PDB Short entry for 2WDA HEADER LYASE 23-MAR-09 2WDA TITLE THE X-RAY STRUCTURE OF THE STREPTOMYCES COELICOLOR A3 CHONDROITIN AC TITLE 2 LYASE IN COMPLEX WITH CHONDROITIN SULPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SECRETED LYASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 33-776; COMPND 5 SYNONYM: PL8; COMPND 6 EC: 4.2.2.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VIOLACEORUBER; SOURCE 3 ORGANISM_TAXID: 1935; SOURCE 4 STRAIN: A3(2); SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28A (NOVAGEN); SOURCE 10 OTHER_DETAILS: GERMAN COLLECTION OF MICROORGANISMS (DSM) DSM NO. SOURCE 11 40783 KEYWDS LYASE, HYALURONATE LYASE, CHONDROITIN LYASE, FAMILY 8 EXPDTA X-RAY DIFFRACTION AUTHOR Z.H.ELMABROUK,E.J.TAYLOR,F.VINCENT,N.L.SMITH,J.P.TURKENBURG, AUTHOR 2 G.J.DAVIES,G.W.BLACK REVDAT 6 13-DEC-23 2WDA 1 HETSYN REVDAT 5 29-JUL-20 2WDA 1 COMPND REMARK HET HETNAM REVDAT 5 2 1 HETSYN FORMUL LINK SITE REVDAT 5 3 1 ATOM REVDAT 4 16-FEB-11 2WDA 1 JRNL REVDAT 3 29-DEC-10 2WDA 1 SOURCE JRNL REVDAT 2 24-NOV-10 2WDA 1 JRNL REMARK DBREF SEQADV REVDAT 2 2 1 HETNAM FORMUL REVDAT 1 21-APR-10 2WDA 0 JRNL AUTH Z.H.ELMABROUK,F.VINCENT,M.ZHANG,N.L.SMITH,J.P.TURKENBURG, JRNL AUTH 2 S.J.CHARNOCK,G.W.BLACK,E.J.TAYLOR JRNL TITL CRYSTAL STRUCTURES OF A FAMILY 8 POLYSACCHARIDE LYASE REVEAL JRNL TITL 2 OPEN AND HIGHLY OCCLUDED SUBSTRATE-BINDING CLEFT JRNL TITL 3 CONFORMATIONS. JRNL REF PROTEINS V. 79 965 2011 JRNL REFN ISSN 0887-3585 JRNL PMID 21287626 JRNL DOI 10.1002/PROT.22938 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43011 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2288 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3121 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 162 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5667 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 127 REMARK 3 SOLVENT ATOMS : 499 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.00000 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): 0.209 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.270 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6000 ; 0.023 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8173 ; 1.953 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 753 ; 6.454 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 262 ;29.103 ;21.489 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 837 ;13.966 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 66 ;17.970 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 889 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4644 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3715 ; 1.034 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5921 ; 1.822 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2285 ; 3.420 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2252 ; 5.084 ; 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 2WDA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1290039132. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-05 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 : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93100 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45361 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 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 ENTRY 2WCO REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 M NA FORMATE,20 % GLYCEROL AS REMARK 280 CRYOPROTECTANT REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 50.38200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 70.25400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 70.25400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 75.57300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 70.25400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 70.25400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.19100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 70.25400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 70.25400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 75.57300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 70.25400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 70.25400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.19100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.38200 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: 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 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 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 REMARK 465 MET A 21 REMARK 465 ALA A 22 REMARK 465 THR A 23 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 ALA A 24 CB REMARK 470 LYS A 231 CD CE NZ REMARK 470 ARG A 702 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 734 CG CD OE1 OE2 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 OD2 ASP A 153 NH2 ARG A 200 1.94 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 ALA A 508 CA ALA A 508 CB 0.140 REMARK 500 TYR A 633 CE2 TYR A 633 CD2 0.092 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 325 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 354 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 568 NE - CZ - NH1 ANGL. DEV. = -3.9 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 VAL A 129 -48.36 -135.40 REMARK 500 ILE A 145 -56.18 -138.60 REMARK 500 THR A 245 -33.25 65.42 REMARK 500 TYR A 249 22.41 -145.34 REMARK 500 THR A 252 -72.26 -118.44 REMARK 500 ASP A 277 118.13 -38.97 REMARK 500 SER A 324 172.23 179.36 REMARK 500 ALA A 443 45.72 -94.55 REMARK 500 GLU A 506 -54.76 -128.21 REMARK 500 LEU A 530 -161.31 -111.55 REMARK 500 ASP A 532 22.74 -144.16 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 A2058 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A2059 DISTANCE = 5.83 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 MG A1783 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 653 O REMARK 620 2 SER A 670 N 130.1 REMARK 620 3 SER A 670 OG 141.7 64.5 REMARK 620 4 HOH A2417 O 106.8 91.6 107.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WCO RELATED DB: PDB REMARK 900 STRUCTURES OF THE STREPTOMYCES COELICOLOR A3( 2) HYALURONAN LYASE REMARK 900 IN COMPLEX WITH OLIGOSACCHARIDE SUBSTRATES AND AN INHIBITOR REMARK 900 RELATED ID: 2X03 RELATED DB: PDB REMARK 900 THE X-RAY STRUCTURE OF THE STREPTOMYCES COELICOLOR A3 CHONDROITIN REMARK 900 AC LYASE Y253A MUTANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CLONED SEQUENCE CONTAINS AN N_TERMINAL VECTOR DERIVED REMARK 999 TAG FROM PET 28A, HOWEVER THIS IN NOT ORDERED IN THE REMARK 999 STRUCTURE. DBREF 2WDA A 22 765 UNP O86516 O86516_STRCO 33 776 SEQADV 2WDA MET A 1 UNP O86516 EXPRESSION TAG SEQADV 2WDA GLY A 2 UNP O86516 EXPRESSION TAG SEQADV 2WDA SER A 3 UNP O86516 EXPRESSION TAG SEQADV 2WDA SER A 4 UNP O86516 EXPRESSION TAG SEQADV 2WDA HIS A 5 UNP O86516 EXPRESSION TAG SEQADV 2WDA HIS A 6 UNP O86516 EXPRESSION TAG SEQADV 2WDA HIS A 7 UNP O86516 EXPRESSION TAG SEQADV 2WDA HIS A 8 UNP O86516 EXPRESSION TAG SEQADV 2WDA HIS A 9 UNP O86516 EXPRESSION TAG SEQADV 2WDA HIS A 10 UNP O86516 EXPRESSION TAG SEQADV 2WDA SER A 11 UNP O86516 EXPRESSION TAG SEQADV 2WDA SER A 12 UNP O86516 EXPRESSION TAG SEQADV 2WDA GLY A 13 UNP O86516 EXPRESSION TAG SEQADV 2WDA LEU A 14 UNP O86516 EXPRESSION TAG SEQADV 2WDA VAL A 15 UNP O86516 EXPRESSION TAG SEQADV 2WDA PRO A 16 UNP O86516 EXPRESSION TAG SEQADV 2WDA ARG A 17 UNP O86516 EXPRESSION TAG SEQADV 2WDA GLY A 18 UNP O86516 EXPRESSION TAG SEQADV 2WDA SER A 19 UNP O86516 EXPRESSION TAG SEQADV 2WDA HIS A 20 UNP O86516 EXPRESSION TAG SEQADV 2WDA MET A 21 UNP O86516 EXPRESSION TAG SEQRES 1 A 765 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 765 LEU VAL PRO ARG GLY SER HIS MET ALA THR ALA ASP PRO SEQRES 3 A 765 TYR ASP ALA LEU ARG ARG ARG TRP LEU GLY ILE THR LEU SEQRES 4 A 765 GLY THR GLY TYR ASP PRO ALA ALA GLU PRO TYR ALA SER SEQRES 5 A 765 ARG LEU ALA GLU THR GLY GLU ARG ALA ARG GLU HIS ARG SEQRES 6 A 765 ALA THR MET ALA PRO THR PRO THR SER LEU TRP PRO GLY SEQRES 7 A 765 HIS PRO PHE ASP PRO PRO ALA GLY ILE THR PHE ALA TYR SEQRES 8 A 765 GLY ARG LEU TRP THR MET THR GLU ALA TYR VAL GLN GLU SEQRES 9 A 765 GLY THR GLY ALA THR GLY ASP PRO ALA LEU LEU ALA ASP SEQRES 10 A 765 ILE LEU ARG GLY LEU ASP HIS LEU SER ALA THR VAL TYR SEQRES 11 A 765 HIS PRO ALA THR THR ARG TYR GLY ASN TRP TRP GLU TRP SEQRES 12 A 765 GLN ILE GLY SER PRO ARG LEU LEU MET ASP ILE THR ALA SEQRES 13 A 765 ALA LEU TYR ASP HIS LEU GLY ALA ASP ARG VAL ALA ALA SEQRES 14 A 765 ALA CYS ALA ALA VAL ASP HIS PHE VAL PRO ASP ALA MET SEQRES 15 A 765 LEU GLY ALA TYR THR GLY THR SER THR GLY ALA ASN ARG SEQRES 16 A 765 VAL ASP LEU CYS ARG SER VAL ALA LEU ARG GLY VAL LEU SEQRES 17 A 765 GLY ARG ALA PRO ALA LYS ILE ALA LEU ALA ARG ASP ALA SEQRES 18 A 765 LEU SER PRO VAL PHE PRO TYR VAL THR LYS GLY ASP GLY SEQRES 19 A 765 LEU TYR ALA ASP GLY SER PHE VAL GLN HIS THR TRP VAL SEQRES 20 A 765 ALA TYR SER GLY THR TYR GLY GLN VAL MET LEU ASP GLY SEQRES 21 A 765 LEU GLY ARG LEU PHE THR LEU LEU ALA GLY SER GLU TRP SEQRES 22 A 765 GLU VAL THR ASP PRO GLY ARG GLN LEU VAL LEU ASP SER SEQRES 23 A 765 VAL GLU HIS ALA TYR ALA PRO LEU ILE HIS ASP GLY LEU SEQRES 24 A 765 VAL MET ASP THR VAL ASN GLY ARG ALA ILE SER ARG GLY SEQRES 25 A 765 TYR LEU LYS SER ASP ASP LEU HIS VAL MET ARG SER ASP SEQRES 26 A 765 HIS PHE HIS GLY GLN GLN LEU ILE ALA ALA MET ALA VAL SEQRES 27 A 765 LEU ALA GLY GLY ALA SER ASN ALA GLU ARG GLU ARG TRP SEQRES 28 A 765 HIS ALA ARG ILE LYS GLY TRP ILE GLU ARG ASP THR VAL SEQRES 29 A 765 THR PRO VAL LEU THR ALA PRO GLN PHE PRO VAL ALA ASP SEQRES 30 A 765 LEU THR ARG LEU HIS ALA ILE ALA ASP ALA PRO GLY GLU SEQRES 31 A 765 ALA ALA PRO GLU PRO VAL GLY HIS HIS LEU PHE ALA ALA SEQRES 32 A 765 MET ASP ARG ALA VAL HIS ARG ARG PRO ALA PHE THR ALA SEQRES 33 A 765 GLY LEU ALA MET ALA SER ASP ARG ILE ALA HIS TYR GLU SEQRES 34 A 765 CYS GLY ASN GLY GLU ASN PRO ARG GLY TRP HIS THR GLY SEQRES 35 A 765 ALA GLY MET LEU THR TRP TRP ALA ASN GLY THR ARG ALA SEQRES 36 A 765 ASP GLN TYR THR ASP TRP PHE TRP PRO THR VAL ASP TRP SEQRES 37 A 765 TYR ARG LEU PRO GLY THR THR VAL SER THR LYS ARG LEU SEQRES 38 A 765 ALA ASP ARG ALA GLY GLY GLU TRP GLY ALA PRO LYS PRO SEQRES 39 A 765 ASP VAL ARG TRP VAL GLY GLY ALA THR ASP GLY GLU TYR SEQRES 40 A 765 ALA ALA VAL GLY GLN HIS LEU LYS GLY LEU GLY SER THR SEQRES 41 A 765 LEU GLU ALA ARG LYS SER TRP PHE PHE LEU ASP ASP ALA SEQRES 42 A 765 VAL VAL CYS LEU GLY ALA GLY ILE THR CYS ALA ASP GLY SEQRES 43 A 765 VAL PRO VAL GLU THR VAL VAL ASP ASN ARG ASN LEU GLY SEQRES 44 A 765 GLU GLY GLY THR GLN ALA LEU VAL ARG GLY ARG HIS TRP SEQRES 45 A 765 ALA HIS LEU GLU GLY HIS GLY GLY TRP ILE VAL PRO GLY SEQRES 46 A 765 GLY ALA LEU ARG THR LEU ARG GLU ASP ARG THR GLY ALA SEQRES 47 A 765 TRP SER ASP ILE ASN THR THR SER THR THR GLU ARG ARG SEQRES 48 A 765 THR ARG ARG TRP GLN THR LEU TRP LEU ASP HIS GLY THR SEQRES 49 A 765 ASP PRO ALA GLY ALA ASP TYR VAL TYR THR VAL MET PRO SEQRES 50 A 765 GLY ALA SER ARG ALA ALA LEU ALA ARG ARG ALA ALA ASP SEQRES 51 A 765 ARG HIS TRP LEU THR VAL LEU ALA ASN ASP ASP ARG ARG SEQRES 52 A 765 GLN ALA VAL SER VAL PRO SER LEU GLY LEU THR ALA ALA SEQRES 53 A 765 ASN PHE TRP GLN ALA GLY THR ALA GLY PRO LEU THR THR SEQRES 54 A 765 THR ALA GLY ALA SER VAL LEU VAL ARG ARG ARG GLY ARG SEQRES 55 A 765 THR ALA THR LEU ARG VAL SER GLU PRO PRO ARG THR GLY SEQRES 56 A 765 GLU ALA LEU GLU ILE VAL TRP ASP HIS PRO VAL GLY ALA SEQRES 57 A 765 VAL LEU ARG ALA ASP GLU THR VAL GLU ILE LEU ALA THR SEQRES 58 A 765 GLY ARG ARG LEU HIS LEU ARG VAL THR PRO GLY VAL VAL SEQRES 59 A 765 CYS THR THR HIS GLU CYS GLU VAL THR LEU SER HET ASG B 1 19 HET GCD B 2 11 HET FMT A1766 3 HET FMT A1767 3 HET FMT A1768 3 HET FMT A1769 3 HET FMT A1770 3 HET GOL A1771 6 HET GOL A1772 6 HET GOL A1773 6 HET PEG A1774 7 HET PEG A1775 7 HET PEG A1776 7 HET PEG A1777 7 HET PEG A1778 7 HET PEG A1779 7 HET PEG A1780 7 HET PEG A1781 7 HET PEG A1782 7 HET MG A1783 1 HETNAM ASG 2-ACETAMIDO-2-DEOXY-4-O-SULFO-BETA-D-GALACTOPYRANOSE HETNAM GCD 4-DEOXY-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC ACID HETNAM FMT FORMIC ACID HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM MG MAGNESIUM ION 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 GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ASG C8 H15 N O9 S FORMUL 2 GCD C6 H8 O6 FORMUL 3 FMT 5(C H2 O2) FORMUL 8 GOL 3(C3 H8 O3) FORMUL 11 PEG 9(C4 H10 O3) FORMUL 20 MG MG 2+ FORMUL 21 HOH *499(H2 O) HELIX 1 1 ALA A 24 GLY A 40 1 17 HELIX 2 2 PRO A 49 MET A 68 1 20 HELIX 3 3 PRO A 84 GLN A 103 1 20 HELIX 4 4 ASP A 111 VAL A 129 1 19 HELIX 5 5 ASN A 139 ILE A 145 1 7 HELIX 6 6 ILE A 145 LEU A 158 1 14 HELIX 7 7 LEU A 158 GLY A 163 1 6 HELIX 8 8 GLY A 163 VAL A 178 1 16 HELIX 9 9 PRO A 179 GLY A 184 5 6 HELIX 10 10 THR A 191 GLY A 209 1 19 HELIX 11 11 ALA A 211 SER A 223 1 13 HELIX 12 12 PRO A 224 PHE A 226 5 3 HELIX 13 13 THR A 252 ALA A 269 1 18 HELIX 14 14 GLY A 279 ALA A 290 1 12 HELIX 15 15 TYR A 291 PRO A 293 5 3 HELIX 16 16 ASP A 302 ARG A 311 5 10 HELIX 17 17 SER A 324 GLY A 341 1 18 HELIX 18 18 SER A 344 ASP A 362 1 19 HELIX 19 19 PRO A 366 ALA A 370 5 5 HELIX 20 20 PRO A 374 ALA A 387 1 14 HELIX 21 21 ALA A 402 MET A 404 5 3 HELIX 22 22 GLY A 438 ALA A 443 5 6 HELIX 23 23 SER A 600 ILE A 602 5 3 HELIX 24 24 SER A 640 ASP A 650 1 11 HELIX 25 25 PRO A 669 LEU A 671 5 3 SHEET 1 AA 3 GLY A 234 LEU A 235 0 SHEET 2 AA 3 PHE A 241 GLN A 243 -1 O VAL A 242 N GLY A 234 SHEET 3 AA 3 VAL A 247 ALA A 248 -1 O VAL A 247 N GLN A 243 SHEET 1 AB 2 ILE A 295 HIS A 296 0 SHEET 2 AB 2 LEU A 299 VAL A 300 -1 O LEU A 299 N HIS A 296 SHEET 1 AC 4 GLY A 397 PHE A 401 0 SHEET 2 AC 4 ARG A 406 ARG A 411 -1 O ARG A 406 N PHE A 401 SHEET 3 AC 4 PHE A 414 ALA A 419 -1 O PHE A 414 N ARG A 411 SHEET 4 AC 4 MET A 445 ALA A 450 -1 O MET A 445 N ALA A 419 SHEET 1 AD 4 THR A 475 SER A 477 0 SHEET 2 AD 4 PRO A 548 GLY A 559 -1 O GLU A 550 N VAL A 476 SHEET 3 AD 4 ARG A 610 THR A 624 -1 O ARG A 614 N LEU A 558 SHEET 4 AD 4 ARG A 589 ALA A 598 -1 O ARG A 589 N TRP A 619 SHEET 1 AE 8 VAL A 499 THR A 503 0 SHEET 2 AE 8 ALA A 508 LYS A 515 -1 O ALA A 509 N ALA A 502 SHEET 3 AE 8 GLU A 522 PHE A 529 -1 O ALA A 523 N LEU A 514 SHEET 4 AE 8 VAL A 534 THR A 542 -1 O VAL A 535 N PHE A 528 SHEET 5 AE 8 ALA A 629 PRO A 637 -1 O ALA A 629 N ILE A 541 SHEET 6 AE 8 GLY A 579 ILE A 582 -1 O GLY A 580 N MET A 636 SHEET 7 AE 8 TRP A 572 LEU A 575 -1 O ALA A 573 N TRP A 581 SHEET 8 AE 8 LEU A 566 GLY A 569 -1 O VAL A 567 N HIS A 574 SHEET 1 AF 7 THR A 655 ASP A 660 0 SHEET 2 AF 7 ARG A 663 VAL A 668 -1 O ARG A 663 N ASP A 660 SHEET 3 AF 7 LEU A 673 PHE A 678 -1 O LEU A 673 N VAL A 668 SHEET 4 AF 7 ALA A 693 ARG A 700 -1 O ALA A 693 N PHE A 678 SHEET 5 AF 7 THR A 703 SER A 709 -1 O THR A 703 N ARG A 700 SHEET 6 AF 7 HIS A 758 LEU A 764 -1 O HIS A 758 N VAL A 708 SHEET 7 AF 7 VAL A 726 ALA A 732 -1 N GLY A 727 O THR A 763 SHEET 1 AG 5 GLY A 682 ALA A 684 0 SHEET 2 AG 5 LEU A 687 THR A 689 -1 O LEU A 687 N ALA A 684 SHEET 3 AG 5 LEU A 718 TRP A 722 -1 O VAL A 721 N THR A 688 SHEET 4 AG 5 LEU A 745 VAL A 749 -1 O LEU A 745 N TRP A 722 SHEET 5 AG 5 VAL A 736 ALA A 740 -1 O GLU A 737 N ARG A 748 LINK O3 ASG B 1 C1 GCD B 2 1555 1555 1.39 LINK O TRP A 653 MG MG A1783 1555 1555 2.65 LINK N SER A 670 MG MG A1783 1555 1555 2.84 LINK OG SER A 670 MG MG A1783 1555 1555 2.64 LINK MG MG A1783 O HOH A2417 1555 1555 2.71 CISPEP 1 GLU A 48 PRO A 49 0 2.38 CISPEP 2 ASP A 82 PRO A 83 0 5.44 CRYST1 140.508 140.508 100.764 90.00 90.00 90.00 P 43 21 2 8 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 0.007117 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007117 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009924 0.00000