HEADER HYDROLASE 12-JUL-16 5GLN TITLE CRYSTAL STRUCTURE OF COXYL43, GH43 BETA-XYLOSIDASE/ALPHA- TITLE 2 ARABINOFURANOSIDASE FROM A COMPOSTMICROBIAL METAGENOME IN COMPLEX TITLE 3 WITH XYLOTRIOSE, CALCIUM-BOUND FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSIDE HYDROLASE FAMILY 43; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 47-369; COMPND 5 SYNONYM: BETA-XYLOSIDASE / ALPHA-ARABINOFURANOSIDASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED BACTERIUM; SOURCE 3 ORGANISM_TAXID: 77133; SOURCE 4 GENE: COXYL43; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS GLYCOSIDE HYDROLASE FAMILY 43, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.MATSUZAWA,N.KISHINE,Z.FUJIMOTO,K.YAOI REVDAT 4 08-NOV-23 5GLN 1 HETSYN LINK REVDAT 3 29-JUL-20 5GLN 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 06-DEC-17 5GLN 1 JRNL REMARK REVDAT 1 15-MAR-17 5GLN 0 JRNL AUTH T.MATSUZAWA,S.KANEKO,N.KISHINE,Z.FUJIMOTO,K.YAOI JRNL TITL CRYSTAL STRUCTURE OF METAGENOMIC BETA-XYLOSIDASE/ JRNL TITL 2 ALPHA-L-ARABINOFURANOSIDASE ACTIVATED BY CALCIUM. JRNL REF J. BIOCHEM. V. 162 173 2017 JRNL REFN ISSN 1756-2651 JRNL PMID 28204531 JRNL DOI 10.1093/JB/MVX012 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.MATSUZAWA,S.KANEKO,K.YAOI REMARK 1 TITL SCREENING, IDENTIFICATION, AND CHARACTERIZATION OF A GH43 REMARK 1 TITL 2 FAMILY BETA-XYLOSIDASE/ALPHA-ARABINOFURANOSIDASE FROM A REMARK 1 TITL 3 COMPOST MICROBIAL METAGENOME. REMARK 1 REF APPL. MICROBIOL. BIOTECHNOL. V. 99 8943 2015 REMARK 1 REFN ESSN 1432-0614 REMARK 1 PMID 25971196 REMARK 1 DOI 10.1007/S00253-015-6647-5 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 78.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 74549 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3854 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) : 5367 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 290 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5190 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 136 REMARK 3 SOLVENT ATOMS : 600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.18000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.729 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5541 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4872 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7554 ; 1.267 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11321 ; 0.910 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 654 ; 6.633 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 268 ;30.652 ;24.142 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 811 ;11.862 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.354 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 801 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6165 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1273 ; 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): 2623 ; 0.844 ; 1.534 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2621 ; 0.841 ; 1.532 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3273 ; 1.502 ; 2.292 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3274 ; 1.502 ; 2.293 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2918 ; 0.951 ; 1.648 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2919 ; 0.951 ; 1.648 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4281 ; 1.609 ; 2.430 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6787 ; 4.302 ;13.224 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6680 ; 4.209 ;13.049 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 5GLN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1300001006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI III REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78466 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.5000 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.60500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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: 5GLL REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 8% TACSIMATE, PH 5.0, REMARK 280 VAPOR DIFFUSION, SITTING 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 30.79350 REMARK 290 SMTRY3 2 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 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 APPLY THE FOLLOWING TO CHAINS: B, 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 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 26 REMARK 465 GLY A 27 REMARK 465 SER A 28 REMARK 465 SER A 29 REMARK 465 HIS A 30 REMARK 465 HIS A 31 REMARK 465 HIS A 32 REMARK 465 HIS A 33 REMARK 465 HIS A 34 REMARK 465 HIS A 35 REMARK 465 SER A 36 REMARK 465 SER A 37 REMARK 465 GLY A 38 REMARK 465 LEU A 39 REMARK 465 MET B 26 REMARK 465 GLY B 27 REMARK 465 SER B 28 REMARK 465 SER B 29 REMARK 465 HIS B 30 REMARK 465 HIS B 31 REMARK 465 HIS B 32 REMARK 465 HIS B 33 REMARK 465 HIS B 34 REMARK 465 HIS B 35 REMARK 465 SER B 36 REMARK 465 SER B 37 REMARK 465 GLY B 38 REMARK 465 LEU B 39 REMARK 465 VAL B 40 REMARK 465 PRO B 41 REMARK 465 ARG B 42 REMARK 465 GLY B 43 REMARK 465 SER B 44 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 HIS B 45 CG ND1 CD2 CE1 NE2 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 HIS A 45 49.77 -142.97 REMARK 500 GLN A 123 81.06 68.90 REMARK 500 SER A 175 -152.48 58.50 REMARK 500 TRP A 196 -118.37 56.56 REMARK 500 THR A 216 -85.25 -129.65 REMARK 500 ASP A 217 -154.58 -144.43 REMARK 500 GLN B 123 79.75 68.55 REMARK 500 SER B 175 -150.98 61.35 REMARK 500 TRP B 196 -118.20 58.72 REMARK 500 THR B 216 -85.24 -128.87 REMARK 500 ASP B 217 -153.43 -143.80 REMARK 500 REMARK 500 REMARK: NULL 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 411 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 363 OG1 REMARK 620 2 HOH A1030 O 81.4 REMARK 620 3 HOH A1097 O 98.1 90.3 REMARK 620 4 HOH A1469 O 79.3 89.7 177.4 REMARK 620 5 HOH A1470 O 85.7 165.8 85.5 93.9 REMARK 620 6 XYP F 3 O4 174.9 102.3 85.5 97.1 90.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1249 O REMARK 620 2 HOH A1250 O 72.9 REMARK 620 3 HOH A1251 O 79.5 87.4 REMARK 620 4 HOH A1252 O 137.9 144.1 82.9 REMARK 620 5 HOH A1388 O 147.7 74.8 100.6 73.2 REMARK 620 6 HOH A1501 O 73.0 145.3 92.8 69.9 138.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 411 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 363 OG1 REMARK 620 2 HOH B1001 O 84.3 REMARK 620 3 HOH B1092 O 80.1 100.0 REMARK 620 4 HOH B1380 O 77.5 159.6 86.2 REMARK 620 5 HOH B1462 O 98.9 84.2 175.6 89.4 REMARK 620 6 HOH B1579 O 170.0 105.7 97.8 92.6 82.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B1013 O REMARK 620 2 HOH B1014 O 74.0 REMARK 620 3 HOH B1016 O 146.5 72.7 REMARK 620 4 HOH B1017 O 102.1 87.1 80.6 REMARK 620 5 HOH B1173 O 72.4 142.1 140.4 83.2 REMARK 620 6 HOH B1174 O 139.2 145.4 73.1 92.6 71.8 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: OLIGOSACCHARIDE METABOLISM REMARK 630 MOLECULE NAME: BETA-D-XYLOPYRANOSE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 XYP A 532 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: NULL REMARK 630 DETAILS: OLIGOSACCHARIDE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GLK RELATED DB: PDB REMARK 900 THE CALCIUM-FREE, LIGAND-FREE FORM OF THE SAME PROTEIN REMARK 900 RELATED ID: 5GLL RELATED DB: PDB REMARK 900 THE CALCIUM-BOUND, LIGAND-FREE FORM OF THE SAME PROTEIN REMARK 900 RELATED ID: 5GLM RELATED DB: PDB REMARK 900 THE CALCIUM-FREE FORM OF THE SAME PROTEIN COMPLEXED WITH XYLOTRIOSE REMARK 900 RELATED ID: 5GLO RELATED DB: PDB REMARK 900 THE CALCIUM-FREE FORM OF THE SAME PROTEIN COMPLEXED WITH L-ARABINOSE REMARK 900 RELATED ID: 5GLP RELATED DB: PDB REMARK 900 THE CALCIUM-BOUND FORM OF THE SAME PROTEIN COMPLEXED WITH L- REMARK 900 ARABINOSE REMARK 900 RELATED ID: 5GLQ RELATED DB: PDB REMARK 900 THE CALCIUM-BOUND FORM OF THE SAME PROTEIN COMPLEXED WITH XYLOTRIOSE REMARK 900 RELATED ID: 5GLR RELATED DB: PDB REMARK 900 THE CALCIUM-BOUND FORM OF THE SAME PROTEIN COMPLEXED WITH REMARK 900 XYLOTRIOSE AND L-ARABINOSE DBREF1 5GLN A 47 369 UNP A0A0H5BL38_9BACT DBREF2 5GLN A A0A0H5BL38 47 369 DBREF1 5GLN B 47 369 UNP A0A0H5BL38_9BACT DBREF2 5GLN B A0A0H5BL38 47 369 SEQADV 5GLN MET A 26 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN GLY A 27 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN SER A 28 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN SER A 29 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS A 30 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS A 31 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS A 32 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS A 33 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS A 34 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS A 35 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN SER A 36 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN SER A 37 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN GLY A 38 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN LEU A 39 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN VAL A 40 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN PRO A 41 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN ARG A 42 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN GLY A 43 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN SER A 44 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS A 45 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN MET A 46 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN MET B 26 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN GLY B 27 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN SER B 28 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN SER B 29 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS B 30 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS B 31 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS B 32 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS B 33 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS B 34 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS B 35 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN SER B 36 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN SER B 37 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN GLY B 38 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN LEU B 39 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN VAL B 40 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN PRO B 41 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN ARG B 42 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN GLY B 43 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN SER B 44 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN HIS B 45 UNP A0A0H5BL3 EXPRESSION TAG SEQADV 5GLN MET B 46 UNP A0A0H5BL3 EXPRESSION TAG SEQRES 1 A 344 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 344 LEU VAL PRO ARG GLY SER HIS MET GLU PRO LEU VAL THR SEQRES 3 A 344 HIS ILE TYR THR ALA ASP PRO SER ALA HIS VAL PHE ASP SEQRES 4 A 344 GLY LYS VAL TYR ILE TYR PRO SER HIS ASP ILE ASP ALA SEQRES 5 A 344 GLY THR PRO GLU ASN ASP MET GLY ASP HIS PHE ASP MET SEQRES 6 A 344 ARG ASP TYR HIS VAL LEU SER MET ASN SER ILE PRO GLY SEQRES 7 A 344 GLU VAL THR ASP HIS GLY VAL ALA LEU ASP ILE LYS ASP SEQRES 8 A 344 ILE PRO TRP ALA GLY ARG GLN LEU TRP ALA PRO ASP ALA SEQRES 9 A 344 ALA SER LYS ASP GLY LYS TYR TYR LEU TYR PHE PRO ALA SEQRES 10 A 344 LYS ASP LYS GLU ASP ILE PHE ARG ILE GLY VAL ALA VAL SEQRES 11 A 344 SER ASP SER PRO ALA GLY PRO PHE LYS PRO GLU SER GLU SEQRES 12 A 344 PRO ILE LYS GLY SER TYR SER ILE ASP PRO ALA VAL PHE SEQRES 13 A 344 LYS ASP ASP ASP GLY LYS TYR TYR MET TYR PHE GLY GLY SEQRES 14 A 344 ILE TRP GLY GLY GLN LEU GLN ARG TRP THR THR GLY GLU SEQRES 15 A 344 TYR ALA GLY HIS ASP ALA SER LYS THR ASP LEU GLU GLN SEQRES 16 A 344 ASP ASP ALA PRO ALA ILE GLY PRO ARG ILE ALA LEU MET SEQRES 17 A 344 SER ASP ASP MET LEU SER PHE ALA GLU PRO VAL LYS GLU SEQRES 18 A 344 ILE SER ILE VAL ASP GLU GLN GLY ASN PRO ILE LEU GLY SEQRES 19 A 344 GLY ASP HIS ASP ARG ARG PHE PHE GLU ALA ALA TRP MET SEQRES 20 A 344 HIS LYS TYR ASN GLY THR TYR TYR LEU SER TYR SER THR SEQRES 21 A 344 GLY ASP THR HIS TYR ILE VAL TYR ALA THR GLY ASP ASN SEQRES 22 A 344 PRO TYR GLY PRO PHE THR TYR ARG GLY VAL ILE LEU ASN SEQRES 23 A 344 PRO VAL ILE GLY TRP THR ASN HIS HIS SER ILE VAL GLU SEQRES 24 A 344 PHE ASN GLY LYS TRP TYR LEU PHE TYR HIS ASP SER SER SEQRES 25 A 344 LEU SER GLY GLY LYS THR HIS LEU ARG CYS ILE LYS VAL SEQRES 26 A 344 THR GLU LEU THR HIS ASN ALA ASP GLY THR ILE GLU THR SEQRES 27 A 344 ILE SER PRO TYR ILE GLU SEQRES 1 B 344 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 344 LEU VAL PRO ARG GLY SER HIS MET GLU PRO LEU VAL THR SEQRES 3 B 344 HIS ILE TYR THR ALA ASP PRO SER ALA HIS VAL PHE ASP SEQRES 4 B 344 GLY LYS VAL TYR ILE TYR PRO SER HIS ASP ILE ASP ALA SEQRES 5 B 344 GLY THR PRO GLU ASN ASP MET GLY ASP HIS PHE ASP MET SEQRES 6 B 344 ARG ASP TYR HIS VAL LEU SER MET ASN SER ILE PRO GLY SEQRES 7 B 344 GLU VAL THR ASP HIS GLY VAL ALA LEU ASP ILE LYS ASP SEQRES 8 B 344 ILE PRO TRP ALA GLY ARG GLN LEU TRP ALA PRO ASP ALA SEQRES 9 B 344 ALA SER LYS ASP GLY LYS TYR TYR LEU TYR PHE PRO ALA SEQRES 10 B 344 LYS ASP LYS GLU ASP ILE PHE ARG ILE GLY VAL ALA VAL SEQRES 11 B 344 SER ASP SER PRO ALA GLY PRO PHE LYS PRO GLU SER GLU SEQRES 12 B 344 PRO ILE LYS GLY SER TYR SER ILE ASP PRO ALA VAL PHE SEQRES 13 B 344 LYS ASP ASP ASP GLY LYS TYR TYR MET TYR PHE GLY GLY SEQRES 14 B 344 ILE TRP GLY GLY GLN LEU GLN ARG TRP THR THR GLY GLU SEQRES 15 B 344 TYR ALA GLY HIS ASP ALA SER LYS THR ASP LEU GLU GLN SEQRES 16 B 344 ASP ASP ALA PRO ALA ILE GLY PRO ARG ILE ALA LEU MET SEQRES 17 B 344 SER ASP ASP MET LEU SER PHE ALA GLU PRO VAL LYS GLU SEQRES 18 B 344 ILE SER ILE VAL ASP GLU GLN GLY ASN PRO ILE LEU GLY SEQRES 19 B 344 GLY ASP HIS ASP ARG ARG PHE PHE GLU ALA ALA TRP MET SEQRES 20 B 344 HIS LYS TYR ASN GLY THR TYR TYR LEU SER TYR SER THR SEQRES 21 B 344 GLY ASP THR HIS TYR ILE VAL TYR ALA THR GLY ASP ASN SEQRES 22 B 344 PRO TYR GLY PRO PHE THR TYR ARG GLY VAL ILE LEU ASN SEQRES 23 B 344 PRO VAL ILE GLY TRP THR ASN HIS HIS SER ILE VAL GLU SEQRES 24 B 344 PHE ASN GLY LYS TRP TYR LEU PHE TYR HIS ASP SER SER SEQRES 25 B 344 LEU SER GLY GLY LYS THR HIS LEU ARG CYS ILE LYS VAL SEQRES 26 B 344 THR GLU LEU THR HIS ASN ALA ASP GLY THR ILE GLU THR SEQRES 27 B 344 ILE SER PRO TYR ILE GLU HET XYP C 1 10 HET XYP C 2 9 HET XYP D 1 10 HET XYP D 2 9 HET XYP E 1 10 HET XYP E 2 9 HET XYP E 3 9 HET XYP F 1 10 HET XYP F 2 9 HET XYP F 3 9 HET CA A 401 1 HET NA A 411 1 HET XYS A 500 10 HET XYP A 532 10 HET ACT A 613 4 HET CA B 401 1 HET NA B 411 1 HET XYS B 500 10 HET ACT B 611 4 HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM XYS ALPHA-D-XYLOPYRANOSE HETNAM ACT ACETATE ION HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE HETSYN XYS ALPHA-D-XYLOSE; D-XYLOSE; XYLOSE; XYLOPYRANOSE FORMUL 3 XYP 11(C5 H10 O5) FORMUL 7 CA 2(CA 2+) FORMUL 8 NA 2(NA 1+) FORMUL 9 XYS 2(C5 H10 O5) FORMUL 11 ACT 2(C2 H3 O2 1-) FORMUL 16 HOH *600(H2 O) HELIX 1 AA1 LYS A 115 ILE A 117 5 3 HELIX 2 AA2 ILE A 195 TRP A 203 5 9 HELIX 3 AA3 GLY A 286 HIS A 289 5 4 HELIX 4 AA4 LYS B 115 ILE B 117 5 3 HELIX 5 AA5 ILE B 195 THR B 204 5 10 HELIX 6 AA6 GLY B 286 HIS B 289 5 4 SHEET 1 AA1 4 TYR A 54 PHE A 63 0 SHEET 2 AA1 4 LYS A 66 ASP A 74 -1 O TYR A 68 N HIS A 61 SHEET 3 AA1 4 ASP A 92 MET A 98 -1 O LEU A 96 N ILE A 69 SHEET 4 AA1 4 VAL A 105 ASP A 113 -1 O ALA A 111 N TYR A 93 SHEET 1 AA2 3 ALA A 120 ARG A 122 0 SHEET 2 AA2 3 LYS A 135 ASP A 144 -1 O LYS A 143 N GLY A 121 SHEET 3 AA2 3 ASP A 128 LYS A 132 -1 N ASP A 128 O TYR A 139 SHEET 1 AA3 4 ALA A 120 ARG A 122 0 SHEET 2 AA3 4 LYS A 135 ASP A 144 -1 O LYS A 143 N GLY A 121 SHEET 3 AA3 4 PHE A 149 SER A 156 -1 O SER A 156 N TYR A 136 SHEET 4 AA3 4 LYS A 164 PRO A 165 -1 O LYS A 164 N VAL A 155 SHEET 1 AA4 4 ALA A 179 LYS A 182 0 SHEET 2 AA4 4 TYR A 188 PHE A 192 -1 O TYR A 191 N ALA A 179 SHEET 3 AA4 4 ARG A 229 LEU A 232 -1 O ARG A 229 N PHE A 192 SHEET 4 AA4 4 LYS A 245 GLU A 246 -1 O LYS A 245 N ILE A 230 SHEET 1 AA5 5 ILE A 249 VAL A 250 0 SHEET 2 AA5 5 PHE A 303 LEU A 310 1 O TYR A 305 N VAL A 250 SHEET 3 AA5 5 ILE A 291 GLY A 296 -1 N ILE A 291 O ILE A 309 SHEET 4 AA5 5 THR A 278 SER A 284 -1 N LEU A 281 O ALA A 294 SHEET 5 AA5 5 GLU A 268 TYR A 275 -1 N HIS A 273 O TYR A 280 SHEET 1 AA6 3 SER A 321 PHE A 325 0 SHEET 2 AA6 3 LYS A 328 ASP A 335 -1 O LYS A 328 N PHE A 325 SHEET 3 AA6 3 CYS A 347 LEU A 353 -1 O THR A 351 N LEU A 331 SHEET 1 AA7 4 TYR B 54 PHE B 63 0 SHEET 2 AA7 4 LYS B 66 ASP B 74 -1 O TYR B 68 N HIS B 61 SHEET 3 AA7 4 ASP B 92 MET B 98 -1 O MET B 98 N VAL B 67 SHEET 4 AA7 4 VAL B 105 ASP B 113 -1 O ALA B 111 N TYR B 93 SHEET 1 AA8 3 ALA B 120 ARG B 122 0 SHEET 2 AA8 3 LYS B 135 ASP B 144 -1 O LYS B 143 N GLY B 121 SHEET 3 AA8 3 ASP B 128 LYS B 132 -1 N ALA B 130 O TYR B 137 SHEET 1 AA9 4 ALA B 120 ARG B 122 0 SHEET 2 AA9 4 LYS B 135 ASP B 144 -1 O LYS B 143 N GLY B 121 SHEET 3 AA9 4 PHE B 149 SER B 156 -1 O SER B 156 N TYR B 136 SHEET 4 AA9 4 LYS B 164 PRO B 165 -1 O LYS B 164 N VAL B 155 SHEET 1 AB1 4 ALA B 179 LYS B 182 0 SHEET 2 AB1 4 TYR B 188 PHE B 192 -1 O TYR B 191 N ALA B 179 SHEET 3 AB1 4 ARG B 229 LEU B 232 -1 O ARG B 229 N PHE B 192 SHEET 4 AB1 4 LYS B 245 GLU B 246 -1 O LYS B 245 N ILE B 230 SHEET 1 AB2 5 ILE B 249 VAL B 250 0 SHEET 2 AB2 5 PHE B 303 LEU B 310 1 O TYR B 305 N VAL B 250 SHEET 3 AB2 5 ILE B 291 GLY B 296 -1 N ILE B 291 O ILE B 309 SHEET 4 AB2 5 THR B 278 SER B 284 -1 N LEU B 281 O ALA B 294 SHEET 5 AB2 5 GLU B 268 TYR B 275 -1 N HIS B 273 O TYR B 280 SHEET 1 AB3 3 SER B 321 PHE B 325 0 SHEET 2 AB3 3 LYS B 328 ASP B 335 -1 O LYS B 328 N PHE B 325 SHEET 3 AB3 3 CYS B 347 LEU B 353 -1 O THR B 351 N LEU B 331 LINK O4 XYP C 1 C1 XYP C 2 1555 1555 1.42 LINK O4 XYP D 1 C1 XYP D 2 1555 1555 1.42 LINK O4 XYP E 1 C1 XYP E 2 1555 1555 1.44 LINK O4 XYP E 2 C1 XYP E 3 1555 1555 1.42 LINK O4 XYP F 1 C1 XYP F 2 1555 1555 1.43 LINK O4 XYP F 2 C1 XYP F 3 1555 1555 1.43 LINK OG1 THR A 363 NA NA A 411 1555 1555 2.35 LINK CA CA A 401 O HOH A1249 1555 1555 2.47 LINK CA CA A 401 O HOH A1250 1555 1555 2.36 LINK CA CA A 401 O HOH A1251 1555 1555 2.44 LINK CA CA A 401 O HOH A1252 1555 1555 2.44 LINK CA CA A 401 O HOH A1388 1555 1555 2.53 LINK CA CA A 401 O HOH A1501 1555 1555 2.52 LINK NA NA A 411 O HOH A1030 1555 1555 2.50 LINK NA NA A 411 O HOH A1097 1555 1555 2.32 LINK NA NA A 411 O HOH A1469 1555 1555 2.51 LINK NA NA A 411 O HOH A1470 1555 1555 2.39 LINK NA NA A 411 O4 XYP F 3 1555 1555 2.53 LINK OG1 THR B 363 NA NA B 411 1555 1555 2.50 LINK CA CA B 401 O HOH B1013 1555 1555 2.55 LINK CA CA B 401 O HOH B1014 1555 1555 2.42 LINK CA CA B 401 O HOH B1016 1555 1555 2.42 LINK CA CA B 401 O HOH B1017 1555 1555 2.34 LINK CA CA B 401 O HOH B1173 1555 1555 2.40 LINK CA CA B 401 O HOH B1174 1555 1555 2.46 LINK NA NA B 411 O HOH B1001 1555 1555 2.37 LINK NA NA B 411 O HOH B1092 1555 1555 2.36 LINK NA NA B 411 O HOH B1380 1555 1555 2.51 LINK NA NA B 411 O HOH B1462 1555 1555 2.34 LINK NA NA B 411 O HOH B1579 1555 1555 2.39 CISPEP 1 ILE A 101 PRO A 102 0 -5.81 CISPEP 2 GLY A 161 PRO A 162 0 -2.27 CISPEP 3 GLY A 301 PRO A 302 0 5.01 CISPEP 4 ILE B 101 PRO B 102 0 -4.07 CISPEP 5 GLY B 161 PRO B 162 0 0.30 CISPEP 6 GLY B 301 PRO B 302 0 6.80 CRYST1 74.760 61.587 78.922 90.00 95.84 90.00 P 1 21 1 4 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 0.013376 0.000000 0.001369 0.00000 SCALE2 0.000000 0.016237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012737 0.00000