HEADER LYASE 15-APR-03 1OFL TITLE CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE TITLE 2 HEXASACCHARIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHONDROITINASE B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CHONDROITIN B LYASE, CHONDROITIN SULFATE B LYASE, COMPND 5 CHONDROITIN B ELIMINASE; COMPND 6 EC: 4.2.2.4; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: HYDROXYPROLINE AT THE N-TERMINUS, GLYCOSYLATION AT COMPND 9 SER234 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PEDOBACTER HEPARINUS; SOURCE 3 ORGANISM_TAXID: 984; SOURCE 4 ATCC: 13125; SOURCE 5 EXPRESSION_SYSTEM: PEDOBACTER HEPARINUS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 984 KEYWDS ACTIVE SITE, BETA-ELIMINATION, DEMATAN SULFATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR G.MICHEL,M.CYGLER REVDAT 8 20-NOV-24 1OFL 1 REMARK REVDAT 7 13-DEC-23 1OFL 1 REMARK HETSYN REVDAT 6 29-JUL-20 1OFL 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 11-MAR-20 1OFL 1 REMARK SEQRES LINK REVDAT 4 23-JAN-13 1OFL 1 COMPND REMARK VERSN HET REVDAT 4 2 1 HETNAM FORMUL LINK SITE REVDAT 4 3 1 SCALE1 SCALE2 SCALE3 TER REVDAT 4 4 1 HETATM CONECT REVDAT 3 24-FEB-09 1OFL 1 VERSN REVDAT 2 29-JUL-04 1OFL 1 JRNL REVDAT 1 10-JUN-04 1OFL 0 JRNL AUTH G.MICHEL,K.POJASEK,Y.LI,T.SULEA,R.J.LINHARDT,R.RAMAN, JRNL AUTH 2 V.PRABHAKAR,R.SASISEKHARAN,M.CYGLER JRNL TITL THE STRUCTURE OF CHONDROITIN B LYASE COMPLEXED WITH JRNL TITL 2 GLYCOSAMINOGLYCAN OLIGOSACCHARIDES UNRAVELS A JRNL TITL 3 CALCIUM-DEPENDENT CATALYTIC MACHINERY JRNL REF J.BIOL.CHEM. V. 279 32882 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15155751 JRNL DOI 10.1074/JBC.M403421200 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.08 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 42015 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) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2211 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2163 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1550 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3784 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 196 REMARK 3 SOLVENT ATOMS : 757 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.107 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.708 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4080 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5544 ; 1.839 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 480 ; 6.922 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 186 ;38.783 ;24.032 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 637 ;12.615 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.062 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 623 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3051 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1981 ; 0.227 ; 0.200 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): 598 ; 0.158 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.081 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 77 ; 0.214 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 66 ; 0.146 ; 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): 2393 ; 1.013 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3839 ; 1.725 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1687 ; 2.789 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1705 ; 4.312 ; 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 : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 1OFL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-APR-03. REMARK 100 THE DEPOSITION ID IS D_1290012591. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.70 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 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 : 44254 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 34.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 2.850 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1DBG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, 2-METHYL-2,4- PENTADIOL, REMARK 280 AMMONIUM ACETATE, TRIS, PH 8.70 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 36.99450 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 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, B, C, D, E, F 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 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 187 CG CD CE NZ REMARK 480 ASP A 188 CG OD1 OD2 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 OG1 THR A 182 O HOH A 2300 1.82 REMARK 500 O HOH A 2043 O HOH A 2064 2.18 REMARK 500 O1S NGK F 1 O HOH A 2754 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 188 CB ASP A 188 CG -0.298 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 ASP A 188 CB - CG - OD1 ANGL. DEV. = -7.4 DEGREES REMARK 500 ASP A 188 CB - CG - OD2 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 301 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 402 CB - CG - OD2 ANGL. DEV. = 8.5 DEGREES REMARK 500 ASP A 468 CB - CG - OD2 ANGL. DEV. = 5.6 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 107 47.17 -164.05 REMARK 500 ASP A 139 -161.64 -163.77 REMARK 500 SER A 143 165.52 175.03 REMARK 500 ASP A 174 163.18 88.49 REMARK 500 LYS A 187 -158.29 54.39 REMARK 500 ASP A 188 19.80 105.11 REMARK 500 SER A 190 -18.71 -32.46 REMARK 500 ASN A 358 45.95 -157.72 REMARK 500 PRO A 393 32.56 -76.89 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 THR A 147 THR A 148 148.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2031 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A2106 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2137 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A2156 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH A2162 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A2163 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A2174 DISTANCE = 7.94 ANGSTROMS REMARK 525 HOH A2377 DISTANCE = 6.22 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 528 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 213 OD1 REMARK 620 2 GLU A 243 OE1 78.3 REMARK 620 3 GLU A 243 OE2 118.7 53.7 REMARK 620 4 GLU A 245 OE1 145.3 136.3 90.2 REMARK 620 5 HOH A2734 O 82.6 105.6 77.2 86.1 REMARK 620 6 HOH A2741 O 99.1 82.7 108.7 87.9 171.6 REMARK 620 7 GCD D 2 O6B 77.5 148.0 158.2 70.2 91.7 80.7 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DBG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CHONDROITINASE B REMARK 900 RELATED ID: 1DBO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE REMARK 900 HEXASACCHARIDE REMARK 900 RELATED ID: 1OFM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO CHONDROITIN 4- REMARK 900 SULFATE TETRASACCHARIDE DBREF 1OFL A 26 26 PDB 1OFL 1OFL 26 26 DBREF 1OFL A 27 506 UNP Q46079 CSLB_PEDHE 27 506 SEQRES 1 A 481 PCA VAL VAL ALA SER ASN GLU THR LEU TYR GLN VAL VAL SEQRES 2 A 481 LYS GLU VAL LYS PRO GLY GLY LEU VAL GLN ILE ALA ASP SEQRES 3 A 481 GLY THR TYR LYS ASP VAL GLN LEU ILE VAL SER ASN SER SEQRES 4 A 481 GLY LYS SER GLY LEU PRO ILE THR ILE LYS ALA LEU ASN SEQRES 5 A 481 PRO GLY LYS VAL PHE PHE THR GLY ASP ALA LYS VAL GLU SEQRES 6 A 481 LEU ARG GLY GLU HIS LEU ILE LEU GLU GLY ILE TRP PHE SEQRES 7 A 481 LYS ASP GLY ASN ARG ALA ILE GLN ALA TRP LYS SER HIS SEQRES 8 A 481 GLY PRO GLY LEU VAL ALA ILE TYR GLY SER TYR ASN ARG SEQRES 9 A 481 ILE THR ALA CYS VAL PHE ASP CYS PHE ASP GLU ALA ASN SEQRES 10 A 481 SER ALA TYR ILE THR THR SER LEU THR GLU ASP GLY LYS SEQRES 11 A 481 VAL PRO GLN HIS CYS ARG ILE ASP HIS CYS SER PHE THR SEQRES 12 A 481 ASP LYS ILE THR PHE ASP GLN VAL ILE ASN LEU ASN ASN SEQRES 13 A 481 THR ALA ARG ALA ILE LYS ASP GLY SER VAL GLY GLY PRO SEQRES 14 A 481 ALA MET TYR HIS ARG VAL ASP HIS CYS PHE PHE SER ASN SEQRES 15 A 481 PRO GLN LYS PRO GLY ASN ALA GLY GLY GLY ILE ARG ILE SEQRES 16 A 481 GLY TYR TYR ARG ASN ASP ILE GLY ARG CYS LEU VAL ASP SEQRES 17 A 481 SER ASN LEU PHE MET ARG GLN ASP SER GLU ALA GLU ILE SEQRES 18 A 481 ILE THR SER LYS SER GLN GLU ASN VAL TYR TYR GLY ASN SEQRES 19 A 481 THR TYR LEU ASN CYS GLN GLY THR MET ASN PHE ARG HIS SEQRES 20 A 481 GLY ASP HIS GLN VAL ALA ILE ASN ASN PHE TYR ILE GLY SEQRES 21 A 481 ASN ASP GLN ARG PHE GLY TYR GLY GLY MET PHE VAL TRP SEQRES 22 A 481 GLY SER ARG HIS VAL ILE ALA CYS ASN TYR PHE GLU LEU SEQRES 23 A 481 SER GLU THR ILE LYS SER ARG GLY ASN ALA ALA LEU TYR SEQRES 24 A 481 LEU ASN PRO GLY ALA MET ALA SER GLU HIS ALA LEU ALA SEQRES 25 A 481 PHE ASP MET LEU ILE ALA ASN ASN ALA PHE ILE ASN VAL SEQRES 26 A 481 ASN GLY TYR ALA ILE HIS PHE ASN PRO LEU ASP GLU ARG SEQRES 27 A 481 ARG LYS GLU TYR CYS ALA ALA ASN ARG LEU LYS PHE GLU SEQRES 28 A 481 THR PRO HIS GLN LEU MET LEU LYS GLY ASN LEU PHE PHE SEQRES 29 A 481 LYS ASP LYS PRO TYR VAL TYR PRO PHE PHE LYS ASP ASP SEQRES 30 A 481 TYR PHE ILE ALA GLY LYS ASN SER TRP THR GLY ASN VAL SEQRES 31 A 481 ALA LEU GLY VAL GLU LYS GLY ILE PRO VAL ASN ILE SER SEQRES 32 A 481 ALA ASN ARG SER ALA TYR LYS PRO VAL LYS ILE LYS ASP SEQRES 33 A 481 ILE GLN PRO ILE GLU GLY ILE ALA LEU ASP LEU ASN ALA SEQRES 34 A 481 LEU ILE SER LYS GLY ILE THR GLY LYS PRO LEU SER TRP SEQRES 35 A 481 ASP GLU VAL ARG PRO TYR TRP LEU LYS GLU MET PRO GLY SEQRES 36 A 481 THR TYR ALA LEU THR ALA ARG LEU SER ALA ASP ARG ALA SEQRES 37 A 481 ALA LYS PHE LYS ALA VAL ILE LYS ARG ASN LYS GLU HIS MODRES 1OFL SER A 234 SER GLYCOSYLATION SITE MODRES 1OFL PCA A 26 GLU PYROGLUTAMIC ACID HET PCA A 26 8 HET MAN B 1 11 HET GCU B 2 12 HET XYP B 3 9 HET MXZ B 4 11 HET GLA B 5 11 HET BGC B 6 11 HET RAM B 7 10 HET ASG C 1 19 HET GCD C 2 11 HET ASG D 1 19 HET GCD D 2 11 HET ASG E 1 19 HET GCD E 2 11 HET NGK F 1 19 HET GCD F 2 11 HET CA A 528 1 HETNAM PCA PYROGLUTAMIC ACID HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM GCU ALPHA-D-GLUCOPYRANURONIC ACID HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM MXZ 2-O-METHYL-ALPHA-L-FUCOPYRANOSE HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM RAM ALPHA-L-RHAMNOPYRANOSE HETNAM ASG 2-ACETAMIDO-2-DEOXY-4-O-SULFO-BETA-D-GALACTOPYRANOSE HETNAM GCD 4-DEOXY-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC ACID HETNAM NGK 2-ACETAMIDO-2-DEOXY-4-O-SULFO-ALPHA-D-GALACTOPYRANOSE HETNAM CA CALCIUM ION HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GCU ALPHA-D-GLUCURONIC ACID; D-GLUCURONIC ACID; GLUCURONIC HETSYN 2 GCU ACID HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE HETSYN MXZ 6-DEOXY-2-O-METHYL-ALPHA-L-GALACTOPYRANOSE; 2-O-METHYL- HETSYN 2 MXZ ALPHA-L-FUCOSE; 2-O-METHYL-L-FUCOSE; 2-O-METHYL-FUCOSE HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN RAM ALPHA-L-RHAMNOSE; 6-DEOXY-ALPHA-L-MANNOPYRANOSE; L- HETSYN 2 RAM RHAMNOSE; RHAMNOSE HETSYN ASG 2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE; N- HETSYN 2 ASG ACETYL-4-O-SULFO-BETA-D-GALACTOSAMINE; 2-ACETAMIDO-2- HETSYN 3 ASG DEOXY-4-O-SULFO-BETA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY- HETSYN 4 ASG 4-O-SULFO-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-4-O-SULFO- HETSYN 5 ASG GALACTOSE HETSYN GCD 4,5-DEHYDRO-D-GLUCURONIC ACID; 4-DEOXY-ALPHA-L-THREO- HETSYN 2 GCD HEX-4-ENURONIC ACID; 4-DEOXY-L-THREO-HEX-4-ENURONIC HETSYN 3 GCD ACID; 4-DEOXY-THREO-HEX-4-ENURONIC ACID HETSYN NGK 2-(ACETYLAMINO)-2-DEOXY-4-O-SULFO-ALPHA-D- HETSYN 2 NGK GALACTOPYRANOSE; N-ACETYL-4-O-SULFO-ALPHA-D- HETSYN 3 NGK GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY-4-O-SULFO-ALPHA-D- HETSYN 4 NGK GALACTOSE; 2-ACETAMIDO-2-DEOXY-4-O-SULFO-D-GALACTOSE; HETSYN 5 NGK 2-ACETAMIDO-2-DEOXY-4-O-SULFO-GALACTOSE FORMUL 1 PCA C5 H7 N O3 FORMUL 2 MAN C6 H12 O6 FORMUL 2 GCU C6 H10 O7 FORMUL 2 XYP C5 H10 O5 FORMUL 2 MXZ C7 H14 O5 FORMUL 2 GLA C6 H12 O6 FORMUL 2 BGC C6 H12 O6 FORMUL 2 RAM C6 H12 O5 FORMUL 3 ASG 3(C8 H15 N O9 S) FORMUL 3 GCD 4(C6 H8 O6) FORMUL 6 NGK C8 H15 N O9 S FORMUL 7 CA CA 2+ FORMUL 8 HOH *757(H2 O) HELIX 1 1 SER A 30 VAL A 41 1 12 HELIX 2 2 ALA A 109 TRP A 113 5 5 HELIX 3 3 ILE A 315 GLY A 319 5 5 HELIX 4 4 LEU A 360 ARG A 372 1 13 HELIX 5 5 ASP A 451 LYS A 458 1 8 HELIX 6 6 SER A 466 ARG A 471 1 6 HELIX 7 7 SER A 489 ASN A 503 1 15 SHEET 1 AA14 VAL A 27 VAL A 28 0 SHEET 2 AA14 LEU A 46 ILE A 49 1 O GLN A 48 N VAL A 28 SHEET 3 AA14 ILE A 71 ALA A 75 1 O THR A 72 N VAL A 47 SHEET 4 AA14 LEU A 96 GLU A 99 1 O ILE A 97 N ILE A 73 SHEET 5 AA14 ARG A 129 THR A 131 1 O ARG A 129 N LEU A 98 SHEET 6 AA14 ARG A 161 ASP A 163 1 O ARG A 161 N ILE A 130 SHEET 7 AA14 ARG A 199 ASP A 201 1 O ARG A 199 N ILE A 162 SHEET 8 AA14 LEU A 231 ASP A 233 1 O LEU A 231 N VAL A 200 SHEET 9 AA14 VAL A 255 TYR A 257 1 O VAL A 255 N VAL A 232 SHEET 10 AA14 VAL A 277 ILE A 279 1 O VAL A 277 N TYR A 256 SHEET 11 AA14 VAL A 303 ALA A 305 1 O VAL A 303 N ALA A 278 SHEET 12 AA14 MET A 340 ALA A 343 1 O LEU A 341 N ILE A 304 SHEET 13 AA14 LEU A 381 LYS A 384 1 O MET A 382 N ILE A 342 SHEET 14 AA14 SER A 410 THR A 412 1 O SER A 410 N LEU A 383 SHEET 1 AB13 GLY A 52 LYS A 55 0 SHEET 2 AB13 VAL A 81 GLY A 85 1 O PHE A 82 N TYR A 54 SHEET 3 AB13 TRP A 102 GLY A 106 1 O TRP A 102 N PHE A 83 SHEET 4 AB13 VAL A 134 ASP A 136 1 O VAL A 134 N PHE A 103 SHEET 5 AB13 SER A 166 THR A 168 1 O SER A 166 N PHE A 135 SHEET 6 AB13 PHE A 204 ASN A 207 1 O PHE A 204 N PHE A 167 SHEET 7 AB13 LEU A 236 GLN A 240 1 O LEU A 236 N PHE A 205 SHEET 8 AB13 THR A 260 LEU A 262 1 O THR A 260 N PHE A 237 SHEET 9 AB13 PHE A 282 GLY A 285 1 O PHE A 282 N TYR A 261 SHEET 10 AB13 TYR A 308 LEU A 311 1 O TYR A 308 N TYR A 283 SHEET 11 AB13 ALA A 346 ILE A 348 1 O ALA A 346 N PHE A 309 SHEET 12 AB13 LEU A 387 PHE A 389 1 O LEU A 387 N PHE A 347 SHEET 13 AB13 VAL A 415 LEU A 417 1 O VAL A 415 N PHE A 388 SHEET 1 AC12 GLN A 58 VAL A 61 0 SHEET 2 AC12 LYS A 88 LEU A 91 1 O LYS A 88 N LEU A 59 SHEET 3 AC12 VAL A 121 ILE A 123 1 O ALA A 122 N LEU A 91 SHEET 4 AC12 ILE A 146 THR A 148 1 O THR A 147 N ILE A 123 SHEET 5 AC12 ILE A 177 LEU A 179 1 O ASN A 178 N THR A 148 SHEET 6 AC12 ILE A 218 ILE A 220 1 O ARG A 219 N LEU A 179 SHEET 7 AC12 GLU A 245 LYS A 250 1 O THR A 248 N ILE A 220 SHEET 8 AC12 THR A 267 HIS A 272 1 O THR A 267 N ILE A 246 SHEET 9 AC12 MET A 295 VAL A 297 1 O PHE A 296 N PHE A 270 SHEET 10 AC12 ALA A 321 LEU A 325 1 O ALA A 322 N MET A 295 SHEET 11 AC12 TYR A 353 HIS A 356 1 O TYR A 353 N ALA A 322 SHEET 12 AC12 PHE A 399 LYS A 400 1 N LYS A 400 O ILE A 355 LINK C PCA A 26 N VAL A 27 1555 1555 1.32 LINK OG SER A 234 C1 MAN B 1 1555 1555 1.42 LINK O2 MAN B 1 C1 GCU B 2 1555 1555 1.54 LINK O4 MAN B 1 C1 RAM B 7 1555 1555 1.44 LINK O4 GCU B 2 C1 XYP B 3 1555 1555 1.43 LINK O4 XYP B 3 C1 MXZ B 4 1555 1555 1.45 LINK O3 MXZ B 4 C1 GLA B 5 1555 1555 1.44 LINK O4 MXZ B 4 C1 BGC B 6 1555 1555 1.68 LINK O3 ASG C 1 C1 GCD C 2 1555 1555 1.44 LINK O3 ASG D 1 C1 GCD D 2 1555 1555 1.43 LINK O3 ASG E 1 C1 GCD E 2 1555 1555 1.44 LINK O3 NGK F 1 C1 GCD F 2 1555 1555 1.45 LINK OD1 ASN A 213 CA CA A 528 1555 1555 2.31 LINK OE1 GLU A 243 CA CA A 528 1555 1555 2.47 LINK OE2 GLU A 243 CA CA A 528 1555 1555 2.37 LINK OE1 GLU A 245 CA CA A 528 1555 1555 2.42 LINK CA CA A 528 O HOH A2734 1555 1555 2.34 LINK CA CA A 528 O HOH A2741 1555 1555 2.46 LINK CA CA A 528 O6B GCD D 2 1555 1555 2.48 CISPEP 1 GLY A 293 GLY A 294 0 6.72 CRYST1 50.574 73.989 59.063 90.00 93.93 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 0.019773 0.000000 0.001358 0.00000 SCALE2 0.000000 0.013516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016971 0.00000 HETATM 1 N PCA A 26 52.479 -8.476 25.811 1.00 10.15 N HETATM 2 CA PCA A 26 53.865 -8.859 25.504 1.00 9.26 C HETATM 3 CB PCA A 26 53.755 -10.283 24.894 1.00 11.10 C HETATM 4 CG PCA A 26 52.518 -10.943 25.525 1.00 12.22 C HETATM 5 CD PCA A 26 51.701 -9.685 25.910 1.00 12.47 C HETATM 6 OE PCA A 26 50.334 -9.622 26.107 1.00 15.09 O HETATM 7 C PCA A 26 54.416 -7.898 24.464 1.00 7.37 C HETATM 8 O PCA A 26 53.666 -7.129 23.833 1.00 7.34 O