HEADER HYDROLASE 11-FEB-10 3LRL TITLE STRUCTURE OF ALFA-GALACTOSIDASE (MEL1) FROM SACCHAROMYCES CEREVISIAE TITLE 2 WITH MELIBIOSE CAVEAT 3LRL GLC D 1 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-D-GALACTOSIDE GALACTOHYDROLASE 1, MELIBIASE 1; COMPND 5 EC: 3.2.1.22; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: MEL1; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: YEPFLAG1 KEYWDS ALPHA-GALACTOSIDASE, TETRAMER, GH27, MELIBIOSE, GLYCOPROTEIN, KEYWDS 2 GLYCOSIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.FERNANDEZ-LEIRO,A.PEREIRA-RODRIGUEZ,M.E.CERDAN,M.BECERRA,J.SANZ- AUTHOR 2 APARICIO REVDAT 6 30-OCT-24 3LRL 1 REMARK REVDAT 5 06-SEP-23 3LRL 1 REMARK REVDAT 4 13-OCT-21 3LRL 1 SEQADV HETSYN REVDAT 3 29-JUL-20 3LRL 1 CAVEAT COMPND REMARK SEQADV REVDAT 3 2 1 HETNAM LINK SITE ATOM REVDAT 2 26-JAN-11 3LRL 1 JRNL REVDAT 1 30-JUN-10 3LRL 0 JRNL AUTH R.FERNANDEZ-LEIRO,A.PEREIRA-RODRIGUEZ,M.E.CERDAN,M.BECERRA, JRNL AUTH 2 J.SANZ-APARICIO JRNL TITL STRUCTURAL ANALYSIS OF SACCHAROMYCES CEREVISIAE JRNL TITL 2 ALPHA-GALACTOSIDASE AND ITS COMPLEXES WITH NATURAL JRNL TITL 3 SUBSTRATES REVEALS NEW INSIGHTS INTO SUBSTRATE SPECIFICITY JRNL TITL 4 OF GH27 GLYCOSIDASES. JRNL REF J.BIOL.CHEM. V. 285 28020 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20592022 JRNL DOI 10.1074/JBC.M110.144584 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 21747 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1174 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1558 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3518 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 136 REMARK 3 SOLVENT ATOMS : 415 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.73000 REMARK 3 B22 (A**2) : 0.73000 REMARK 3 B33 (A**2) : -1.47000 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): 0.420 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.268 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.184 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.832 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3759 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5108 ; 1.546 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 451 ; 6.121 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;38.826 ;24.778 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 560 ;15.453 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;19.220 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 552 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2870 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1860 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2555 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 363 ; 0.168 ; 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): 67 ; 0.173 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.238 ; 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): 2231 ; 0.608 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3561 ; 1.163 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1612 ; 1.931 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1546 ; 2.806 ; 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 3LRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057641. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-09 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 : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22940 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 111.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : 0.11100 REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : 0.43300 REMARK 200 FOR SHELL : 5.800 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 (%): 53.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DEGLYCOSYLATED SAMPLE. 19% PEG3350, REMARK 280 0.1 M BISTRIS, 0.2 M SCNK, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 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+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.36450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.36450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.36450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.36450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.36450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.36450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.36450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.36450 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 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: 22990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 62280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 77.0 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 100.72900 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 50.36450 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 50.36450 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 -50.36450 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 50.36450 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 808 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 MET A 1 REMARK 465 PHE A 2 REMARK 465 ALA A 3 REMARK 465 PHE A 4 REMARK 465 TYR A 5 REMARK 465 PHE A 6 REMARK 465 LEU A 7 REMARK 465 THR A 8 REMARK 465 ALA A 9 REMARK 465 CYS A 10 REMARK 465 ILE A 11 REMARK 465 SER A 12 REMARK 465 LEU A 13 REMARK 465 LYS A 14 REMARK 465 GLY A 15 REMARK 465 VAL A 16 REMARK 465 PHE A 17 REMARK 465 GLY A 18 REMARK 465 SER A 471 REMARK 465 ASP A 472 REMARK 465 TYR A 473 REMARK 465 LYS A 474 REMARK 465 ASP A 475 REMARK 465 ASP A 476 REMARK 465 ASP A 477 REMARK 465 ASP A 478 REMARK 465 LYS A 479 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 209 O2 GLA D 2 1.71 REMARK 500 NZ LYS A 147 O3 GLA D 2 2.04 REMARK 500 ND2 ASN A 270 O5 NAG B 1 2.05 REMARK 500 ND2 ASN A 370 O5 NAG A 6001 2.15 REMARK 500 C3 NAG B 1 C1 NAG B 2 2.18 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 TRP A 37 -72.30 -76.13 REMARK 500 ASN A 38 -13.64 -35.21 REMARK 500 ALA A 41 -140.69 40.58 REMARK 500 ASP A 72 -153.25 -107.59 REMARK 500 ASP A 73 171.02 -56.68 REMARK 500 ASP A 262 164.80 90.72 REMARK 500 ASN A 298 36.64 -140.58 REMARK 500 ILE A 419 -62.17 -94.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LRK RELATED DB: PDB REMARK 900 RELATED ID: 3LRM RELATED DB: PDB DBREF 3LRL A 1 471 UNP P04824 MEL1_YEAST 1 471 SEQADV 3LRL VAL A 181 UNP P04824 ILE 181 ENGINEERED MUTATION SEQADV 3LRL ASP A 472 UNP P04824 EXPRESSION TAG SEQADV 3LRL TYR A 473 UNP P04824 EXPRESSION TAG SEQADV 3LRL LYS A 474 UNP P04824 EXPRESSION TAG SEQADV 3LRL ASP A 475 UNP P04824 EXPRESSION TAG SEQADV 3LRL ASP A 476 UNP P04824 EXPRESSION TAG SEQADV 3LRL ASP A 477 UNP P04824 EXPRESSION TAG SEQADV 3LRL ASP A 478 UNP P04824 EXPRESSION TAG SEQADV 3LRL LYS A 479 UNP P04824 EXPRESSION TAG SEQRES 1 A 479 MET PHE ALA PHE TYR PHE LEU THR ALA CYS ILE SER LEU SEQRES 2 A 479 LYS GLY VAL PHE GLY VAL SER PRO SER TYR ASN GLY LEU SEQRES 3 A 479 GLY LEU THR PRO GLN MET GLY TRP ASP ASN TRP ASN THR SEQRES 4 A 479 PHE ALA CYS ASP VAL SER GLU GLN LEU LEU LEU ASP THR SEQRES 5 A 479 ALA ASP ARG ILE SER ASP LEU GLY LEU LYS ASP MET GLY SEQRES 6 A 479 TYR LYS TYR ILE ILE LEU ASP ASP CYS TRP SER SER GLY SEQRES 7 A 479 ARG ASP SER ASP GLY PHE LEU VAL ALA ASP GLU GLN LYS SEQRES 8 A 479 PHE PRO ASN GLY MET GLY HIS VAL ALA ASP HIS LEU HIS SEQRES 9 A 479 ASN ASN SER PHE LEU PHE GLY MET TYR SER SER ALA GLY SEQRES 10 A 479 GLU TYR THR CYS ALA GLY TYR PRO GLY SER LEU GLY ARG SEQRES 11 A 479 GLU GLU GLU ASP ALA GLN PHE PHE ALA ASN ASN ARG VAL SEQRES 12 A 479 ASP TYR LEU LYS TYR ASP ASN CYS TYR ASN LYS GLY GLN SEQRES 13 A 479 PHE GLY THR PRO GLU ILE SER TYR HIS ARG TYR LYS ALA SEQRES 14 A 479 MET SER ASP ALA LEU ASN LYS THR GLY ARG PRO VAL PHE SEQRES 15 A 479 TYR SER LEU CYS ASN TRP GLY GLN ASP LEU THR PHE TYR SEQRES 16 A 479 TRP GLY SER GLY ILE ALA ASN SER TRP ARG MET SER GLY SEQRES 17 A 479 ASP VAL THR ALA GLU PHE THR ARG PRO ASP SER ARG CYS SEQRES 18 A 479 PRO CYS ASP GLY ASP GLU TYR ASP CYS LYS TYR ALA GLY SEQRES 19 A 479 PHE HIS CYS SER ILE MET ASN ILE LEU ASN LYS ALA ALA SEQRES 20 A 479 PRO MET GLY GLN ASN ALA GLY VAL GLY GLY TRP ASN ASP SEQRES 21 A 479 LEU ASP ASN LEU GLU VAL GLY VAL GLY ASN LEU THR ASP SEQRES 22 A 479 ASP GLU GLU LYS ALA HIS PHE SER MET TRP ALA MET VAL SEQRES 23 A 479 LYS SER PRO LEU ILE ILE GLY ALA ASN VAL ASN ASN LEU SEQRES 24 A 479 LYS ALA SER SER TYR SER ILE TYR SER GLN ALA SER VAL SEQRES 25 A 479 ILE ALA ILE ASN GLN ASP SER ASN GLY ILE PRO ALA THR SEQRES 26 A 479 ARG VAL TRP ARG TYR TYR VAL SER ASP THR ASP GLU TYR SEQRES 27 A 479 GLY GLN GLY GLU ILE GLN MET TRP SER GLY PRO LEU ASP SEQRES 28 A 479 ASN GLY ASP GLN VAL VAL ALA LEU LEU ASN GLY GLY SER SEQRES 29 A 479 VAL SER ARG PRO MET ASN THR THR LEU GLU GLU ILE PHE SEQRES 30 A 479 PHE ASP SER ASN LEU GLY SER LYS LYS LEU THR SER THR SEQRES 31 A 479 TRP ASP ILE TYR ASP LEU TRP ALA ASN ARG VAL ASP ASN SEQRES 32 A 479 SER THR ALA SER ALA ILE LEU GLY ARG ASN LYS THR ALA SEQRES 33 A 479 THR GLY ILE LEU TYR ASN ALA THR GLU GLN SER TYR LYS SEQRES 34 A 479 ASP GLY LEU SER LYS ASN ASP THR ARG LEU PHE GLY GLN SEQRES 35 A 479 LYS ILE GLY SER LEU SER PRO ASN ALA ILE LEU ASN THR SEQRES 36 A 479 THR VAL PRO ALA HIS GLY ILE ALA PHE TYR ARG LEU ARG SEQRES 37 A 479 PRO SER SER ASP TYR LYS ASP ASP ASP ASP LYS MODRES 3LRL ASN A 105 ASN GLYCOSYLATION SITE MODRES 3LRL ASN A 270 ASN GLYCOSYLATION SITE MODRES 3LRL ASN A 422 ASN GLYCOSYLATION SITE MODRES 3LRL ASN A 175 ASN GLYCOSYLATION SITE MODRES 3LRL ASN A 403 ASN GLYCOSYLATION SITE MODRES 3LRL ASN A 370 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET GLC D 1 12 HET GLA D 2 11 HET NAG A1001 14 HET NAG A2001 14 HET NAG A4001 14 HET NAG A6001 14 HET NA A8001 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM NA SODIUM 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 GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE FORMUL 2 NAG 8(C8 H15 N O6) FORMUL 4 GLC C6 H12 O6 FORMUL 4 GLA C6 H12 O6 FORMUL 9 NA NA 1+ FORMUL 10 HOH *415(H2 O) HELIX 1 1 ASN A 36 ALA A 41 1 6 HELIX 2 2 SER A 45 LEU A 59 1 15 HELIX 3 3 LEU A 61 GLY A 65 5 5 HELIX 4 4 GLY A 95 ASN A 106 1 12 HELIX 5 5 ARG A 130 ASN A 141 1 12 HELIX 6 6 THR A 159 THR A 177 1 19 HELIX 7 7 LEU A 192 GLY A 197 1 6 HELIX 8 8 SER A 198 ILE A 200 5 3 HELIX 9 9 SER A 238 ALA A 247 1 10 HELIX 10 10 PRO A 248 ALA A 253 5 6 HELIX 11 11 THR A 272 VAL A 286 1 15 HELIX 12 12 ALA A 301 TYR A 307 1 7 HELIX 13 13 GLN A 309 GLN A 317 1 9 HELIX 14 14 THR A 372 PHE A 377 1 6 HELIX 15 15 SER A 384 SER A 389 1 6 HELIX 16 16 ASP A 402 GLY A 411 1 10 HELIX 17 17 SER A 427 LYS A 434 1 8 HELIX 18 18 ASP A 436 GLY A 441 1 6 SHEET 1 A 8 TRP A 258 ASP A 260 0 SHEET 2 A 8 SER A 203 ARG A 205 1 N TRP A 204 O ASP A 260 SHEET 3 A 8 PHE A 182 LEU A 185 1 N LEU A 185 O SER A 203 SHEET 4 A 8 TYR A 145 ASP A 149 1 N LEU A 146 O PHE A 182 SHEET 5 A 8 LEU A 109 SER A 115 1 N SER A 114 O ASP A 149 SHEET 6 A 8 TYR A 68 ILE A 70 1 N ILE A 69 O GLY A 111 SHEET 7 A 8 MET A 32 ASP A 35 1 N TRP A 34 O ILE A 70 SHEET 8 A 8 LEU A 290 ILE A 292 1 O ILE A 292 N GLY A 33 SHEET 1 B 2 SER A 76 ARG A 79 0 SHEET 2 B 2 LEU A 85 ALA A 87 -1 O VAL A 86 N SER A 77 SHEET 1 C 6 THR A 325 TYR A 331 0 SHEET 2 C 6 GLU A 342 PRO A 349 -1 O ILE A 343 N TYR A 330 SHEET 3 C 6 GLN A 355 ASN A 361 -1 O LEU A 360 N GLN A 344 SHEET 4 C 6 GLY A 461 PRO A 469 -1 O LEU A 467 N GLN A 355 SHEET 5 C 6 TRP A 391 ASP A 395 -1 N ASP A 392 O ARG A 468 SHEET 6 C 6 GLN A 442 LEU A 447 -1 O GLN A 442 N ASP A 395 SHEET 1 D 2 ARG A 367 THR A 371 0 SHEET 2 D 2 LEU A 453 VAL A 457 -1 O THR A 455 N MET A 369 SSBOND 1 CYS A 42 CYS A 74 1555 1555 2.03 SSBOND 2 CYS A 121 CYS A 151 1555 1555 2.05 SSBOND 3 CYS A 221 CYS A 237 1555 1555 2.05 SSBOND 4 CYS A 223 CYS A 230 1555 1555 2.03 LINK ND2 ASN A 105 C1 NAG A1001 1555 1555 1.44 LINK ND2 ASN A 175 C1 NAG A2001 1555 1555 1.45 LINK ND2 ASN A 270 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 370 C1 NAG A6001 1555 1555 1.44 LINK ND2 ASN A 403 C1 NAG A4001 1555 1555 1.46 LINK ND2 ASN A 422 C1 NAG C 1 1555 1555 1.45 LINK O3 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O6 GLC D 1 C1 GLA D 2 1555 1555 1.43 CRYST1 100.729 100.729 111.280 90.00 90.00 90.00 P 4 21 2 8 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 0.009928 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009928 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008986 0.00000