIS LEU THR LEU GLU LEU ASP ASN VAL TYR SEQRES 51 A 737 GLU ILE ASN LYS VAL LYS TYR ALA PRO ARG GLN ASP SER SEQRES 52 A 737 LYS ASN GLY ARG ILE THR GLY TYR LYS VAL SER VAL SER SEQRES 53 A 737 LEU ASP GLY GLU ASN PHE THR GLU VAL LYS THR GLY THR SEQRES 54 A 737 LEU GLU ASP ASN ALA ALA ILE LYS PHE ILE GLU PHE ASP SEQRES 55 A 737 SER VAL ASP ALA LYS TYR VAL ARG LEU ASP VAL THR ASP SEQRES 56 A 737 SER VAL SER ASP GLN ALA ASN GLY ARG GLY LYS PHE ALA SEQRES 57 A 737 THR ALA ALA GLU VAL ASN VAL HIS GLY HET CA A1768 1 HET CA A1769 1 HET CA A1770 1 HETNAM CA CALCIUM ION FORMUL 2 CA 3(CA 2+) FORMUL 3 HOH *27(H2 O1) HELIX 1 1 ASP A 75 ASN A 89 1 15 HELIX 2 2 ILE A 113 ASN A 121 1 9 HELIX 3 3 ASP A 148 VAL A 163 1 16 HELIX 4 4 THR A 194 ASN A 208 1 15 HELIX 5 5 GLU A 235 ASN A 249 1 15 HELIX 6 6 PRO A 259 ILE A 263 5 5 HELIX 7 7 GLY A 270 GLY A 288 1 19 HELIX 8 8 SER A 303 PHE A 318 1 16 HELIX 9 9 PHE A 318 GLY A 323 1 6 HELIX 10 10 ASP A 336 VAL A 341 1 6 HELIX 11 11 ARG A 347 VAL A 357 1 11 HELIX 12 12 PRO A 376 ASN A 388 1 13 HELIX 13 13 SER A 437 ASN A 450 1 14 HELIX 14 14 ASP A 455 GLY A 469 1 15 HELIX 15 15 LEU A 471 HIS A 481 1 11 HELIX 16 16 ALA A 498 SER A 513 1 16 HELIX 17 17 ALA A 518 LEU A 543 1 26 HELIX 18 18 PRO A 544 ASN A 577 1 34 HELIX 19 19 ASP A 579 SER A 600 1 22 HELIX 20 20 VAL A 608 PHE A 619 1 12 HELIX 21 21 PRO A 644 ASP A 650 5 7 SHEET 1 AA 7 ASN A 52 VAL A 55 0 SHEET 2 AA 7 VAL A 171 ASP A 175 -1 O ASN A 172 N GLU A 54 SHEET 3 AA 7 TYR A 133 SER A 137 -1 O TYR A 133 N ASP A 175 SHEET 4 AA 7 LYS A 141 GLY A 146 -1 O ALA A 143 N VAL A 136 SHEET 5 AA 7 THR A 103 GLU A 108 1 O THR A 103 N ILE A 142 SHEET 6 AA 7 SER A 65 VAL A 69 1 O ASN A 67 N LEU A 104 SHEET 7 AA 7 GLU A 92 ILE A 93 1 O GLU A 92 N ILE A 66 SHEET 1 AB 2 PHE A 60 LYS A 61 0 SHEET 2 AB 2 ASN A 167 ILE A 168 -1 O ILE A 168 N PHE A 60 SHEET 1 AC 9 ALA A 181 VAL A 185 0 SHEET 2 AC 9 VAL A 423 VAL A 428 1 O ASP A 424 N ALA A 181 SHEET 3 AC 9 MET A 391 TRP A 395 1 O MET A 391 N ASP A 424 SHEET 4 AC 9 GLU A 362 TRP A 365 1 O VAL A 363 N ALA A 392 SHEET 5 AC 9 ILE A 329 VAL A 331 1 O THR A 330 N MET A 364 SHEET 6 AC 9 SER A 291 TYR A 295 1 O PHE A 292 N ILE A 329 SHEET 7 AC 9 ASP A 252 PHE A 255 1 O PHE A 253 N SER A 291 SHEET 8 AC 9 THR A 212 ILE A 214 1 O TYR A 213 N VAL A 254 SHEET 9 AC 9 ALA A 181 VAL A 185 1 O ILE A 184 N ILE A 214 SHEET 1 AD 2 MET A 485 ASP A 486 0 SHEET 2 AD 2 LYS A 492 SER A 493 -1 O SER A 493 N MET A 485 SHEET 1 AE 8 THR A 632 ALA A 633 0 SHEET 2 AE 8 HIS A 671 ALA A 688 -1 O THR A 673 N THR A 632 SHEET 3 AE 8 LYS A 716 THR A 719 SHEET 4 AE 8 ARG A 697 SER A 706 -1 O TYR A 701 N GLY A 718 SHEET 5 AE 8 LYS A 727 VAL A 747 -1 N LYS A 737 O SER A 706 SHEET 6 AE 8 HIS A 671 ALA A 688 -1 O LEU A 672 N LEU A 741 SHEET 7 AE 8 GLU A 762 HIS A 766 -1 O GLU A 762 N ALA A 688 SHEET 8 AE 8 HIS A 671 ALA A 688 -1 N ASN A 683 O HIS A 766 SHEET 1 AF 2 TRP A 657 HIS A 658 0 SHEET 2 AF 2 THR A 759 ALA A 760 -1 O ALA A 760 N TRP A 657 LINK CA CA A1768 OE1 GLU A 557 1555 1555 3.15 LINK CA CA A1768 O ALA A 597 1555 1555 2.49 LINK CA CA A1768 O SER A 600 1555 1555 2.85 LINK CA CA A1768 O ALA A 602 1555 1555 2.53 LINK CA CA A1769 O GLU A 73 1555 1555 2.98 LINK CA CA A1769 OE2 GLU A 108 1555 1555 2.60 LINK CA CA A1769 OD1 ASP A 111 1555 1555 3.01 LINK CA CA A1770 O THR A 655 1555 1555 2.76 LINK CA CA A1770 OG1 THR A 655 1555 1555 2.64 LINK CA CA A1770 OE1 GLU A 762 1555 1555 2.73 LINK CA CA A1770 O PHE A 647 1555 1555 2.25 LINK CA CA A1770 O ALA A 761 1555 1555 2.42 LINK CA CA A1770 O ASP A 652 1555 1555 2.61 CISPEP 1 ASN A 47 PRO A 48 0 -2.90 CISPEP 2 ALA A 216 PRO A 217 0 -11.71 CISPEP 3 PRO A 217 LYS A 218 0 16.60 CISPEP 4 ASP A 268 ALA A 269 0 -9.58 CISPEP 5 ALA A 269 GLY A 270 0 -0.21 CISPEP 6 SER A 342 ASN A 343 0 1.55 CISPEP 7 ASN A 343 GLY A 344 0 1.24 CISPEP 8 TYR A 397 PRO A 398 0 7.96 CISPEP 9 LEU A 621 THR A 622 0 -21.65 CISPEP 10 PRO A 626 ARG A 627 0 -8.65 CISPEP 11 ARG A 627 THR A 628 0 -7.95 CISPEP 12 THR A 628 VAL A 629 0 -6.08 CISPEP 13 SER A 663 PRO A 664 0 4.64 CISPEP 14 GLY A 668 PRO A 669 0 -5.76 SITE 1 AC1 5 GLU A 557 ALA A 597 SER A 600 ALA A 602 SITE 2 AC1 5 VAL A 603 SITE 1 AC2 3 GLU A 73 GLU A 108 ASP A 111 SITE 1 AC3 5 PHE A 647 ASP A 652 THR A 655 ALA A 761 SITE 2 AC3 5 GLU A 762 CRYST1 46.851 69.546 136.780 90.00 95.78 90.00 P 1 21 1 2 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 0.021344 0.000000 0.002161 0.00000 SCALE2 0.000000 0.014379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007348 0.00000