HEADER LYASE 11-MAR-03 1UAI TITLE CRYSTAL STRUCTURE OF THE ALGINATE LYASE FROM CORYNEBACTERIUM SP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYGULURONATE LYASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALGINATE LYASE; COMPND 5 EC: 4.2.2.11 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM SP.; SOURCE 3 ORGANISM_TAXID: 1720 KEYWDS JELLYROLL BETA-SANDWICH, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.KAKUTA REVDAT 6 27-DEC-23 1UAI 1 REMARK REVDAT 5 04-OCT-17 1UAI 1 REMARK REVDAT 4 16-APR-14 1UAI 1 REMARK VERSN REVDAT 3 24-FEB-09 1UAI 1 VERSN REVDAT 2 22-FEB-05 1UAI 1 JRNL REVDAT 1 27-JUL-04 1UAI 0 JRNL AUTH T.OSAWA,Y.MATSUBARA,T.MURAMATSU,M.KIMURA,Y.KAKUTA JRNL TITL CRYSTAL STRUCTURE OF THE ALGINATE (POLY ALPHA-L-GULURONATE) JRNL TITL 2 LYASE FROM CORYNEBACTERIUM SP. AT 1.2 A RESOLUTION JRNL REF J.MOL.BIOL. V. 345 1111 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15644208 JRNL DOI 10.1016/J.JMB.2004.10.081 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 656713.420 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 59170 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 SET) : 0.170 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2982 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9005 REMARK 3 BIN R VALUE (WORKING SET) : 0.1780 REMARK 3 BIN FREE R VALUE : 0.1820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 456 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1709 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 346 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.19000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.05000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.11 REMARK 3 ESD FROM SIGMAA (A) : 0.04 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.13 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.04 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 50.08 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UAI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000005617. 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 : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59499 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 13.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 20000, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 23.61700 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 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 ALA A 1 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 SER A 73 N - CA - C ANGL. DEV. = -16.9 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 ASP A 15 51.85 -100.97 REMARK 500 SER A 66 -26.92 71.95 REMARK 500 VAL A 109 -52.54 66.69 REMARK 500 ASP A 120 -160.64 -128.04 REMARK 500 ASP A 123 -172.32 -178.55 REMARK 500 SER A 186 -167.49 -102.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 1UAI A 1 224 UNP Q9RB42 Q9RB42_9CORY 33 256 SEQRES 1 A 224 ALA GLU PRO CYS ASP TYR PRO ALA GLN GLN LEU ASP LEU SEQRES 2 A 224 THR ASP TRP LYS VAL THR LEU PRO ILE GLY SER SER GLY SEQRES 3 A 224 LYS PRO SER GLU ILE GLU GLN PRO ALA LEU ASP THR PHE SEQRES 4 A 224 ALA THR ALA PRO TRP PHE GLN VAL ASN ALA LYS CYS THR SEQRES 5 A 224 GLY VAL GLN PHE ARG ALA ALA VAL ASN GLY VAL THR THR SEQRES 6 A 224 SER GLY SER GLY TYR PRO ARG SER GLU LEU ARG GLU MET SEQRES 7 A 224 THR ASP GLY GLY GLU GLU LYS ALA SER TRP SER ALA THR SEQRES 8 A 224 SER GLY THR HIS THR MET VAL PHE ARG GLU ALA PHE ASN SEQRES 9 A 224 HIS LEU PRO GLU VAL LYS PRO HIS LEU VAL GLY ALA GLN SEQRES 10 A 224 ILE HIS ASP GLY ASP ASP ASP VAL THR VAL PHE ARG LEU SEQRES 11 A 224 GLU GLY THR SER LEU TYR ILE THR LYS GLY ASP ASP THR SEQRES 12 A 224 HIS HIS LYS LEU VAL THR SER ASP TYR LYS LEU ASN THR SEQRES 13 A 224 VAL PHE GLU GLY LYS PHE VAL VAL SER GLY GLY LYS ILE SEQRES 14 A 224 LYS VAL TYR TYR ASN GLY VAL LEU GLN THR THR ILE SER SEQRES 15 A 224 HIS THR SER SER GLY ASN TYR PHE LYS ALA GLY ALA TYR SEQRES 16 A 224 THR GLN ALA ASN CYS SER ASN SER SER PRO CYS SER SER SEQRES 17 A 224 SER ASN TYR GLY GLN VAL SER LEU TYR LYS LEU GLN VAL SEQRES 18 A 224 THR HIS SER FORMUL 2 HOH *346(H2 O) HELIX 1 1 TYR A 6 GLN A 10 5 5 HELIX 2 2 PRO A 34 PHE A 39 5 6 SHEET 1 A 4 LYS A 27 ILE A 31 0 SHEET 2 A 4 TRP A 16 SER A 24 -1 N SER A 24 O LYS A 27 SHEET 3 A 4 ARG A 72 THR A 79 -1 O ARG A 76 N LYS A 17 SHEET 4 A 4 GLU A 84 LYS A 85 -1 O GLU A 84 N THR A 79 SHEET 1 B 8 LYS A 27 ILE A 31 0 SHEET 2 B 8 TRP A 16 SER A 24 -1 N SER A 24 O LYS A 27 SHEET 3 B 8 ARG A 72 THR A 79 -1 O ARG A 76 N LYS A 17 SHEET 4 B 8 TYR A 189 THR A 196 -1 O ALA A 192 N LEU A 75 SHEET 5 B 8 HIS A 112 HIS A 119 -1 N HIS A 119 O TYR A 189 SHEET 6 B 8 ASP A 124 GLU A 131 -1 O LEU A 130 N LEU A 113 SHEET 7 B 8 SER A 134 LYS A 139 -1 O TYR A 136 N ARG A 129 SHEET 8 B 8 ASP A 142 THR A 149 -1 O VAL A 148 N LEU A 135 SHEET 1 C 7 PHE A 45 VAL A 47 0 SHEET 2 C 7 VAL A 54 ALA A 59 -1 O GLN A 55 N GLN A 46 SHEET 3 C 7 TYR A 211 SER A 224 -1 O VAL A 214 N PHE A 56 SHEET 4 C 7 THR A 94 HIS A 105 -1 N ARG A 100 O TYR A 217 SHEET 5 C 7 PHE A 158 SER A 165 -1 O VAL A 164 N HIS A 95 SHEET 6 C 7 LYS A 168 TYR A 173 -1 O LYS A 170 N VAL A 163 SHEET 7 C 7 VAL A 176 SER A 182 -1 O GLN A 178 N VAL A 171 SSBOND 1 CYS A 4 CYS A 51 1555 1555 2.03 SSBOND 2 CYS A 200 CYS A 206 1555 1555 2.03 CISPEP 1 GLU A 2 PRO A 3 0 -0.40 CISPEP 2 GLN A 33 PRO A 34 0 0.18 CISPEP 3 ALA A 42 PRO A 43 0 0.14 CISPEP 4 SER A 204 PRO A 205 0 0.15 CRYST1 40.925 47.234 50.307 90.00 90.22 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 0.024435 0.000000 0.000095 0.00000 SCALE2 0.000000 0.021171 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019878 0.00000