HEADER OXIDOREDUCTASE 21-JAN-20 6XUV TITLE CRYSTALLOGRAPHIC STRUCTURE OF OLIGOSACCHARIDE DEHYDROGENASE FROM TITLE 2 PYCNOPORUS CINNABARINUS, LAMINARIBIOSE-BOUND FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: OLIGOSACCHARIDE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.5.9; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRAMETES CINNABARINA; SOURCE 3 ORGANISM_TAXID: 5643; SOURCE 4 EXPRESSION_SYSTEM: ASPERGILLUS NIGER; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 5061 KEYWDS GLUCOSE DEHYDROGENASE, PYCNOPORUS CINNABARINUS, LAMINARIBIOSE, KEYWDS 2 OXIDOREDUCTASE, OLIGOSACCHARIDE DEHYDROGENASE EXPDTA X-RAY DIFFRACTION AUTHOR G.CERUTTI,C.SAVINO,L.C.MONTEMIGLIO,B.VALLONE,G.SCIARA REVDAT 2 11-AUG-21 6XUV 1 JRNL REVDAT 1 03-FEB-21 6XUV 0 JRNL AUTH G.CERUTTI,E.GUGOLE,L.C.MONTEMIGLIO,A.TURBE-DOAN,D.CHENA, JRNL AUTH 2 D.NAVARRO,A.LOMASCOLO,F.PIUMI,C.EXERTIER,I.FREDA,B.VALLONE, JRNL AUTH 3 E.RECORD,C.SAVINO,G.SCIARA JRNL TITL CRYSTAL STRUCTURE AND FUNCTIONAL CHARACTERIZATION OF AN JRNL TITL 2 OLIGOSACCHARIDE DEHYDROGENASE FROM PYCNOPORUS CINNABARINUS JRNL TITL 3 PROVIDES INSIGHTS INTO FUNGAL BREAKDOWN OF LIGNOCELLULOSE. JRNL REF BIOTECHNOL BIOFUELS V. 14 161 2021 JRNL REFN ESSN 1754-6834 JRNL PMID 34294139 JRNL DOI 10.1186/S13068-021-02003-Y REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 97.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 56520 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3022 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4042 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.4320 REMARK 3 BIN FREE R VALUE SET COUNT : 216 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4399 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 242 REMARK 3 SOLVENT ATOMS : 302 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.74000 REMARK 3 B22 (A**2) : 3.90000 REMARK 3 B33 (A**2) : -1.16000 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): 0.122 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.152 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.205 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5570 ; 0.014 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4970 ; 0.003 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7766 ; 2.005 ; 1.692 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11733 ; 1.436 ; 1.620 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 797 ;16.816 ; 5.376 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 260 ;36.978 ;24.038 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 849 ;16.938 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.050 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 807 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7121 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1130 ; 0.002 ; 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): 2621 ; 1.569 ; 2.799 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2620 ; 1.568 ; 2.798 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3329 ; 2.199 ; 4.193 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3330 ; 2.200 ; 4.193 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2949 ; 1.976 ; 3.118 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2937 ; 1.895 ; 3.087 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4328 ; 2.829 ; 4.575 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6192 ; 5.393 ;33.854 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6108 ; 5.217 ;33.169 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 : 1 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 3 A 591 REMARK 3 ORIGIN FOR THE GROUP (A): -12.6317 4.1841 -21.8624 REMARK 3 T TENSOR REMARK 3 T11: 0.0056 T22: 0.1754 REMARK 3 T33: 0.0366 T12: -0.0071 REMARK 3 T13: 0.0085 T23: -0.0667 REMARK 3 L TENSOR REMARK 3 L11: 2.6521 L22: 0.8476 REMARK 3 L33: 0.9498 L12: -0.1263 REMARK 3 L13: -0.1622 L23: 0.2617 REMARK 3 S TENSOR REMARK 3 S11: -0.0094 S12: 0.6315 S13: -0.2468 REMARK 3 S21: 0.0047 S22: 0.0066 S23: -0.0341 REMARK 3 S31: -0.0031 S32: 0.0862 S33: 0.0028 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6XUV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-19 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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9685 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59350 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 97.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 294K 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 24.45700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 97.14300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.46450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 97.14300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.45700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.46450 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 TOTAL BURIED SURFACE AREA: 6170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G 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 465 SER A 2 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 OD1 ASP A 253 O HOH A 701 1.97 REMARK 500 O PRO A 258 O HOH A 702 2.08 REMARK 500 O HOH A 958 O HOH A 992 2.15 REMARK 500 O HOH A 949 O HOH A 969 2.15 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 PHE A 252 C PHE A 252 O 0.127 REMARK 500 GLY A 273 C GLY A 273 O 0.183 REMARK 500 ASP A 306 N ASP A 306 CA 0.157 REMARK 500 ILE A 313 N ILE A 313 CA 0.236 REMARK 500 TYR A 551 C TYR A 551 O 0.153 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 ILE A 313 CA - C - O ANGL. DEV. = 17.5 DEGREES REMARK 500 ILE A 313 CA - C - N ANGL. DEV. = -13.2 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 ALA A 78 -167.07 -106.76 REMARK 500 LYS A 88 77.78 -107.24 REMARK 500 LYS A 282 -72.36 -105.26 REMARK 500 LYS A 282 -72.03 -105.44 REMARK 500 ASP A 350 61.02 -151.56 REMARK 500 ASN A 501 -168.30 -161.41 REMARK 500 ASN A 501 -168.55 -161.41 REMARK 500 ALA A 527 37.80 73.94 REMARK 500 ASP A 552 15.56 80.83 REMARK 500 ASN A 555 26.67 -145.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 257 PRO A 258 -41.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 254 10.99 REMARK 500 GLY A 254 12.14 REMARK 500 LEU A 259 -12.67 REMARK 500 LEU A 259 -13.77 REMARK 500 GLY A 273 -10.52 REMARK 500 ASN A 503 13.06 REMARK 500 TYR A 551 15.43 REMARK 500 TYR A 551 15.48 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 A1001 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A1002 DISTANCE = 7.69 ANGSTROMS REMARK 630 REMARK 630 MOLECULE TYPE: OLIGOSACCHARIDE ANTIMICROBIAL REMARK 630 MOLECULE NAME: FLAVIN-ADENINE DINUCLEOTIDE 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 FAD A 601 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: NULL REMARK 630 DETAILS: OLIGOSACCHARIDE REMARK 630 MOLECULE TYPE: OLIGOSACCHARIDE ANTIMICROBIAL REMARK 630 MOLECULE NAME: BETA-D-GLUCOPYRANOSE 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 BGC F 1 REMARK 630 BGC F 2 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: 6XUT RELATED DB: PDB REMARK 900 6XUT CONTAINS THE SAME PROTEIN IN THE LIGAND-FREE FORM REMARK 900 RELATED ID: 6XUU RELATED DB: PDB REMARK 900 6XUU CONTAINS THE SAME PROTEIN IN THE GLUCOSE-BOUND FORM DBREF1 6XUV A 1 591 UNP A0A060SC37_PYCCI DBREF2 6XUV A A0A060SC37 30 620 SEQRES 1 A 591 ALA SER SER GLY ILE THR SER ASP PRO THR VAL VAL ASN SEQRES 2 A 591 GLY GLN THR TYR ASP TYR ILE VAL VAL GLY GLY GLY LEU SEQRES 3 A 591 THR GLY THR THR VAL ALA ALA ARG LEU ALA GLU ASN SER SEQRES 4 A 591 SER LEU GLN ILE LEU MET ILE GLU ALA GLY GLY ASP ASP SEQRES 5 A 591 ARG THR ASN PRO GLN ILE TYR ASP ILE TYR GLU TYR GLY SEQRES 6 A 591 ALA VAL PHE ASN GLY PRO LEU ASP TRP ALA TRP GLU ALA SEQRES 7 A 591 ASP GLN GLY LYS VAL ILE HIS GLY GLY LYS THR LEU GLY SEQRES 8 A 591 GLY SER SER SER ILE ASN GLY ALA ALA TRP THR ARG GLY SEQRES 9 A 591 LEU ASN ALA GLN TYR ASP SER TRP SER SER LEU LEU GLU SEQRES 10 A 591 PRO GLU GLU ALA SER VAL GLY TRP ASN TRP ASN ASN LEU SEQRES 11 A 591 PHE GLY TYR MET LYS LYS ALA GLU ALA PHE SER ALA PRO SEQRES 12 A 591 ASN ASP GLN GLN ARG ALA LYS GLY ALA ASP SER ILE ALA SEQRES 13 A 591 SER TYR HIS GLY THR THR GLY PRO VAL GLN ALA THR PHE SEQRES 14 A 591 PRO ASP GLU MET TYR GLY GLY PRO GLN MET PRO ALA PHE SEQRES 15 A 591 VAL ASN THR VAL VAL ASN VAL THR GLY MET PRO HIS TYR SEQRES 16 A 591 LYS ASP LEU ASN GLY GLY THR PRO ASN CYS VAL SER ILE SEQRES 17 A 591 THR PRO LEU SER ILE ASN TRP HIS ASP ASP ASP HIS ARG SEQRES 18 A 591 SER SER SER ILE GLU ALA TYR TYR THR PRO VAL GLU ASN SEQRES 19 A 591 ASN ARG GLN GLY TRP THR LEU LEU ILE ASP HIS MET ALA SEQRES 20 A 591 THR LYS VAL LEU PHE ASP GLY THR ASN ALA PRO LEU THR SEQRES 21 A 591 ALA VAL GLY ILE GLU PHE GLY ALA SER ASP ALA THR GLY SEQRES 22 A 591 ASN ARG TYR LYS ALA PHE ALA ARG LYS GLU VAL ILE LEU SEQRES 23 A 591 ALA ALA GLY ALA ILE GLN THR PRO ALA LEU LEU GLN LEU SEQRES 24 A 591 SER GLY ILE GLY ASP SER ASP VAL LEU GLY PRO LEU GLY SEQRES 25 A 591 ILE SER THR LEU SER ASP LEU LYS THR VAL GLY LYS ASN SEQRES 26 A 591 LEU GLN GLU GLN THR GLN ASN ALA ILE GLY ALA LYS GLY SEQRES 27 A 591 ASN GLY PHE ASP PRO ASP GLY HIS GLY PRO THR ASP ALA SEQRES 28 A 591 ILE ALA PHE PRO ASN ILE TYR GLN VAL PHE GLY SER GLN SEQRES 29 A 591 ALA THR SER ALA VAL GLN THR ILE GLN SER SER LEU SER SEQRES 30 A 591 ALA TRP ALA LYS THR GLN ALA ALA ALA GLY ALA LEU SER SEQRES 31 A 591 ALA ASP ALA LEU ASN THR ILE TYR GLN THR GLN ALA ASP SEQRES 32 A 591 LEU ILE ILE ASN HIS ASN ALA PRO VAL VAL GLU LEU PHE SEQRES 33 A 591 PHE ASP SER GLY PHE PRO ASP ASP VAL GLY ILE VAL MET SEQRES 34 A 591 TRP PRO LEU LEU PRO PHE SER ARG GLY ASN VAL THR ILE SEQRES 35 A 591 THR SER ASN ASN PRO PHE ALA LYS PRO SER VAL ASN VAL SEQRES 36 A 591 ASN TYR PHE SER VAL ASP PHE ASP LEU THR MET HIS ILE SEQRES 37 A 591 ALA GLY ALA ARG LEU SER ARG LYS LEU LEU GLY SER PRO SEQRES 38 A 591 PRO LEU SER SER LEU LEU VAL GLY GLU THR VAL PRO GLY SEQRES 39 A 591 PHE LYS THR VAL PRO ASN ASN GLY ASN GLY GLY THR ASP SEQRES 40 A 591 ALA ASP TRP LYS LYS TRP ILE LEU LYS PRO GLY ASN SER SEQRES 41 A 591 ALA GLY PHE ALA SER VAL ALA HIS PRO ILE GLY THR ALA SEQRES 42 A 591 ALA MET MET LYS ARG SER LEU GLY GLY VAL VAL ASP ALA SEQRES 43 A 591 GLN LEU LYS VAL TYR ASP THR THR ASN LEU ARG VAL VAL SEQRES 44 A 591 ASP ALA SER MET MET PRO LEU GLN ILE SER ALA HIS LEU SEQRES 45 A 591 SER SER THR LEU TYR GLY VAL ALA GLU LYS ALA ALA ASP SEQRES 46 A 591 LEU ILE LYS ALA ALA GLN HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET BGC D 1 12 HET BGC D 2 11 HET BGC E 1 12 HET BGC E 2 11 HET BGC G 1 12 HET BGC G 2 11 HET FAD A 601 53 HET GLC A 612 12 HET NAG A 615 28 HET SO4 A 616 5 HET SO4 A 617 5 HET SO4 A 618 5 HET BGC F 1 12 HET BGC F 2 22 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION 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 BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 NAG 5(C8 H15 N O6) FORMUL 4 BGC 8(C6 H12 O6) FORMUL 7 FAD C27 H33 N9 O15 P2 FORMUL 8 GLC C6 H12 O6 FORMUL 10 SO4 3(O4 S 2-) FORMUL 15 HOH *302(H2 O) HELIX 1 AA1 ASP A 8 ASN A 13 1 6 HELIX 2 AA2 GLY A 25 ALA A 36 1 12 HELIX 3 AA3 ASN A 55 ASP A 60 1 6 HELIX 4 AA4 ILE A 61 TYR A 64 5 4 HELIX 5 AA5 ASP A 79 GLY A 81 5 3 HELIX 6 AA6 GLY A 91 ILE A 96 5 6 HELIX 7 AA7 LEU A 105 LEU A 115 1 11 HELIX 8 AA8 LEU A 116 GLY A 124 5 9 HELIX 9 AA9 ASN A 126 ALA A 137 1 12 HELIX 10 AB1 ASN A 144 LYS A 150 1 7 HELIX 11 AB2 ILE A 155 HIS A 159 5 5 HELIX 12 AB3 PRO A 177 GLY A 191 1 15 HELIX 13 AB4 ASN A 214 ASP A 218 5 5 HELIX 14 AB5 SER A 223 TYR A 229 1 7 HELIX 15 AB6 THR A 230 GLU A 233 5 4 HELIX 16 AB7 ALA A 288 SER A 300 1 13 HELIX 17 AB8 ASP A 304 GLY A 309 1 6 HELIX 18 AB9 ASN A 356 GLY A 362 1 7 HELIX 19 AC1 GLN A 364 ALA A 388 1 25 HELIX 20 AC2 SER A 390 HIS A 408 1 19 HELIX 21 AC3 VAL A 460 GLY A 479 1 20 HELIX 22 AC4 PRO A 482 SER A 485 5 4 HELIX 23 AC5 PRO A 493 VAL A 498 1 6 HELIX 24 AC6 THR A 506 LEU A 515 1 10 HELIX 25 AC7 LYS A 537 GLY A 541 5 5 HELIX 26 AC8 ASP A 560 MET A 564 5 5 HELIX 27 AC9 LEU A 572 GLN A 591 1 20 SHEET 1 AA1 7 ILE A 5 THR A 6 0 SHEET 2 AA1 7 TRP A 239 ILE A 243 1 O LEU A 241 N THR A 6 SHEET 3 AA1 7 ILE A 43 GLU A 47 1 N ILE A 43 O THR A 240 SHEET 4 AA1 7 THR A 16 VAL A 22 1 N VAL A 21 O LEU A 44 SHEET 5 AA1 7 TYR A 276 LEU A 286 1 O PHE A 279 N TYR A 17 SHEET 6 AA1 7 ALA A 261 ALA A 268 -1 N ILE A 264 O ALA A 278 SHEET 7 AA1 7 HIS A 245 PHE A 252 -1 N LEU A 251 O GLY A 263 SHEET 1 AA2 6 ILE A 5 THR A 6 0 SHEET 2 AA2 6 TRP A 239 ILE A 243 1 O LEU A 241 N THR A 6 SHEET 3 AA2 6 ILE A 43 GLU A 47 1 N ILE A 43 O THR A 240 SHEET 4 AA2 6 THR A 16 VAL A 22 1 N VAL A 21 O LEU A 44 SHEET 5 AA2 6 TYR A 276 LEU A 286 1 O PHE A 279 N TYR A 17 SHEET 6 AA2 6 LEU A 556 VAL A 558 1 O ARG A 557 N LEU A 286 SHEET 1 AA3 2 TRP A 76 GLU A 77 0 SHEET 2 AA3 2 VAL A 83 ILE A 84 -1 O ILE A 84 N TRP A 76 SHEET 1 AA4 2 GLU A 138 PHE A 140 0 SHEET 2 AA4 2 VAL A 165 ALA A 167 1 O VAL A 165 N ALA A 139 SHEET 1 AA5 6 VAL A 206 ILE A 208 0 SHEET 2 AA5 6 ALA A 351 ALA A 353 -1 O ILE A 352 N SER A 207 SHEET 3 AA5 6 VAL A 413 SER A 419 -1 O LEU A 415 N ALA A 353 SHEET 4 AA5 6 VAL A 425 PRO A 431 -1 O VAL A 428 N PHE A 416 SHEET 5 AA5 6 THR A 330 GLY A 338 -1 N ALA A 336 O VAL A 425 SHEET 6 AA5 6 LEU A 487 VAL A 492 -1 O VAL A 492 N GLY A 335 SHEET 1 AA6 6 VAL A 206 ILE A 208 0 SHEET 2 AA6 6 ALA A 351 ALA A 353 -1 O ILE A 352 N SER A 207 SHEET 3 AA6 6 VAL A 413 SER A 419 -1 O LEU A 415 N ALA A 353 SHEET 4 AA6 6 VAL A 425 PRO A 431 -1 O VAL A 428 N PHE A 416 SHEET 5 AA6 6 THR A 330 GLY A 338 -1 N ALA A 336 O VAL A 425 SHEET 6 AA6 6 ALA A 524 SER A 525 -1 O ALA A 524 N GLN A 331 SHEET 1 AA7 2 ASN A 439 THR A 441 0 SHEET 2 AA7 2 SER A 452 ASN A 454 -1 O ASN A 454 N ASN A 439 LINK ND2 ASN A 38 C1 NAG B 1 1555 1555 1.45 LINK ND2AASN A 188 C1 ANAG A 615 1555 1555 1.43 LINK ND2BASN A 188 C1 BNAG A 615 1555 1555 1.49 LINK ND2 ASN A 439 C1 NAG C 1 1555 1555 1.43 LINK O3 BGLC A 612 C1 BBGC F 2 1555 1555 1.34 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.41 LINK O3 BGC D 1 C1 BGC D 2 1555 1555 1.39 LINK O3 BGC E 1 C1 BGC E 2 1555 1555 1.42 LINK O3 ABGC F 1 C1 ABGC F 2 1555 1555 1.52 LINK O3 BGC G 1 C1 BGC G 2 1555 1555 1.42 CISPEP 1 ALA A 257 PRO A 258 0 7.76 CISPEP 2 GLY A 347 PRO A 348 0 3.56 CISPEP 3 PHE A 421 PRO A 422 0 3.87 CISPEP 4 PHE A 421 PRO A 422 0 3.85 CISPEP 5 PRO A 481 PRO A 482 0 -4.47 CISPEP 6 VAL A 492 PRO A 493 0 1.84 CRYST1 48.914 60.929 194.286 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 0.020444 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005147 0.00000