HEADER HYDROLASE 01-NOV-13 3WKX TITLE CRYSTAL STRUCTURE OF GH127 BETA-L-ARABINOFURANOSIDASE HYPBA1 FROM TITLE 2 BIFIDOBACTERIUM LONGUM ARABINOSE COMPLEX FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-REDUCING END BETA-L-ARABINOFURANOSIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-L-ARABINOFURANOSIDASE HYPBA1; COMPND 5 EC: 3.2.1.185; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BIFIDOBACTERIUM LONGUM; SOURCE 3 ORGANISM_TAXID: 565042; SOURCE 4 STRAIN: JCM 1217; SOURCE 5 GENE: HYPBA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C43 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-23B KEYWDS (ALPHA/ALPHA)6 BARREL, HYDROLASE, INTRACELLULAR EXPDTA X-RAY DIFFRACTION AUTHOR T.ITO,K.SAIKAWA,T.ARAKAWA,T.WAKAGI,K.FUJITA REVDAT 3 24-AUG-22 3WKX 1 JRNL HETSYN REVDAT 2 29-JUL-20 3WKX 1 REMARK SEQADV LINK SITE REVDAT 2 2 1 ATOM REVDAT 1 30-APR-14 3WKX 0 JRNL AUTH T.ITO,K.SAIKAWA,S.KIM,K.FUJITA,A.ISHIWATA,S.KAEOTHIP, JRNL AUTH 2 T.ARAKAWA,T.WAKAGI,G.T.BECKHAM,Y.ITO,S.FUSHINOBU JRNL TITL CRYSTAL STRUCTURE OF GLYCOSIDE HYDROLASE FAMILY 127 JRNL TITL 2 BETA-L-ARABINOFURANOSIDASE FROM BIFIDOBACTERIUM LONGUM. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 447 32 2014 JRNL REFN ESSN 1090-2104 JRNL PMID 24680821 JRNL DOI 10.1016/J.BBRC.2014.03.096 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.FUJITA,Y.TAKASHI,E.OBUCHI,K.KITAHARA,T.SUGANUMA REMARK 1 TITL CHARACTERIZATION OF A NOVEL BETA-L-ARABINOFURANOSIDASE IN REMARK 1 TITL 2 BIFIDOBACTERIUM LONGUM: FUNCTIONAL ELUCIDATION OF A DUF1680 REMARK 1 TITL 3 PROTEIN FAMILY MEMBER REMARK 1 REF J.BIOL.CHEM. V. 289 5240 2014 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 24385433 REMARK 1 DOI 10.1074/JBC.M113.528711 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 54418 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2892 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4063 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.3550 REMARK 3 BIN FREE R VALUE SET COUNT : 206 REMARK 3 BIN FREE R VALUE : 0.4240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5140 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.01000 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): 0.191 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.006 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5271 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4825 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7169 ; 1.846 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11079 ; 0.919 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 655 ; 6.812 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 266 ;38.990 ;24.135 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 819 ;16.726 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;18.935 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 773 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6112 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1248 ; 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): 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): 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 : BABINET MODEL WITH 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 3WKX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000096464. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59588 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 43.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.69300 REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7M SODIUM CITRATE, 0.1M MES, 10MM REMARK 280 DTT, 20% L-ARABINOSE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 168.44533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 84.22267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 84.22267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 168.44533 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 958 LIES ON A SPECIAL POSITION. 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 ASP A 246 REMARK 465 LEU A 247 REMARK 465 ALA A 660 REMARK 465 ALA A 661 REMARK 465 LEU A 662 REMARK 465 GLU A 663 REMARK 465 HIS A 664 REMARK 465 HIS A 665 REMARK 465 HIS A 666 REMARK 465 HIS A 667 REMARK 465 HIS A 668 REMARK 465 HIS A 669 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 175 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 380 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 402 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 402 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 424 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 424 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 489 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 580 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 611 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 637 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 45 97.48 -44.50 REMARK 500 LEU A 46 111.77 71.18 REMARK 500 LYS A 50 -144.83 -91.71 REMARK 500 ASP A 94 97.50 -170.35 REMARK 500 GLU A 185 137.99 -38.81 REMARK 500 HIS A 189 67.31 -111.38 REMARK 500 GLU A 196 -42.72 167.65 REMARK 500 PHE A 249 23.51 -63.73 REMARK 500 THR A 325 -90.31 -122.87 REMARK 500 ASN A 371 -74.75 -135.71 REMARK 500 ALA A 416 45.85 -94.05 REMARK 500 PHE A 448 67.82 -102.30 REMARK 500 SER A 482 31.71 -51.92 REMARK 500 ALA A 483 -130.21 16.92 REMARK 500 THR A 484 87.13 58.62 REMARK 500 ASP A 485 109.46 88.88 REMARK 500 SER A 501 85.68 -164.84 REMARK 500 ASN A 507 64.53 31.59 REMARK 500 PRO A 510 -33.31 -32.77 REMARK 500 ALA A 511 99.71 8.59 REMARK 500 ASP A 517 56.37 37.06 REMARK 500 PRO A 620 173.44 -58.09 REMARK 500 ALA A 625 48.05 -146.13 REMARK 500 PRO A 628 131.83 -37.38 REMARK 500 ARG A 647 -153.31 -130.78 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 ZN A 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 338 OE2 REMARK 620 2 CYS A 340 SG 109.0 REMARK 620 3 CYS A 417 SG 95.4 111.3 REMARK 620 4 CYS A 418 SG 113.2 106.5 120.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WKW RELATED DB: PDB DBREF 3WKX A 1 658 UNP E8MGH8 HYBA1_BIFL2 1 658 SEQADV 3WKX ALA A 659 UNP E8MGH8 EXPRESSION TAG SEQADV 3WKX ALA A 660 UNP E8MGH8 EXPRESSION TAG SEQADV 3WKX ALA A 661 UNP E8MGH8 EXPRESSION TAG SEQADV 3WKX LEU A 662 UNP E8MGH8 EXPRESSION TAG SEQADV 3WKX GLU A 663 UNP E8MGH8 EXPRESSION TAG SEQADV 3WKX HIS A 664 UNP E8MGH8 EXPRESSION TAG SEQADV 3WKX HIS A 665 UNP E8MGH8 EXPRESSION TAG SEQADV 3WKX HIS A 666 UNP E8MGH8 EXPRESSION TAG SEQADV 3WKX HIS A 667 UNP E8MGH8 EXPRESSION TAG SEQADV 3WKX HIS A 668 UNP E8MGH8 EXPRESSION TAG SEQADV 3WKX HIS A 669 UNP E8MGH8 EXPRESSION TAG SEQRES 1 A 669 MET ASN VAL THR ILE THR SER PRO PHE TRP LYS ARG ARG SEQRES 2 A 669 ARG ASP GLN ILE VAL GLU SER VAL ILE PRO TYR GLN TRP SEQRES 3 A 669 GLY VAL MET ASN ASP GLU ILE ASP THR THR VAL PRO ASP SEQRES 4 A 669 ASP PRO ALA GLY ASN GLN LEU ALA ASP SER LYS SER HIS SEQRES 5 A 669 ALA VAL ALA ASN LEU LYS VAL ALA ALA GLY GLU LEU ASP SEQRES 6 A 669 ASP GLU PHE HIS GLY MET VAL PHE GLN ASP SER ASP VAL SEQRES 7 A 669 TYR LYS TRP LEU GLU GLU ALA ALA TYR ALA LEU ALA TYR SEQRES 8 A 669 HIS PRO ASP PRO GLU LEU LYS ALA LEU CYS ASP ARG THR SEQRES 9 A 669 VAL ASP LEU ILE ALA ARG ALA GLN GLN SER ASP GLY TYR SEQRES 10 A 669 LEU ASP THR PRO TYR GLN ILE LYS SER GLY VAL TRP ALA SEQRES 11 A 669 ASP ARG PRO ARG PHE SER LEU ILE GLN GLN SER HIS GLU SEQRES 12 A 669 MET TYR VAL MET GLY HIS TYR ILE GLU ALA ALA VAL ALA SEQRES 13 A 669 TYR HIS GLN VAL THR GLY ASN GLU GLN ALA LEU GLU VAL SEQRES 14 A 669 ALA LYS LYS MET ALA ASP CYS LEU ASP ALA ASN PHE GLY SEQRES 15 A 669 PRO GLU GLU GLY LYS ILE HIS GLY ALA ASP GLY HIS PRO SEQRES 16 A 669 GLU ILE GLU LEU ALA LEU ALA LYS LEU TYR GLU GLU THR SEQRES 17 A 669 GLY GLU LYS ARG TYR LEU THR LEU SER GLN TYR LEU ILE SEQRES 18 A 669 ASP VAL ARG GLY GLN ASP PRO GLN PHE TYR ALA LYS GLN SEQRES 19 A 669 LEU LYS ALA MET ASN GLY ASP ASN ILE PHE HIS ASP LEU SEQRES 20 A 669 GLY PHE TYR LYS PRO THR TYR PHE GLN ALA ALA GLU PRO SEQRES 21 A 669 VAL ARG ASP GLN GLN THR ALA ASP GLY HIS ALA VAL ARG SEQRES 22 A 669 VAL GLY TYR LEU CYS THR GLY VAL ALA HIS VAL GLY ARG SEQRES 23 A 669 LEU LEU GLY ASP GLN GLY LEU ILE ASP THR ALA LYS ARG SEQRES 24 A 669 PHE TRP LYS ASN ILE VAL THR ARG ARG MET TYR VAL THR SEQRES 25 A 669 GLY ALA ILE GLY SER THR HIS VAL GLY GLU SER PHE THR SEQRES 26 A 669 TYR ASP TYR ASP LEU PRO ASN ASP THR MET TYR GLY GLU SEQRES 27 A 669 THR CYS ALA SER VAL ALA MET SER MET PHE ALA GLN GLN SEQRES 28 A 669 MET LEU ASP LEU GLU PRO LYS GLY GLU TYR ALA ASP VAL SEQRES 29 A 669 LEU GLU LYS GLU LEU PHE ASN GLY SER ILE ALA GLY ILE SEQRES 30 A 669 SER LEU ASP GLY LYS GLN TYR TYR TYR VAL ASN ALA LEU SEQRES 31 A 669 GLU THR THR PRO ASP GLY LEU ASP ASN PRO ASP ARG HIS SEQRES 32 A 669 HIS VAL LEU SER HIS ARG VAL ASP TRP PHE GLY CYS ALA SEQRES 33 A 669 CYS CYS PRO ALA ASN ILE ALA ARG LEU ILE ALA SER VAL SEQRES 34 A 669 ASP ARG TYR ILE TYR THR GLU ARG ASP GLY GLY LYS THR SEQRES 35 A 669 VAL LEU SER HIS GLN PHE ILE ALA ASN THR ALA GLU PHE SEQRES 36 A 669 ALA SER GLY LEU THR VAL GLU GLN ARG SER ASN PHE PRO SEQRES 37 A 669 TRP ASP GLY HIS VAL GLU TYR THR VAL SER LEU PRO ALA SEQRES 38 A 669 SER ALA THR ASP SER SER VAL ARG PHE GLY LEU ARG ILE SEQRES 39 A 669 PRO GLY TRP SER ARG GLY SER TYR THR LEU THR VAL ASN SEQRES 40 A 669 GLY LYS PRO ALA VAL GLY SER LEU GLU ASP GLY PHE VAL SEQRES 41 A 669 TYR LEU VAL VAL ASN ALA GLY ASP THR LEU GLU ILE ALA SEQRES 42 A 669 LEU GLU LEU ASP MET SER VAL LYS PHE VAL ARG ALA ASN SEQRES 43 A 669 SER ARG VAL ARG SER ASP ALA GLY GLN VAL ALA VAL MET SEQRES 44 A 669 ARG GLY PRO LEU VAL TYR CYS ALA GLU GLN VAL ASP ASN SEQRES 45 A 669 PRO GLY ASP LEU TRP ASN TYR ARG LEU ALA ASP GLY VAL SEQRES 46 A 669 THR GLY ALA ASP ALA ALA VAL ALA PHE GLN ALA ASP LEU SEQRES 47 A 669 LEU GLY GLY VAL ASP THR VAL ASP LEU PRO ALA VAL ARG SEQRES 48 A 669 GLU HIS ALA ASP GLU ASP ASP ALA PRO LEU TYR VAL ASP SEQRES 49 A 669 ALA ASP GLU PRO ARG ALA GLY GLU PRO ALA THR LEU ARG SEQRES 50 A 669 LEU VAL PRO TYR TYR SER TRP ALA ASN ARG GLU ILE GLY SEQRES 51 A 669 GLU MET ARG VAL PHE GLN ARG ARG ALA ALA ALA LEU GLU SEQRES 52 A 669 HIS HIS HIS HIS HIS HIS HET FUB A 701 10 HET ZN A 702 1 HETNAM FUB BETA-L-ARABINOFURANOSE HETNAM ZN ZINC ION HETSYN FUB BETA-L-ARABINOSE; L-ARABINOSE; ARABINOSE FORMUL 2 FUB C5 H10 O5 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *262(H2 O) HELIX 1 1 SER A 7 SER A 20 1 14 HELIX 2 2 SER A 20 ASN A 30 1 11 HELIX 3 3 HIS A 52 GLY A 62 1 11 HELIX 4 4 GLN A 74 HIS A 92 1 19 HELIX 5 5 ASP A 94 GLN A 112 1 19 HELIX 6 6 THR A 120 LYS A 125 1 6 HELIX 7 7 SER A 126 ARG A 132 5 7 HELIX 8 8 LEU A 137 HIS A 142 1 6 HELIX 9 9 HIS A 142 GLY A 162 1 21 HELIX 10 10 ASN A 163 PHE A 181 1 19 HELIX 11 11 GLU A 196 GLY A 209 1 14 HELIX 12 12 GLU A 210 ARG A 224 1 15 HELIX 13 13 GLN A 229 MET A 238 1 10 HELIX 14 14 PRO A 260 GLN A 264 5 5 HELIX 15 15 HIS A 270 GLY A 289 1 20 HELIX 16 16 ASP A 290 ARG A 308 1 19 HELIX 17 17 HIS A 319 SER A 323 5 5 HELIX 18 18 GLU A 338 GLU A 356 1 19 HELIX 19 19 LYS A 358 ASN A 371 1 14 HELIX 20 20 SER A 373 ILE A 377 5 5 HELIX 21 21 THR A 393 ASN A 399 5 7 HELIX 22 22 CYS A 418 SER A 428 1 11 HELIX 23 23 VAL A 429 TYR A 432 5 4 HELIX 24 24 ASP A 438 GLY A 440 5 3 HELIX 25 25 PRO A 495 ARG A 499 5 5 HELIX 26 26 VAL A 549 ALA A 553 5 5 HELIX 27 27 VAL A 570 ASN A 572 5 3 HELIX 28 28 ASP A 575 TRP A 577 5 3 HELIX 29 29 THR A 586 ALA A 590 5 5 HELIX 30 30 TYR A 642 TRP A 644 5 3 SHEET 1 A 6 ASN A 2 ILE A 5 0 SHEET 2 A 6 ASN A 451 GLU A 454 -1 O THR A 452 N THR A 4 SHEET 3 A 6 THR A 460 SER A 465 -1 O VAL A 461 N ALA A 453 SHEET 4 A 6 HIS A 472 SER A 478 -1 O GLU A 474 N ARG A 464 SHEET 5 A 6 THR A 529 GLU A 535 -1 O LEU A 534 N VAL A 473 SHEET 6 A 6 THR A 503 VAL A 506 -1 N THR A 503 O GLU A 535 SHEET 1 B 8 GLU A 391 THR A 392 0 SHEET 2 B 8 MET A 652 ARG A 653 -1 O MET A 652 N THR A 392 SHEET 3 B 8 LEU A 563 GLU A 568 -1 N ALA A 567 O ARG A 653 SHEET 4 B 8 GLN A 555 ARG A 560 -1 N VAL A 558 O TYR A 565 SHEET 5 B 8 GLN A 656 ARG A 657 -1 O GLN A 656 N VAL A 556 SHEET 6 B 8 TYR A 579 LEU A 581 1 N LEU A 581 O ARG A 657 SHEET 7 B 8 VAL A 602 GLU A 612 -1 O VAL A 610 N ARG A 580 SHEET 8 B 8 ALA A 591 GLN A 595 -1 N ALA A 593 O THR A 604 SHEET 1 C 6 ALA A 591 GLN A 595 0 SHEET 2 C 6 VAL A 602 GLU A 612 -1 O THR A 604 N ALA A 593 SHEET 3 C 6 GLY A 631 PRO A 640 -1 O LEU A 638 N VAL A 605 SHEET 4 C 6 LEU A 563 GLU A 568 -1 N CYS A 566 O VAL A 639 SHEET 5 C 6 GLN A 555 ARG A 560 -1 N VAL A 558 O TYR A 565 SHEET 6 C 6 VAL A 540 VAL A 543 -1 N LYS A 541 O MET A 559 SHEET 1 D 4 TYR A 434 ARG A 437 0 SHEET 2 D 4 THR A 442 SER A 445 -1 O LEU A 444 N THR A 435 SHEET 3 D 4 SER A 487 ARG A 493 1 O GLY A 491 N SER A 445 SHEET 4 D 4 PHE A 519 ASN A 525 -1 O VAL A 524 N VAL A 488 LINK OE2 GLU A 338 ZN ZN A 702 1555 1555 2.25 LINK SG CYS A 340 ZN ZN A 702 1555 1555 2.12 LINK SG CYS A 417 ZN ZN A 702 1555 1555 2.38 LINK SG CYS A 418 ZN ZN A 702 1555 1555 2.11 CISPEP 1 SER A 49 LYS A 50 0 -11.21 CISPEP 2 PHE A 467 PRO A 468 0 2.91 CRYST1 77.726 77.726 252.668 90.00 90.00 120.00 P 32 2 1 6 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 0.012866 0.007428 0.000000 0.00000 SCALE2 0.000000 0.014856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003958 0.00000