HEADER HYDROLASE 03-DEC-08 2W52 TITLE 2 BETA-GLUCANS (6-O-GLUCOSYL-LAMINARITRIOSE) IN BOTH DONOR AND TITLE 2 ACCEPTOR SITES OF GH16 LAMINARINASE 16A FROM PHANEROCHAETE TITLE 3 CHRYSOSPORIUM. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE LAMINARINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 21-318; COMPND 5 SYNONYM: LAMINARINASE 16A; COMPND 6 EC: 3.2.1.6; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHANEROCHAETE CHRYSOSPORIUM; SOURCE 3 ORGANISM_COMMON: WHITE-ROT FUNGUS; SOURCE 4 ORGANISM_TAXID: 5306; SOURCE 5 STRAIN: K-3; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: KM71H; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZALPHAA KEYWDS LAMINARIN, FAMILY 16, EXTRACELLULAR, BETA SANDWICH, BASIDIOMYCETE, KEYWDS 2 BETA- GLUCANASE, GLYCOSYL HYDROLASE, 3/1, GH7, GH16, LAM16A, BETA- KEYWDS 3 1\, 6-GLUCAN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.VASUR,R.KAWAI,E.ANDERSSON,K.IGARASHI,M.SANDGREN,M.SAMEJIMA, AUTHOR 2 J.STAHLBERG REVDAT 5 23-OCT-24 2W52 1 HETSYN REVDAT 4 29-JUL-20 2W52 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 17-JAN-18 2W52 1 REMARK REVDAT 2 04-APR-12 2W52 1 KEYWDS JRNL REMARK VERSN REVDAT 2 2 1 FORMUL REVDAT 1 21-JUL-09 2W52 0 JRNL AUTH J.VASUR,R.KAWAI,E.ANDERSSON,K.IGARASHI,M.SANDGREN, JRNL AUTH 2 M.SAMEJIMA,J.STAHLBERG JRNL TITL X-RAY CRYSTAL STRUCTURES OF PHANEROCHAETE CHRYSOSPORIUM JRNL TITL 2 LAMINARINASE 16A IN COMPLEX WITH PRODUCTS FROM LICHENIN AND JRNL TITL 3 LAMINARIN HYDROLYSIS JRNL REF FEBS J. V. 276 3858 2009 JRNL REFN ISSN 1742-464X JRNL PMID 19769746 JRNL DOI 10.1111/J.1742-4658.2009.07099.X REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : RESTRAINED REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.562 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 39468 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) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1981 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) : 1.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2560 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 144 REMARK 3 BIN FREE R VALUE : 0.2350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2247 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 162 REMARK 3 SOLVENT ATOMS : 422 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : 0.07100 REMARK 3 B33 (A**2) : -0.04100 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): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.075 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.181 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2536 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3493 ; 1.485 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 308 ; 6.875 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;36.985 ;24.530 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 305 ;10.681 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;16.937 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 411 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1931 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1266 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1772 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 337 ; 0.134 ; 0.200 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): 50 ; 0.172 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 50 ; 0.197 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1534 ; 0.796 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2427 ; 1.288 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1137 ; 1.904 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1063 ; 2.733 ; 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 BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2W52 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1290038061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.041 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39543 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 34.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.12000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.780 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45 MG/ML LAM16A CRYSTALIZED IN 20% PEG REMARK 280 3350, 0.2 M AMMONIUM NITRATE AND 10 MM NAOAC PH 5, THEN SOAKED REMARK 280 WITH 10 MM LIGAND FOR 90 MIN REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 19.02800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.43550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.34500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.43550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.02800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.34500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 2149 O HOH A 2307 2.17 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 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 55 NE - CZ - NH2 ANGL. DEV. = -3.5 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 THR A 81 -96.98 -119.40 REMARK 500 THR A 151 -81.40 -102.23 REMARK 500 ASP A 243 -149.45 -118.20 REMARK 500 CYS A 254 -134.77 58.17 REMARK 500 TRP A 257 -64.55 -98.35 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 A2046 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A2167 DISTANCE = 6.26 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 6-O-GLUCOSYL-LAMINARITRIOSE: GLCP-BETA-1-6-GLCP-BETA-1-3- REMARK 600 GLCP-BETA1-3-GLCP, A.K.A. G6G3G3G FROM LAMINARIA DIGITATA. REMARK 600 BETA-D-MANNOSE (BMA): PART OF N-GLYCOSYLATION REMARK 600 BETA GLUCOSE (BGC): ACCEPTOR-SITE G6G3G3 LIGAND COMPRISED REMARK 600 OF A401, A402, A403, A404. DONOR LIGAND A405, A406, A407, REMARK 600 NO BETA-1-6 GLUCOSE BRANCH DETECTED REMARK 600 N-ACETYL-D-GLUCOSAMINE (NAG): PART OF N-GLYCOSYLATION REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 650 THE FOLLOWING HELIX RECORDS HAVE BEEN GENERATED BY BETA-SPIDER, REMARK 650 VERSION ALPHA 2.0. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 THE FOLLOWING SHEET RECORDS HAVE BEEN GENERATED BY BETA-SPIDER, REMARK 700 VERSION ALPHA 2.0 WITH AN ENERGY THRESHOLD OF -8.2 KCAL/MOL REMARK 700 USING COULOMB ELECTROSTATICS USING 12-6 L-J VAN DER WAALS REMARK 700 USING BETA-SPIDER RULE SETS. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W39 RELATED DB: PDB REMARK 900 GLC(BETA-1-3)GLC DISACCHARIDE IN -1 AND -2 SITES OF LAMINARINASE REMARK 900 16A FROM PHANEROCHAETE CHRYSOSPORIUM REMARK 900 RELATED ID: 2CL2 RELATED DB: PDB REMARK 900 ENDO-1,3(4)-BETA-GLUCANASE FROM PHANEROCHAETE CHRYSOSPORIUM, SOLVED REMARK 900 USING NATIVE SULFUR SAD, EXHIBITING INTACT HEPTASACCHARIDE REMARK 900 GLYCOSYLATION DBREF 2W52 A 1 298 UNP Q874E3 Q874E3_PHACH 21 318 SEQRES 1 A 298 ALA THR TYR HIS LEU GLU ASP ASN TRP VAL GLY SER ALA SEQRES 2 A 298 PHE LEU SER THR PHE THR HIS GLU ALA ILE ALA ASP PRO SEQRES 3 A 298 THR HIS GLY ARG VAL ASN TYR VAL ASP GLN ALA THR ALA SEQRES 4 A 298 LEU ALA LYS ASN LEU THR TYR ALA SER GLY ASP THR LEU SEQRES 5 A 298 ILE LEU ARG ALA ASP HIS THR THR THR LEU SER PRO SER SEQRES 6 A 298 GLY PRO GLY ARG ASN SER VAL ARG ILE ARG SER ILE LYS SEQRES 7 A 298 THR TYR THR THR HIS VAL ALA VAL PHE ASP VAL ARG HIS SEQRES 8 A 298 MET PRO GLN GLY CYS GLY THR TRP PRO ALA ALA TRP GLU SEQRES 9 A 298 THR ASP GLU GLY ASP TRP PRO ASN GLY GLY GLU VAL ASP SEQRES 10 A 298 ILE ILE GLU GLY VAL ASN ASP GLN SER PRO ASN ALA MET SEQRES 11 A 298 THR LEU HIS THR GLY ALA ASN CYS ALA MET PRO ALA SER SEQRES 12 A 298 ARG THR MET THR GLY HIS ALA THR ASN ASN ASN CYS ASP SEQRES 13 A 298 VAL ASN THR ASP GLY ASN THR GLY CYS GLY VAL GLN ALA SEQRES 14 A 298 PRO THR ALA ASN SER TYR GLY PRO SER PHE ASN ALA ASN SEQRES 15 A 298 GLY GLY GLY TRP TYR ALA MET GLU ARG THR ASN SER PHE SEQRES 16 A 298 ILE LYS VAL TRP PHE PHE PRO ARG ASN ALA GLY ASN VAL SEQRES 17 A 298 PRO ASN ASP ILE ALA SER GLY PRO ALA THR ILE ASN THR SEQRES 18 A 298 ASP ASN TRP GLY THR PRO THR ALA PHE PHE PRO ASN THR SEQRES 19 A 298 ASN CYS ASP ILE GLY SER HIS PHE ASP ALA ASN ASN ILE SEQRES 20 A 298 ILE ILE ASN LEU THR PHE CYS GLY ASP TRP ALA GLY GLN SEQRES 21 A 298 ALA SER ILE PHE ASN GLY ALA GLY CYS PRO GLY SER CYS SEQRES 22 A 298 VAL ASP TYR VAL ASN ASN ASN PRO SER ALA PHE ALA ASN SEQRES 23 A 298 ALA TYR TRP ASP ILE ALA SER VAL ARG VAL TYR GLN MODRES 2W52 ASN A 43 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET MAN B 4 11 HET MAN B 5 11 HET MAN B 6 11 HET MAN B 7 11 HET BGC C 1 12 HET BGC C 2 11 HET BGC C 3 11 HET BGC C 4 11 HET BGC D 1 12 HET BGC D 2 11 HET BGC D 3 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM BGC BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 2 MAN 4(C6 H12 O6) FORMUL 3 BGC 7(C6 H12 O6) FORMUL 5 HOH *422(H2 O) HELIX 1 1 GLY A 11 THR A 17 1 7 HELIX 2 2 GLN A 36 ALA A 41 1 6 HELIX 3 3 GLU A 107 ASP A 109 1 3 HELIX 4 4 ASP A 160 ASN A 162 1 3 HELIX 5 5 ALA A 172 SER A 174 1 3 HELIX 6 6 GLY A 176 ALA A 181 1 6 HELIX 7 7 ASN A 210 SER A 214 1 5 HELIX 8 8 THR A 221 ASN A 223 1 3 HELIX 9 9 ILE A 238 HIS A 241 1 4 HELIX 10 10 GLY A 255 ALA A 258 1 4 HELIX 11 11 ALA A 261 GLY A 266 1 6 HELIX 12 12 CYS A 273 ASN A 279 1 7 HELIX 13 13 PRO A 281 PHE A 284 1 4 SHEET 1 A1 3 THR A 2 VAL A 10 0 SHEET 2 A1 3 ALA A 217 ASN A 220 -1 N ALA A 217 O LEU A 5 SHEET 3 A1 3 ALA A 287 GLN A 298 -1 N VAL A 296 O GLU A 6 SHEET 1 A2 2 PHE A 18 GLU A 21 0 SHEET 2 A2 2 PRO A 67 MET A 92 -1 N ARG A 73 O GLU A 21 SHEET 1 A3 3 GLY A 29 VAL A 34 0 SHEET 2 A3 3 PRO A 67 MET A 92 1 N ARG A 69 O ASN A 32 SHEET 3 A3 3 PHE A 242 CYS A 254 -1 N PHE A 253 O ARG A 30 SHEET 1 A4 2 LEU A 44 SER A 48 0 SHEET 2 A4 2 THR A 51 ASP A 57 -1 O ILE A 53 N TYR A 46 SHEET 1 A5 3 THR A 51 ASP A 57 0 SHEET 2 A5 3 PRO A 67 MET A 92 -1 N ASN A 70 O ASP A 57 SHEET 3 A5 3 ALA A 287 GLN A 298 -1 O TRP A 289 N LEU A 54 SHEET 1 A6 4 PRO A 67 MET A 92 0 SHEET 2 A6 4 GLY A 183 THR A 192 -1 N TYR A 187 O PHE A 87 SHEET 3 A6 4 PHE A 242 CYS A 254 -1 N ILE A 247 O SER A 76 SHEET 4 A6 4 ALA A 287 GLN A 298 -1 N ARG A 295 O VAL A 86 SHEET 1 A7 3 GLY A 97 ASP A 106 0 SHEET 2 A7 3 GLY A 113 ASN A 123 -1 O VAL A 116 N GLU A 104 SHEET 3 A7 3 PHE A 242 CYS A 254 -1 O ILE A 248 N TRP A 103 SHEET 1 A8 4 ASN A 128 MET A 140 0 SHEET 2 A8 4 MET A 146 VAL A 157 -1 N ASN A 153 O MET A 140 SHEET 3 A8 4 GLY A 164 ALA A 169 -1 O ALA A 169 N ASN A 128 SHEET 4 A8 4 ASN A 235 CYS A 236 -1 N ASN A 235 O ALA A 139 SHEET 1 A9 4 MET A 146 VAL A 157 0 SHEET 2 A9 4 GLY A 164 ALA A 169 -1 O GLN A 168 N HIS A 149 SHEET 3 A9 4 PRO A 227 ASN A 233 1 N THR A 228 O GLY A 148 SHEET 4 A9 4 ASN A 235 CYS A 236 -1 O ALA A 229 N VAL A 198 SHEET 1 AA 3 GLY A 183 THR A 192 0 SHEET 2 AA 3 SER A 194 ARG A 203 -1 O TRP A 199 N ALA A 188 SHEET 3 AA 3 PRO A 227 ASN A 233 -1 O PHE A 231 N ILE A 196 SSBOND 1 CYS A 96 CYS A 269 1555 1555 2.09 SSBOND 2 CYS A 138 CYS A 236 1555 1555 2.06 SSBOND 3 CYS A 155 CYS A 165 1555 1555 2.04 SSBOND 4 CYS A 254 CYS A 273 1555 1555 2.06 LINK ND2 ASN A 43 C1 NAG B 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.43 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.45 LINK O6 BMA B 3 C1 MAN B 4 1555 1555 1.44 LINK O6 MAN B 4 C1 MAN B 5 1555 1555 1.44 LINK O3 MAN B 4 C1 MAN B 7 1555 1555 1.44 LINK O2 MAN B 5 C1 MAN B 6 1555 1555 1.45 LINK O3 BGC C 1 C1 BGC C 2 1555 1555 1.35 LINK O3 BGC C 2 C1 BGC C 3 1555 1555 1.36 LINK O6 BGC C 3 C1 BGC C 4 1555 1555 1.34 LINK O3 BGC D 1 C1 BGC D 2 1555 1555 1.32 LINK O3 BGC D 2 C1 BGC D 3 1555 1555 1.34 CISPEP 1 TRP A 110 PRO A 111 0 1.62 CISPEP 2 SER A 126 PRO A 127 0 -0.06 CRYST1 38.056 46.690 152.871 90.00 90.00 90.00 P 21 21 21 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 0.026277 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021418 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006541 0.00000