HEADER LYASE 04-MAR-13 3ZPY TITLE CRYSTAL STRUCTURE OF THE MARINE PL7 ALGINATE LYASE ALYA1 FROM ZOBELLIA TITLE 2 GALACTANIVORANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALGINATE LYASE, FAMILY PL7; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 199-446; COMPND 5 EC: 4.2.2.3, 4.2.2.11; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZOBELLIA GALACTANIVORANS; SOURCE 3 ORGANISM_TAXID: 63186; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PFO4; SOURCE 9 OTHER_DETAILS: INHOUSE ISOLATE OF ROSCOFF MARINE INSTITUTE AND DSM KEYWDS LYASE, POLYSACCHARIDASES, MARINE BACTERIAL ENZYME EXPDTA X-RAY DIFFRACTION AUTHOR F.THOMAS,A.JEUDY,G.MICHEL,M.CZJZEK REVDAT 4 20-DEC-23 3ZPY 1 REMARK LINK REVDAT 3 28-AUG-13 3ZPY 1 JRNL REVDAT 2 03-JUL-13 3ZPY 1 JRNL REVDAT 1 26-JUN-13 3ZPY 0 JRNL AUTH F.THOMAS,L.C.E.LUNDQVIST,M.JAM,A.JEUDY,T.BARBEYRON, JRNL AUTH 2 C.SANDSTROM,G.MICHEL,M.CZJZEK JRNL TITL COMPARATIVE CHARACTERIZATION OF TWO MARINE ALGINATE LYASES JRNL TITL 2 FROM ZOBELLIA GALACTANIVORANS REVEALS DISTINCT MODES OF JRNL TITL 3 ACTION AND EXQUISITE ADAPTATION TO THEIR NATURAL SUBSTRATE. JRNL REF J.BIOL.CHEM. V. 288 23021 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23782694 JRNL DOI 10.1074/JBC.M113.467217 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 74936 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3944 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) : 1.43 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5455 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.1370 REMARK 3 BIN FREE R VALUE SET COUNT : 287 REMARK 3 BIN FREE R VALUE : 0.2140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3810 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 632 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.68000 REMARK 3 B22 (A**2) : 0.75000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : -0.20000 REMARK 3 B13 (A**2) : -0.20000 REMARK 3 B23 (A**2) : -0.04000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.074 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.005 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3926 ; 0.022 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5335 ; 2.102 ; 1.932 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 506 ; 7.690 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 193 ;36.517 ;25.337 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 615 ;11.051 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;22.446 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 565 ; 0.186 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3082 ; 0.015 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 3926 ; 8.848 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3839 ; 8.254 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 210 A 440 5 REMARK 3 1 B 210 B 440 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 919 ; 0.08 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 919 ; 0.08 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 853 ; 0.27 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 B (A): 853 ; 0.27 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 919 ; 1.98 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 919 ; 1.98 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 853 ; 2.74 ; 10.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 853 ; 2.74 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 200 A 440 REMARK 3 ORIGIN FOR THE GROUP (A): 29.3000 26.2040 18.7520 REMARK 3 T TENSOR REMARK 3 T11: 0.0151 T22: 0.0037 REMARK 3 T33: 0.0098 T12: 0.0046 REMARK 3 T13: -0.0007 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.1456 L22: 0.1690 REMARK 3 L33: 0.1855 L12: 0.0871 REMARK 3 L13: -0.0234 L23: 0.0635 REMARK 3 S TENSOR REMARK 3 S11: -0.0053 S12: 0.0008 S13: 0.0117 REMARK 3 S21: -0.0193 S22: 0.0065 S23: 0.0099 REMARK 3 S31: -0.0274 S32: -0.0140 S33: -0.0011 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 200 B 440 REMARK 3 ORIGIN FOR THE GROUP (A): 49.7150 47.7970 0.0010 REMARK 3 T TENSOR REMARK 3 T11: 0.0138 T22: 0.0021 REMARK 3 T33: 0.0138 T12: 0.0036 REMARK 3 T13: 0.0006 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.1214 L22: 0.0808 REMARK 3 L33: 0.2784 L12: 0.0676 REMARK 3 L13: -0.0479 L23: -0.0077 REMARK 3 S TENSOR REMARK 3 S11: -0.0058 S12: 0.0046 S13: -0.0160 REMARK 3 S21: 0.0100 S22: 0.0053 S23: -0.0230 REMARK 3 S31: 0.0265 S32: -0.0048 S33: 0.0005 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. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U REMARK 3 VALUES WITH TLS ADDED REMARK 4 REMARK 4 3ZPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1290055914. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78881 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 43.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1UAI REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M KSCN AND 28% PEG-MME 2000, PH 7 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 GLY B 199 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 2288 O HOH A 2309 1.93 REMARK 500 NZ LYS A 404 O HOH A 2288 2.02 REMARK 500 O HOH B 2138 O HOH B 2259 2.07 REMARK 500 O HOH B 2140 O HOH B 2262 2.08 REMARK 500 O HOH B 2069 O HOH B 2082 2.09 REMARK 500 O HOH B 2139 O HOH B 2258 2.16 REMARK 500 O HOH A 2083 O HOH A 2084 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2235 O HOH B 2286 1545 1.89 REMARK 500 O HOH A 2124 O HOH B 2003 1446 2.12 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 GLU A 276 CD GLU A 276 OE2 -0.067 REMARK 500 HIS B 323 CG HIS B 323 CD2 0.071 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 309 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 PHE A 342 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 TYR A 420 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG B 274 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP B 309 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 TYR B 386 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP B 408 CB - CG - OD1 ANGL. DEV. = 6.3 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 TYR A 248 -44.36 -131.41 REMARK 500 SER A 287 109.08 -160.85 REMARK 500 ASP A 335 -135.69 51.59 REMARK 500 SER A 358 -164.42 -124.36 REMARK 500 GLN A 365 51.47 -142.82 REMARK 500 GLU A 412 40.74 74.45 REMARK 500 TYR B 248 -43.32 -136.13 REMARK 500 SER B 287 109.50 -160.15 REMARK 500 ASP B 313 85.09 39.34 REMARK 500 ASP B 335 -136.75 50.40 REMARK 500 GLN B 365 53.50 -143.28 REMARK 500 GLU B 406 60.74 -100.18 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 A2136 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A2143 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 NA A 450 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 233 O REMARK 620 2 ALA A 235 O 86.8 REMARK 620 3 ILE A 238 O 81.8 96.2 REMARK 620 4 SER A 352 OG 138.3 125.5 70.3 REMARK 620 5 HOH A2344 O 87.0 142.3 119.6 81.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 450 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 233 OG1 REMARK 620 2 ASP B 234 OD1 112.1 REMARK 620 3 SER B 372 OG 111.7 108.8 REMARK 620 4 HOH B2049 O 108.4 116.7 98.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 450 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BE3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EXOLYTIC PL7 ALGINATE LYASE ALYA5 FROM REMARK 900 ZOBELLIA GALACTANIVORANS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CRYSTAL STRUCTURE CONTAINS THE C-TERMINAL CATALYTIC REMARK 999 DOMAIN ONLY DBREF 3ZPY A 199 446 UNP G0LAE1 G0LAE1_ZOBGA 199 446 DBREF 3ZPY B 199 446 UNP G0LAE1 G0LAE1_ZOBGA 199 446 SEQRES 1 A 248 GLY ASN SER PRO ALA SER VAL LEU GLY ILE THR ALA ASN SEQRES 2 A 248 THR TRP LYS ILE ASN SER PHE ILE GLY SER PRO GLY SER SEQRES 3 A 248 SER ALA THR TYR TYR ASP ASP ILE THR ASP ALA SER GLY SEQRES 4 A 248 ILE SER TYR ASN THR TYR SER ASP ASP ASN TYR PHE TYR SEQRES 5 A 248 THR ASP GLY GLU TRP VAL TYR PHE LYS CYS TYR ARG GLY SEQRES 6 A 248 LEU GLY GLY SER ALA ASN SER GLN ASN PRO ARG VAL GLU SEQRES 7 A 248 LEU ARG GLU MET ASP ASN GLY ASN LEU ALA SER TRP THR SEQRES 8 A 248 GLY ASP SER GLY THR HIS THR MET GLU TRP THR VAL GLN SEQRES 9 A 248 VAL ASN GLN LEU PRO GLN ASP THR ASP GLY ASP GLY GLY SEQRES 10 A 248 VAL LEU CYS PHE GLY GLN ILE HIS GLY PRO SER LYS ASN SEQRES 11 A 248 SER ASP GLY VAL GLU VAL ASP ASP VAL VAL ARG VAL GLN SEQRES 12 A 248 PHE ILE GLY GLU GLU ASN GLN SER SER GLY SER VAL LYS SEQRES 13 A 248 LEU LYS ILE SER GLY TYR VAL THR GLU GLU GLN GLY GLY SEQRES 14 A 248 SER GLN THR PHE SER GLY TYR SER LEU ASP THR THR TYR SEQRES 15 A 248 ASN CYS LYS LEU VAL TYR SER GLY GLY TYR VAL GLU LEU SEQRES 16 A 248 PHE MET ASN GLY SER SER VAL PHE ARG LYS LYS MET GLU SEQRES 17 A 248 VAL ASP ASP LEU SER GLU ASN TYR PHE LYS VAL GLY ASN SEQRES 18 A 248 TYR LEU GLN SER VAL LYS GLY ALA SER TYR THR GLY SER SEQRES 19 A 248 TYR GLY LEU VAL ARG ILE LYS ASN LEU SER VAL THR HIS SEQRES 20 A 248 ASN SEQRES 1 B 248 GLY ASN SER PRO ALA SER VAL LEU GLY ILE THR ALA ASN SEQRES 2 B 248 THR TRP LYS ILE ASN SER PHE ILE GLY SER PRO GLY SER SEQRES 3 B 248 SER ALA THR TYR TYR ASP ASP ILE THR ASP ALA SER GLY SEQRES 4 B 248 ILE SER TYR ASN THR TYR SER ASP ASP ASN TYR PHE TYR SEQRES 5 B 248 THR ASP GLY GLU TRP VAL TYR PHE LYS CYS TYR ARG GLY SEQRES 6 B 248 LEU GLY GLY SER ALA ASN SER GLN ASN PRO ARG VAL GLU SEQRES 7 B 248 LEU ARG GLU MET ASP ASN GLY ASN LEU ALA SER TRP THR SEQRES 8 B 248 GLY ASP SER GLY THR HIS THR MET GLU TRP THR VAL GLN SEQRES 9 B 248 VAL ASN GLN LEU PRO GLN ASP THR ASP GLY ASP GLY GLY SEQRES 10 B 248 VAL LEU CYS PHE GLY GLN ILE HIS GLY PRO SER LYS ASN SEQRES 11 B 248 SER ASP GLY VAL GLU VAL ASP ASP VAL VAL ARG VAL GLN SEQRES 12 B 248 PHE ILE GLY GLU GLU ASN GLN SER SER GLY SER VAL LYS SEQRES 13 B 248 LEU LYS ILE SER GLY TYR VAL THR GLU GLU GLN GLY GLY SEQRES 14 B 248 SER GLN THR PHE SER GLY TYR SER LEU ASP THR THR TYR SEQRES 15 B 248 ASN CYS LYS LEU VAL TYR SER GLY GLY TYR VAL GLU LEU SEQRES 16 B 248 PHE MET ASN GLY SER SER VAL PHE ARG LYS LYS MET GLU SEQRES 17 B 248 VAL ASP ASP LEU SER GLU ASN TYR PHE LYS VAL GLY ASN SEQRES 18 B 248 TYR LEU GLN SER VAL LYS GLY ALA SER TYR THR GLY SER SEQRES 19 B 248 TYR GLY LEU VAL ARG ILE LYS ASN LEU SER VAL THR HIS SEQRES 20 B 248 ASN HET NA A 450 1 HET NA B 450 1 HETNAM NA SODIUM ION FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *632(H2 O) HELIX 1 1 SER A 201 GLY A 207 1 7 HELIX 2 2 ASP A 231 ALA A 235 5 5 HELIX 3 3 SER A 239 TYR A 243 5 5 HELIX 4 4 GLY A 359 GLU A 364 1 6 HELIX 5 5 SER B 201 GLY B 207 1 7 HELIX 6 6 ASP B 231 ALA B 235 5 5 HELIX 7 7 GLY B 359 GLU B 364 1 6 SHEET 1 AA 4 THR A 227 TYR A 229 0 SHEET 2 AA 4 TRP A 213 ILE A 219 -1 O SER A 217 N TYR A 229 SHEET 3 AA 4 ARG A 274 ASP A 281 -1 O GLU A 276 N ASN A 216 SHEET 4 AA 4 ASN A 284 LEU A 285 -1 O ASN A 284 N ASP A 281 SHEET 1 AB 8 THR A 227 TYR A 229 0 SHEET 2 AB 8 TRP A 213 ILE A 219 -1 O SER A 217 N TYR A 229 SHEET 3 AB 8 ARG A 274 ASP A 281 -1 O GLU A 276 N ASN A 216 SHEET 4 AB 8 TYR A 414 LEU A 421 -1 O PHE A 415 N GLU A 279 SHEET 5 AB 8 GLY A 315 HIS A 323 -1 O CYS A 318 N TYR A 420 SHEET 6 AB 8 ASP A 336 GLY A 344 -1 N VAL A 337 O ILE A 322 SHEET 7 AB 8 SER A 352 SER A 358 -1 O LYS A 354 N ILE A 343 SHEET 8 AB 8 GLN A 369 SER A 375 -1 O GLN A 369 N ILE A 357 SHEET 1 AC 2 ASN A 284 LEU A 285 0 SHEET 2 AC 2 ARG A 274 ASP A 281 -1 O ASP A 281 N ASN A 284 SHEET 1 AD 7 PHE A 249 THR A 251 0 SHEET 2 AD 7 VAL A 256 TYR A 261 -1 O TYR A 257 N TYR A 250 SHEET 3 AD 7 TYR A 433 ASN A 446 -1 O GLY A 434 N CYS A 260 SHEET 4 AD 7 THR A 294 GLN A 305 -1 O THR A 294 N ASN A 446 SHEET 5 AD 7 TYR A 380 SER A 387 -1 O TYR A 380 N VAL A 301 SHEET 6 AD 7 TYR A 390 MET A 395 -1 O TYR A 390 N SER A 387 SHEET 7 AD 7 SER A 398 LYS A 404 -1 O SER A 398 N MET A 395 SHEET 1 BA 4 THR B 227 TYR B 229 0 SHEET 2 BA 4 TRP B 213 ILE B 219 -1 O SER B 217 N TYR B 229 SHEET 3 BA 4 ARG B 274 ASP B 281 -1 O GLU B 276 N ASN B 216 SHEET 4 BA 4 ASN B 284 LEU B 285 -1 O ASN B 284 N ASP B 281 SHEET 1 BB 8 THR B 227 TYR B 229 0 SHEET 2 BB 8 TRP B 213 ILE B 219 -1 O SER B 217 N TYR B 229 SHEET 3 BB 8 ARG B 274 ASP B 281 -1 O GLU B 276 N ASN B 216 SHEET 4 BB 8 TYR B 414 LEU B 421 -1 O PHE B 415 N GLU B 279 SHEET 5 BB 8 GLY B 315 HIS B 323 -1 O CYS B 318 N TYR B 420 SHEET 6 BB 8 ASP B 336 GLY B 344 -1 N VAL B 337 O ILE B 322 SHEET 7 BB 8 SER B 352 SER B 358 -1 O LYS B 354 N ILE B 343 SHEET 8 BB 8 GLN B 369 SER B 375 -1 O GLN B 369 N ILE B 357 SHEET 1 BC 2 ASN B 284 LEU B 285 0 SHEET 2 BC 2 ARG B 274 ASP B 281 -1 O ASP B 281 N ASN B 284 SHEET 1 BD 7 PHE B 249 THR B 251 0 SHEET 2 BD 7 VAL B 256 TYR B 261 -1 O TYR B 257 N TYR B 250 SHEET 3 BD 7 TYR B 433 ASN B 446 -1 O GLY B 434 N CYS B 260 SHEET 4 BD 7 THR B 294 GLN B 305 -1 O THR B 294 N ASN B 446 SHEET 5 BD 7 TYR B 380 SER B 387 -1 O TYR B 380 N VAL B 301 SHEET 6 BD 7 TYR B 390 MET B 395 -1 O TYR B 390 N SER B 387 SHEET 7 BD 7 SER B 398 LYS B 404 -1 O SER B 398 N MET B 395 LINK O THR A 233 NA NA A 450 1555 1555 2.75 LINK O ALA A 235 NA NA A 450 1555 1555 2.70 LINK O ILE A 238 NA NA A 450 1555 1555 2.80 LINK OG SER A 352 NA NA A 450 1455 1555 2.78 LINK NA NA A 450 O HOH A2344 1555 1555 2.95 LINK OG1 THR B 233 NA NA B 450 1555 1555 2.67 LINK OD1 ASP B 234 NA NA B 450 1555 1555 2.82 LINK OG SER B 372 NA NA B 450 1655 1555 2.62 LINK NA NA B 450 O HOH B2049 1555 1555 2.73 SITE 1 AC1 5 THR A 233 ALA A 235 ILE A 238 SER A 352 SITE 2 AC1 5 HOH A2344 SITE 1 AC2 5 THR B 233 ASP B 234 LYS B 354 SER B 372 SITE 2 AC2 5 HOH B2049 CRYST1 43.860 50.390 55.520 69.14 90.02 84.92 P 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 0.022800 -0.002027 0.000784 0.00000 SCALE2 0.000000 0.019923 -0.007627 0.00000 SCALE3 0.000000 0.000000 0.019286 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.999991 -0.004242 0.000898 79.25528 1 MTRIX2 2 0.003756 -0.743863 0.668322 61.61369 1 MTRIX3 2 -0.002167 0.668319 0.743872 -13.06502 1