HEADER HYDROLASE 10-DEC-15 5FQH TITLE THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURAL ANALYSIS TITLE 2 OF A FAMILY 123 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-N-ACETYLGALACTOSAMINIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS BETA-N-ACETYLGALACTOSAMINIDASE, GLYCOSIDE HYDROLASE, GH123, KEYWDS 2 GLYCOSPHINGOLIPID, GANGLIOSIDE, GLOBOSIDE, SUBSTRATE- ASSISTED KEYWDS 3 CATALYSIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.NOACH,B.PLUVINAGE,C.LAURIE,K.T.ABE,M.ALTEEN,D.J.VOCADLO, AUTHOR 2 A.B.BORASTON REVDAT 5 10-JAN-24 5FQH 1 HETSYN REVDAT 4 29-JUL-20 5FQH 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 24-AUG-16 5FQH 1 JRNL REVDAT 2 13-APR-16 5FQH 1 JRNL REVDAT 1 30-MAR-16 5FQH 0 JRNL AUTH I.NOACH,B.PLUVINAGE,C.LAURIE,K.T.ABE,M.ALTEEN,D.J.VOCADLO, JRNL AUTH 2 A.B.BORASTON JRNL TITL THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE JRNL TITL 2 STRUCTURAL ANALYSIS OF A FAMILY 123 GLYCOSIDE HYDROLASE FROM JRNL TITL 3 CLOSTRIDIUM PERFRINGENS JRNL REF J.MOL.BIOL. V. 428 3253 2016 JRNL REFN ISSN 0022-2836 JRNL PMID 27038508 JRNL DOI 10.1016/J.JMB.2016.03.020 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 96.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 38008 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1962 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2776 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4693 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.92000 REMARK 3 B22 (A**2) : 0.92000 REMARK 3 B33 (A**2) : -2.98000 REMARK 3 B12 (A**2) : 0.46000 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): 0.199 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.185 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.152 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.024 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4862 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4390 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6612 ; 1.475 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10122 ; 0.759 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 580 ; 6.568 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 241 ;38.114 ;24.979 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 800 ;14.012 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.201 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 708 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5530 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1162 ; 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): 2323 ; 2.942 ; 4.488 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2322 ; 2.929 ; 4.488 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2902 ; 4.167 ; 6.726 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2537 ; 3.655 ; 4.807 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 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 5FQH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1290065747. 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 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39970 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 48.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 11.00 REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: PDB ENTR 5FQE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.84667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.92333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.92333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.84667 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 A2035 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 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 VAL A -8 REMARK 465 PRO A -7 REMARK 465 ARG A -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 LYS A 3 REMARK 465 ASP A 4 REMARK 465 LEU A 587 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 THR A 5 OG1 CG2 REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 SER A 54 OG REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 GLU A 117 CG CD OE1 OE2 REMARK 470 LYS A 118 CG CD CE NZ REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 GLU A 151 CG CD OE1 OE2 REMARK 470 GLU A 378 CG CD OE1 OE2 REMARK 470 ASN A 381 CG OD1 ND2 REMARK 470 ILE A 493 CG1 CG2 CD1 REMARK 470 LYS A 555 CG CD CE NZ REMARK 470 THR A 586 CA C O CB OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2112 O HOH A 2113 1.62 REMARK 500 O HOH A 2010 O HOH A 2023 1.90 REMARK 500 O HOH A 2156 O HOH A 2157 2.07 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 585 O - C - N ANGL. DEV. = -16.1 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 30 63.51 -157.77 REMARK 500 ASN A 53 -148.86 -116.18 REMARK 500 SER A 95 45.94 33.86 REMARK 500 HIS A 109 -122.48 -90.39 REMARK 500 GLU A 149 1.48 -64.71 REMARK 500 GLU A 228 48.49 38.50 REMARK 500 ASN A 290 19.35 58.63 REMARK 500 ALA A 299 -72.36 -62.69 REMARK 500 THR A 300 2.50 -68.30 REMARK 500 ASN A 301 63.42 39.06 REMARK 500 MET A 343 -163.78 -115.43 REMARK 500 ASN A 363 -166.20 -79.43 REMARK 500 ASN A 402 34.89 -77.08 REMARK 500 ASP A 462 33.29 -157.02 REMARK 500 TRP A 477 161.82 70.83 REMARK 500 GLU A 585 -117.89 92.41 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 SER A 373 ALA A 374 149.88 REMARK 500 TRP A 459 SER A 460 -146.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AD" 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FQE RELATED DB: PDB REMARK 900 THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURAL REMARK 900 ANALYSIS OF A FAMILY 123 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM REMARK 900 PERFRINGENS REMARK 900 RELATED ID: 5FQF RELATED DB: PDB REMARK 900 THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURAL REMARK 900 ANALYSIS OF A FAMILY 123 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM REMARK 900 PERFRINGENS REMARK 900 RELATED ID: 5FQG RELATED DB: PDB REMARK 900 THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURAL REMARK 900 ANALYSIS OF A FAMILY 123 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM REMARK 900 PERFRINGENS REMARK 900 RELATED ID: 5FR0 RELATED DB: PDB REMARK 900 THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURAL REMARK 900 ANALYSIS OF A FAMILY 123 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM REMARK 900 PERFRINGENS DBREF1 5FQH A 1 587 UNP A0A0H2YNR7_CLOP1 DBREF2 5FQH A A0A0H2YNR7 1 587 SEQADV 5FQH MET A -22 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH GLY A -21 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH SER A -20 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH SER A -19 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH HIS A -18 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH HIS A -17 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH HIS A -16 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH HIS A -15 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH HIS A -14 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH HIS A -13 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH SER A -12 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH SER A -11 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH GLY A -10 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH LEU A -9 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH VAL A -8 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH PRO A -7 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH ARG A -6 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH GLY A -5 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH SER A -4 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH HIS A -3 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH MET A -2 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH ALA A -1 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH SER A 0 UNP A0A0H2YNR EXPRESSION TAG SEQADV 5FQH ASN A 344 UNP A0A0H2YNR ASP 344 ENGINEERED MUTATION SEQADV 5FQH GLN A 345 UNP A0A0H2YNR GLU 345 ENGINEERED MUTATION SEQRES 1 A 610 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 610 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET LYS LYS SEQRES 3 A 610 ASP THR THR LEU GLY ALA SER ILE GLY SER THR ASP PHE SEQRES 4 A 610 HIS TYR LEU GLN LYS ASP TYR ASP GLU ILE LYS LYS LEU SEQRES 5 A 610 ASN LEU ASN THR TRP ASN GLU VAL ALA TRP ILE GLY ASP SEQRES 6 A 610 GLU LEU ASN SER LYS ILE VAL MET TRP THR ASN SER SER SEQRES 7 A 610 PRO VAL ASN ASN VAL THR LEU SER SER SER ASP PHE ILE SEQRES 8 A 610 ASN GLU ASN GLY ASP LEU ILE SER SER ASN ASN ILE LYS SEQRES 9 A 610 ILE SER TRP LEU LYS GLU THR LEU ALA ASN ILE GLY ARG SEQRES 10 A 610 SER ASN PRO SER ALA PRO LEU GLU PRO PHE PRO ASP ILE SEQRES 11 A 610 ILE HIS ASN SER GLY SER LEU ASN ILE GLU LYS ASN LYS SEQRES 12 A 610 ILE ALA SER ALA TRP ILE ASN ILE LYS ILE PRO ARG ASN SEQRES 13 A 610 ALA LYS PRO GLY ILE TYR ASN GLY SER ILE GLU VAL THR SEQRES 14 A 610 ALA ASP GLU LEU GLU LYS SER TYR THR PHE ASP TYR SER SEQRES 15 A 610 PHE GLU VAL LEU ASN LEU VAL GLN PRO LEU PRO SER GLU SEQRES 16 A 610 THR ASN THR GLN ILE GLU PHE TRP GLN HIS PRO TYR THR SEQRES 17 A 610 ILE ALA ARG TYR TYR LYS ILE CYS LYS GLU ASP LEU PHE SEQRES 18 A 610 THR GLU LYS HIS PHE LYS TYR LEU ARG GLY ASN LEU LYS SEQRES 19 A 610 GLU TYR ARG ASN MET GLY GLY ARG GLY VAL ILE ALA THR SEQRES 20 A 610 ILE VAL HIS GLU ALA TRP ASN HIS GLN SER TYR ASP SER SEQRES 21 A 610 ASP PRO SER MET ILE LYS TRP ARG LYS ASN SER TYR GLY SEQRES 22 A 610 THR PHE GLU PHE ASP TYR SER HIS PHE ASP LYS TRP ILE SEQRES 23 A 610 GLN LEU ASN ILE ASP LEU GLY ILE LEU ASP PRO GLU LYS SEQRES 24 A 610 GLY PHE GLY GLN ILE LYS CYS TYR SER ILE VAL PRO TRP SEQRES 25 A 610 ASN ASN ARG ILE GLN TYR PHE ASN GLU ALA THR ASN LYS SEQRES 26 A 610 GLU GLU ALA ILE ASN PRO THR PRO GLY SER ASP LEU TRP SEQRES 27 A 610 ILE ASN ILE TRP THR GLN PHE LEU THR SER PHE MET SER SEQRES 28 A 610 HIS LEU GLU GLU LYS GLY TRP PHE ASN ILE THR TYR ILE SEQRES 29 A 610 SER MET ASN GLN ARG SER MET ASP ASP LEU LYS ALA CYS SEQRES 30 A 610 VAL ASP LEU ILE GLU ASN ILE THR ASN ASN SER TYR GLU SEQRES 31 A 610 HIS PHE LYS ILE SER SER ALA MET ASP TYR GLU SER GLY SEQRES 32 A 610 ASN ASP TYR SER PHE LEU ASP ARG ILE ASP ASP ILE SER SEQRES 33 A 610 ILE GLY LEU SER HIS ILE ASN HIS ASN SER ASP ASP MET SEQRES 34 A 610 LYS ASN MET ALA THR HIS ARG GLN GLU LEU GLY LEU LEU SEQRES 35 A 610 THR THR ILE TYR THR CYS THR GLY ASP TYR PRO SER SER SEQRES 36 A 610 PHE THR ILE SER ASP PRO SER GLU GLY ALA PHE THR ILE SEQRES 37 A 610 TRP TYR SER LEU TYR GLN ASN THR ASN GLY PHE LEU ARG SEQRES 38 A 610 TRP SER TRP ASP GLY TRP VAL GLU ASN PRO LEU GLU ASN SEQRES 39 A 610 VAL SER TYR LYS TYR TRP GLU PRO GLY ASP PRO PHE LEU SEQRES 40 A 610 ILE TYR PRO ALA GLU LYS ASP SER ILE GLY LYS THR PHE SEQRES 41 A 610 TYR SER THR PRO ARG LEU GLU LYS LEU LYS GLU GLY ILE SEQRES 42 A 610 ARG ASP ILE ASN LYS ALA LYS TYR LEU MET GLU LYS ALA SEQRES 43 A 610 PRO ASN LEU LYS ASN SER ILE GLU ASN LEU ILE TYR SER SEQRES 44 A 610 LEU LYS ARG PRO ASN LYS GLY GLU ASN ALA TYR GLY SER SEQRES 45 A 610 ALA VAL ALA ALA SER LYS GLU ASP ARG ASP LEU THR ILE SEQRES 46 A 610 SER GLU ALA ASN ARG ILE LYS ASN GLY ILE ASN ASN PHE SEQRES 47 A 610 ALA ARG GLU PHE ILE SER LEU THR MET GLU THR LEU HET BGC B 1 12 HET GAL B 2 11 HET NGA B 3 14 HET PO4 A1589 5 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM NGA 2-ACETAMIDO-2-DEOXY-BETA-D-GALACTOPYRANOSE HETNAM PO4 PHOSPHATE ION HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN NGA N-ACETYL-BETA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NGA BETA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 NGA ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-D-GALACTOSAMINE FORMUL 2 BGC C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 2 NGA C8 H15 N O6 FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *166(H2 O) HELIX 1 1 LEU A 19 LYS A 21 5 3 HELIX 2 2 ASP A 22 LYS A 27 1 6 HELIX 3 3 SER A 76 ASN A 78 5 3 HELIX 4 4 LEU A 169 THR A 173 5 5 HELIX 5 5 HIS A 182 TYR A 190 1 9 HELIX 6 6 CYS A 193 LEU A 197 5 5 HELIX 7 7 THR A 199 MET A 216 1 18 HELIX 8 8 TYR A 256 LEU A 269 1 14 HELIX 9 9 PRO A 288 ARG A 292 5 5 HELIX 10 10 SER A 312 GLY A 334 1 23 HELIX 11 11 TRP A 335 ASN A 337 5 3 HELIX 12 12 SER A 347 ILE A 361 1 15 HELIX 13 13 PHE A 385 ILE A 389 5 5 HELIX 14 14 SER A 397 ILE A 399 5 3 HELIX 15 15 ASP A 404 LEU A 416 1 13 HELIX 16 16 PRO A 438 GLN A 451 1 14 HELIX 17 17 THR A 500 ALA A 523 1 24 HELIX 18 18 LEU A 526 SER A 536 1 11 HELIX 19 19 SER A 554 GLU A 585 1 32 SHEET 1 AA 5 LEU A 7 GLY A 12 0 SHEET 2 AA 5 GLU A 43 THR A 52 -1 O LYS A 47 N GLY A 12 SHEET 3 AA 5 ILE A 121 LYS A 129 -1 O ALA A 122 N MET A 50 SHEET 4 AA 5 ILE A 80 ASN A 91 -1 O LYS A 81 N ASN A 127 SHEET 5 AA 5 LEU A 101 ILE A 108 -1 O GLU A 102 N ALA A 90 SHEET 1 AB 5 THR A 33 ILE A 40 0 SHEET 2 AB 5 SER A 153 VAL A 166 1 O ASP A 157 N TRP A 34 SHEET 3 AB 5 GLY A 137 THR A 146 -1 O GLY A 137 N VAL A 162 SHEET 4 AB 5 VAL A 57 SER A 64 -1 O THR A 61 N THR A 146 SHEET 5 AB 5 LEU A 114 ILE A 116 -1 O LEU A 114 N VAL A 60 SHEET 1 AC 2 PHE A 67 ILE A 68 0 SHEET 2 AC 2 LEU A 74 ILE A 75 -1 O ILE A 75 N PHE A 67 SHEET 1 AD 9 GLN A 176 PHE A 179 0 SHEET 2 AD 9 GLY A 455 ARG A 458 1 O PHE A 456 N GLU A 178 SHEET 3 AD 9 LEU A 419 TYR A 423 1 O ILE A 422 N LEU A 457 SHEET 4 AD 9 ASP A 391 GLY A 395 1 O ILE A 392 N THR A 421 SHEET 5 AD 9 LYS A 370 MET A 375 1 O ILE A 371 N ASP A 391 SHEET 6 AD 9 THR A 339 SER A 342 1 O THR A 339 N LYS A 370 SHEET 7 AD 9 GLN A 280 TYR A 284 1 O ILE A 281 N TYR A 340 SHEET 8 AD 9 GLY A 220 THR A 224 1 O VAL A 221 N LYS A 282 SHEET 9 AD 9 GLN A 176 PHE A 179 1 N PHE A 179 O GLY A 220 SHEET 1 AE 4 PHE A 252 ASP A 255 0 SHEET 2 AE 4 LYS A 243 LYS A 246 -1 O LYS A 243 N ASP A 255 SHEET 3 AE 4 ILE A 293 ASN A 297 1 O PHE A 296 N LYS A 246 SHEET 4 AE 4 LYS A 302 ILE A 306 -1 O LYS A 302 N ASN A 297 SHEET 1 AF 2 TYR A 486 PRO A 487 0 SHEET 2 AF 2 PHE A 497 TYR A 498 -1 O TYR A 498 N TYR A 486 SHEET 1 AG 2 LYS A 542 GLU A 544 0 SHEET 2 AG 2 ALA A 550 ALA A 552 -1 O VAL A 551 N GLY A 543 SSBOND 1 CYS A 193 CYS A 193 1555 5555 1.86 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.44 LINK O4 GAL B 2 C1 NGA B 3 1555 1555 1.43 CISPEP 1 TYR A 284 SER A 285 0 -3.14 CISPEP 2 TYR A 429 PRO A 430 0 -3.83 CISPEP 3 ILE A 493 GLY A 494 0 -11.03 CRYST1 111.130 111.130 95.770 90.00 90.00 120.00 P 32 2 1 6 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 0.008998 0.005195 0.000000 0.00000 SCALE2 0.000000 0.010391 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010442 0.00000