HEADER HYDROLASE 12-AUG-09 3A5V TITLE CRYSTAL STRUCTURE OF ALPHA-GALACTOSIDASE I FROM MORTIERELLA VINACEA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UMBELOPSIS VINACEA; SOURCE 3 ORGANISM_TAXID: 44442; SOURCE 4 OTHER_DETAILS: SYNONYM: MORTIERELLA VINACEA KEYWDS BETA/ALPHA BARREL, N-GLYCOSYLATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.FUJIMOTO,S.KANEKO,H.KOBAYASHI REVDAT 7 01-NOV-23 3A5V 1 HETSYN REVDAT 6 29-JUL-20 3A5V 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 11-OCT-17 3A5V 1 REMARK REVDAT 4 13-JUL-11 3A5V 1 VERSN REVDAT 3 03-NOV-09 3A5V 1 JRNL REVDAT 2 20-OCT-09 3A5V 1 JRNL REVDAT 1 25-AUG-09 3A5V 0 JRNL AUTH Z.FUJIMOTO,S.KANEKO,W.-D.KIM,G.-G.PARK,M.MOMMA,H.KOBAYASHI JRNL TITL THE TETRAMER STRUCTURE OF THE GLYCOSIDE HYDROLASE FAMILY 27 JRNL TITL 2 ALPHA-GALACTOSIDASE I FROM UMBELOPSIS VINACEA JRNL REF BIOSCI.BIOTECHNOL.BIOCHEM. V. 73 2360 2009 JRNL REFN ISSN 0916-8451 JRNL PMID 19809163 JRNL DOI 10.1271/BBB.90604 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.FUJIMOTO,W.-D.KIM,S.KANEKO,G.-G.PARK,M.MOMMA,H.KOBAYASHI, REMARK 1 AUTH 2 H.MIZUNO REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC REMARK 1 TITL 2 STUDIES OF ALPHA-GALACTOSIDASE I FROM MORTIERELLA VINACEA REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 2289 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 14646097 REMARK 1 DOI 10.1107/S0907444903019681 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.SHIBUYA,H.KOBAYASHI,T.SATO,W.S.KIM,S.YOSHIDA,S.KANEKO, REMARK 1 AUTH 2 K.KASAMO,I.KUSAKABE REMARK 1 TITL PURIFICATION, CHARACTERIZATION, AND CDNA CLONING OF A NOVEL REMARK 1 TITL 2 ALPHA-GALACTOSIDASE FROM MORTIERELLA VINACEA REMARK 1 REF BIOSCI.BIOTECHNOL.BIOCHEM. V. 61 592 1997 REMARK 1 REFN ISSN 0916-8451 REMARK 1 PMID 9145516 REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45392 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) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2291 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) : 3103 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.1580 REMARK 3 BIN FREE R VALUE SET COUNT : 172 REMARK 3 BIN FREE R VALUE : 0.2040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3087 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 213 REMARK 3 SOLVENT ATOMS : 556 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.067 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3424 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4655 ; 1.291 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 396 ; 6.547 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;38.627 ;25.267 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 538 ;12.030 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;11.122 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 533 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2464 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1577 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2345 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 463 ; 0.128 ; 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): 49 ; 0.164 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 36 ; 0.180 ; 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): 2050 ; 0.660 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3194 ; 1.067 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1607 ; 1.826 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1457 ; 2.957 ; 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 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 3A5V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000028849. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0313 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 : DPS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45399 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.08400 REMARK 200 FOR THE DATA SET : 8.4000 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34300 REMARK 200 R SYM FOR SHELL (I) : 0.31400 REMARK 200 FOR SHELL : 2.400 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: PDB ENTRY 1UAS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M TRISODIUM CITRATE DIHYDRATE, 0.1M REMARK 280 TRIS BUFFER PH 8.5, 30% POLYETHYLENE GLYCOL 400, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 71.23500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 71.23500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 65.29000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 71.23500 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 71.23500 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 65.29000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 71.23500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 71.23500 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 65.29000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 71.23500 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 71.23500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 65.29000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 71.23500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 71.23500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 65.29000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 71.23500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 71.23500 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 65.29000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 71.23500 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 71.23500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 65.29000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 71.23500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 71.23500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 65.29000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 53800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 809 LIES ON A SPECIAL POSITION. 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 OG SER A 187 O HOH A 562 2.16 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 CYS A 21 CA - CB - SG ANGL. DEV. = 8.4 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 ASP A 51 -153.33 -86.37 REMARK 500 CYS A 53 18.22 85.07 REMARK 500 LYS A 63 -8.00 85.22 REMARK 500 ASN A 195 6.59 -150.27 REMARK 500 ASP A 240 176.16 81.10 REMARK 500 ASN A 374 -52.13 74.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PG A 851 REMARK 610 1PG A 852 REMARK 610 1PG A 853 REMARK 610 1PG A 854 REMARK 999 REMARK 999 SEQUENCE REMARK 999 HOWEVER, SINCE MANY CONFLICTS ROSE UP DURING REFINEMENT, REMARK 999 THE DEPOSITORS BUILT THIS STRUCTURE BASED ON THE ELECTRON REMARK 999 DENSITY INSTEAD. THEY THINK THE DNA SEQUENCE IN Q02402_9FUNG REMARK 999 COMES FROM ONE OF THE ISOZYME OF THE ANALYZED PROTEIN. DBREF 3A5V A 1 397 PDB 3A5V 3A5V 1 397 SEQRES 1 A 397 ALA ASN ASN GLY LEU ALA ILE THR PRO GLN MET GLY TRP SEQRES 2 A 397 ASN THR TRP ASN LYS TYR GLY CYS ASN VAL ASP GLU GLN SEQRES 3 A 397 LEU ILE LEU ASP ALA ALA LYS ALA ILE ALA SER SER GLY SEQRES 4 A 397 LEU LYS ASP LEU GLY TYR ASN TYR VAL ILE ILE ASP ASP SEQRES 5 A 397 CYS TRP GLN LYS ASN GLU ARG GLU SER SER LYS THR LEU SEQRES 6 A 397 LEU ALA ASP PRO THR LYS PHE PRO ARG GLY ILE LYS PRO SEQRES 7 A 397 LEU VAL ASP ASP ILE HIS ASN LEU GLY LEU LYS ALA GLY SEQRES 8 A 397 ILE TYR SER SER ALA GLY THR LEU THR CYS GLY GLY HIS SEQRES 9 A 397 ILE ALA SER LEU GLY TYR GLU ASP ILE ASP ALA LYS THR SEQRES 10 A 397 TRP ALA LYS TRP GLY ILE ASP TYR LEU LYS TYR ASP ASN SEQRES 11 A 397 CYS TYR ASN GLN GLY GLN SER GLY THR PRO LYS LEU SER SEQRES 12 A 397 TYR ASP ARG TYR LYS ALA MET GLY ASN ALA LEU ASN LYS SEQRES 13 A 397 THR GLY ARG PRO MET LEU TYR SER LEU CYS ASN TRP GLY SEQRES 14 A 397 GLU ASP GLY PRO TRP ASN PHE ALA SER THR ILE SER ASN SEQRES 15 A 397 SER TRP ARG ILE SER GLY ASP VAL TYR ASP ASN PHE ASN SEQRES 16 A 397 ARG PRO ASP PRO ALA CYS PRO CYS THR THR TYR ASP CYS SEQRES 17 A 397 VAL LEU ALA GLY PHE ARG CYS SER VAL MET ASN ILE ILE SEQRES 18 A 397 ASN LYS ALA VAL ALA VAL SER GLN LYS ALA ARG SER GLY SEQRES 19 A 397 GLY TRP ASN ASP LEU ASP MET LEU GLU VAL GLY ASN GLY SEQRES 20 A 397 GLY MET ASN GLN GLU GLU TYR ARG VAL HIS TYR THR ILE SEQRES 21 A 397 TRP ALA ALA LEU LYS SER PRO LEU ILE LEU GLY ASN ASP SEQRES 22 A 397 VAL THR ASN ILE THR ASN THR THR LYS GLU ILE ILE MET SEQRES 23 A 397 ASN LYS GLU VAL ILE ALA VAL ASN GLN ASP SER SER PHE SEQRES 24 A 397 SER PRO ALA ASN ARG ILE TRP VAL LYS GLY ASP GLN GLN SEQRES 25 A 397 LEU PHE SER GLY ASN LEU ALA ASN ASN THR GLN VAL VAL SEQRES 26 A 397 ILE LEU LEU ASN ALA GLY ASP SER ALA ALA LYS MET THR SEQRES 27 A 397 ALA THR TRP ASP ASP ILE TRP VAL TYR ASN LEU PRO ASN SEQRES 28 A 397 VAL ASP SER SER ARG SER ILE GLU VAL ARG ASP LEU TRP SEQRES 29 A 397 LYS GLN LYS SER LEU GLY ASN PHE SER ASN HIS ILE THR SEQRES 30 A 397 LEU ASP VAL PRO ALA HIS GLY VAL ARG LEU LEU LYS PHE SEQRES 31 A 397 MET ASP SER ALA THR SER SER MODRES 3A5V ASN A 155 ASN GLYCOSYLATION SITE MODRES 3A5V ASN A 276 ASN GLYCOSYLATION SITE MODRES 3A5V ASN A 371 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 NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET 1PG A 851 16 HET 1PG A 852 16 HET 1PG A 853 16 HET 1PG A 854 7 HET TRS A 841 8 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM 1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)- HETNAM 2 1PG ETHANOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 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 TRS TRIS BUFFER FORMUL 2 NAG 6(C8 H15 N O6) FORMUL 2 BMA 2(C6 H12 O6) FORMUL 2 MAN 4(C6 H12 O6) FORMUL 5 1PG 4(C11 H24 O6) FORMUL 9 TRS C4 H12 N O3 1+ FORMUL 10 HOH *556(H2 O) HELIX 1 1 THR A 15 GLY A 20 1 6 HELIX 2 2 CYS A 21 VAL A 23 5 3 HELIX 3 3 ASP A 24 SER A 38 1 15 HELIX 4 4 GLY A 39 GLY A 44 1 6 HELIX 5 5 GLY A 75 LEU A 86 1 12 HELIX 6 6 TYR A 110 GLY A 122 1 13 HELIX 7 7 THR A 139 THR A 157 1 19 HELIX 8 8 GLY A 172 ALA A 177 1 6 HELIX 9 9 SER A 216 SER A 228 1 13 HELIX 10 10 GLN A 229 ALA A 231 5 3 HELIX 11 11 ASN A 250 LEU A 264 1 15 HELIX 12 12 THR A 278 MET A 286 1 9 HELIX 13 13 ASN A 287 GLN A 295 1 9 HELIX 14 14 TRP A 341 TRP A 345 1 5 HELIX 15 15 VAL A 346 LEU A 349 5 4 SHEET 1 A 8 TRP A 236 ASP A 238 0 SHEET 2 A 8 SER A 183 ARG A 185 1 N TRP A 184 O ASP A 238 SHEET 3 A 8 LEU A 162 LEU A 165 1 N LEU A 165 O SER A 183 SHEET 4 A 8 TYR A 125 ASP A 129 1 N LEU A 126 O SER A 164 SHEET 5 A 8 LYS A 89 SER A 95 1 N SER A 94 O ASP A 129 SHEET 6 A 8 TYR A 47 ILE A 49 1 N VAL A 48 O LYS A 89 SHEET 7 A 8 MET A 11 ASN A 14 1 N TRP A 13 O ILE A 49 SHEET 8 A 8 LEU A 268 LEU A 270 1 O LEU A 270 N GLY A 12 SHEET 1 B 6 ASN A 303 LYS A 308 0 SHEET 2 B 6 GLN A 311 LEU A 318 -1 O GLN A 311 N LYS A 308 SHEET 3 B 6 THR A 322 ASN A 329 -1 O VAL A 324 N GLY A 316 SHEET 4 B 6 GLY A 384 PHE A 390 -1 O LEU A 388 N VAL A 325 SHEET 5 B 6 ILE A 358 ASP A 362 -1 N ARG A 361 O LYS A 389 SHEET 6 B 6 LYS A 367 PHE A 372 -1 O LEU A 369 N VAL A 360 SHEET 1 C 2 ALA A 335 THR A 340 0 SHEET 2 C 2 HIS A 375 VAL A 380 -1 O LEU A 378 N MET A 337 SSBOND 1 CYS A 21 CYS A 53 1555 1555 2.06 SSBOND 2 CYS A 101 CYS A 131 1555 1555 2.02 SSBOND 3 CYS A 201 CYS A 215 1555 1555 2.04 SSBOND 4 CYS A 203 CYS A 208 1555 1555 2.06 LINK ND2 ASN A 155 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN A 276 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 371 C1 NAG D 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.43 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.43 LINK O6 BMA B 3 C1 MAN B 4 1555 1555 1.45 LINK O3 BMA B 3 C1 MAN B 7 1555 1555 1.45 LINK O3 MAN B 4 C1 MAN B 5 1555 1555 1.45 LINK O6 MAN B 4 C1 MAN B 6 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.45 CISPEP 1 LEU A 349 PRO A 350 0 6.97 CRYST1 142.470 142.470 130.580 90.00 90.00 90.00 I 4 2 2 16 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 0.007019 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007658 0.00000