HEADER HYDROLASE 04-SEP-15 5DKY TITLE CRYSTAL STRUCTURE OF GLUCOSIDASE II ALPHA SUBUNIT (DNJ-BOUND FROM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA GLUCOSIDASE-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-977; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS SOURCE 3 144.50 / IMI 039719); SOURCE 4 ORGANISM_TAXID: 759272; SOURCE 5 STRAIN: DSM 1495 / CBS 144.50 / IMI 039719; SOURCE 6 GENE: CTHT_0064960; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCOLD-GST (MODIFIED) KEYWDS ENDOPLASMIC RETICULUM, GLYCOSIDE HYDROLASE, GLYCOSYLATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.SATOH,T.TOSHIMORI,G.YAN,T.YAMAGUCHI,K.KATO REVDAT 4 20-MAR-24 5DKY 1 REMARK REVDAT 3 19-FEB-20 5DKY 1 REMARK REVDAT 2 17-FEB-16 5DKY 1 JRNL REVDAT 1 27-JAN-16 5DKY 0 JRNL AUTH T.SATOH,T.TOSHIMORI,G.YAN,T.YAMAGUCHI,K.KATO JRNL TITL STRUCTURAL BASIS FOR TWO-STEP GLUCOSE TRIMMING BY JRNL TITL 2 GLUCOSIDASE II INVOLVED IN ER GLYCOPROTEIN QUALITY CONTROL. JRNL REF SCI REP V. 6 20575 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 26847925 JRNL DOI 10.1038/SREP20575 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 133918 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7092 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9757 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 516 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7485 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 819 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.16000 REMARK 3 B12 (A**2) : -0.03000 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): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.075 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.482 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7744 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7140 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10505 ; 1.427 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16483 ; 0.795 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1085 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8757 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1866 ; 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): 3720 ; 1.255 ; 1.851 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3719 ; 1.253 ; 1.851 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4649 ; 1.901 ; 2.772 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4650 ; 1.901 ; 2.773 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4022 ; 1.934 ; 2.058 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 4022 ; 1.934 ; 2.058 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5850 ; 3.059 ; 2.991 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7357 ; 4.551 ;19.762 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6958 ; 4.234 ;19.330 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 5DKY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213362. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 141836 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 51.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M SODIUM CITRATE TRIBASIC, 0.1 M REMARK 280 TRIS-HCL (PH 7.0), 2.5 MM DNJ, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 94.76150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.71058 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 52.59467 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 94.76150 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 54.71058 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 52.59467 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 94.76150 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 54.71058 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 52.59467 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 94.76150 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 54.71058 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 52.59467 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 94.76150 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 54.71058 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 52.59467 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 94.76150 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 54.71058 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 52.59467 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 109.42116 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 105.18933 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 109.42116 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 105.18933 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 109.42116 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 105.18933 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 109.42116 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 105.18933 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 109.42116 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 105.18933 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 109.42116 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 105.18933 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 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 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 A1771 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 GLY A 27 REMARK 465 SER A 28 REMARK 465 PRO A 215 REMARK 465 GLU A 216 REMARK 465 PRO A 217 REMARK 465 GLU A 218 REMARK 465 LYS A 219 REMARK 465 LYS A 220 REMARK 465 GLU A 221 REMARK 465 GLY A 222 REMARK 465 GLU A 223 REMARK 465 GLN A 224 REMARK 465 GLN A 225 REMARK 465 PRO A 226 REMARK 465 ASP A 227 REMARK 465 LYS A 228 REMARK 465 LYS A 229 REMARK 465 GLU A 230 REMARK 465 GLU A 231 REMARK 465 ALA A 232 REMARK 465 PRO A 233 REMARK 465 ARG A 234 REMARK 465 GLU A 235 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 SG CYS A 45 NE1 TRP A 342 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CZ PHE A 30 CZ PHE A 30 12555 1.77 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 PRO A 64 45.93 -82.54 REMARK 500 GLU A 121 53.08 -92.99 REMARK 500 ASP A 159 -156.43 -137.48 REMARK 500 TRP A 241 -136.54 -115.33 REMARK 500 GLU A 257 23.07 -157.35 REMARK 500 ILE A 274 47.48 38.34 REMARK 500 TYR A 300 86.47 -153.77 REMARK 500 LEU A 315 -143.23 -117.12 REMARK 500 CYS A 516 -150.24 -148.05 REMARK 500 ARG A 699 36.99 -145.33 REMARK 500 ASP A 736 21.78 -153.53 REMARK 500 ALA A 803 -16.45 79.54 REMARK 500 ALA A 812 62.67 -154.44 REMARK 500 ASP A 867 -44.09 -139.73 REMARK 500 LYS A 953 -123.51 54.53 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 ASN A 416 TYR A 417 149.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NOJ A 1000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DKX RELATED DB: PDB REMARK 900 RELATED ID: 5DKZ RELATED DB: PDB REMARK 900 RELATED ID: 5DL0 RELATED DB: PDB DBREF 5DKY A 31 977 UNP G0SG42 G0SG42_CHATD 31 977 SEQADV 5DKY GLY A 27 UNP G0SG42 EXPRESSION TAG SEQADV 5DKY SER A 28 UNP G0SG42 EXPRESSION TAG SEQADV 5DKY GLU A 29 UNP G0SG42 EXPRESSION TAG SEQADV 5DKY PHE A 30 UNP G0SG42 EXPRESSION TAG SEQRES 1 A 951 GLY SER GLU PHE VAL LYS GLU HIS ASP TRP LYS LYS CYS SEQRES 2 A 951 ASP GLN SER GLY PHE CYS ARG ARG ASN ARG ALA TYR ALA SEQRES 3 A 951 ASP HIS ALA LEU SER ALA ILE SER TRP GLU SER PRO TYR SEQRES 4 A 951 LYS ILE ALA PRO GLU THR GLY SER PHE LYS ASP GLY GLN SEQRES 5 A 951 TYR GLN ALA ILE ILE LEU LYS THR ILE ASN ASP HIS GLY SEQRES 6 A 951 GLU THR VAL ARG LEU PRO LEU THR VAL SER PHE LEU GLU SEQRES 7 A 951 SER GLY THR ALA ARG VAL THR ILE ASP GLU GLU LYS ARG SEQRES 8 A 951 GLN LYS GLY GLU ILE GLU LEU ARG HIS ASP SER LYS ALA SEQRES 9 A 951 ARG LYS GLU ARG TYR ASN GLU ALA GLU GLN TRP VAL ILE SEQRES 10 A 951 VAL GLY GLY MET THR LEU ASP LYS GLY ALA LYS VAL ASP SEQRES 11 A 951 TYR GLU ASP LYS THR GLN MET THR VAL LYS TYR GLY PRO SEQRES 12 A 951 SER SER LYS PHE GLU ALA THR ILE LYS PHE ALA PRO PHE SEQRES 13 A 951 SER ILE ASP PHE LYS ARG ASP GLY ALA SER HIS ILE LYS SEQRES 14 A 951 PHE ASN ASP GLN GLY LEU LEU ASN ILE GLU HIS TRP ARG SEQRES 15 A 951 PRO LYS ILE ASP PRO PRO PRO GLU PRO GLU LYS LYS GLU SEQRES 16 A 951 GLY GLU GLN GLN PRO ASP LYS LYS GLU GLU ALA PRO ARG SEQRES 17 A 951 GLU ASP ASP SER THR TRP TRP GLU GLU SER PHE GLY GLY SEQRES 18 A 951 ASN THR ASP SER LYS PRO ARG GLY PRO GLU SER VAL GLY SEQRES 19 A 951 LEU ASP ILE SER PHE VAL GLY TYR GLU HIS VAL PHE GLY SEQRES 20 A 951 ILE PRO SER HIS ALA SER PRO LEU SER LEU LYS GLN THR SEQRES 21 A 951 ARG GLY GLY GLU GLY ASN TYR ASN GLU PRO TYR ARG MET SEQRES 22 A 951 TYR ASN ALA ASP VAL PHE GLU TYR ILE LEU ASP SER PRO SEQRES 23 A 951 MET THR LEU TYR GLY SER ILE PRO PHE MET GLN ALA HIS SEQRES 24 A 951 ARG LYS ASP SER SER VAL GLY ILE PHE TRP LEU ASN ALA SEQRES 25 A 951 ALA GLU THR TRP VAL ASP ILE THR LYS GLY LYS ASP SER SEQRES 26 A 951 LYS ASN PRO LEU ALA LEU GLY VAL LYS SER LYS ILE THR SEQRES 27 A 951 THR ARG THR HIS TRP PHE SER GLU SER GLY LEU LEU ASP SEQRES 28 A 951 VAL PHE VAL PHE LEU GLY PRO THR PRO LYS ASP ILE ILE SEQRES 29 A 951 SER LYS TYR ALA GLU LEU THR GLY THR THR ALA MET PRO SEQRES 30 A 951 GLN GLU PHE SER LEU GLY TYR HIS GLN CYS ARG TRP ASN SEQRES 31 A 951 TYR VAL SER ASP GLU ASP VAL LYS ASP VAL ASP ARG LYS SEQRES 32 A 951 MET ASP LYS PHE ASN MET PRO TYR ASP VAL ILE TRP LEU SEQRES 33 A 951 ASP ILE GLU TYR THR ASP GLU LYS LYS TYR PHE THR TRP SEQRES 34 A 951 ASP LYS HIS SER PHE LYS ASP PRO ILE GLY MET GLY LYS SEQRES 35 A 951 GLN LEU GLU ALA HIS GLY ARG LYS LEU VAL THR ILE ILE SEQRES 36 A 951 ASP PRO HIS ILE LYS ASN THR ASN ASN TYR PRO VAL VAL SEQRES 37 A 951 ASP GLU LEU LYS SER LYS ASP LEU ALA VAL LYS THR LYS SEQRES 38 A 951 ASP GLY SER ILE PHE GLU GLY TRP CYS TRP PRO GLY SER SEQRES 39 A 951 SER HIS TRP ILE ASP ALA PHE ASN PRO ALA ALA ARG GLU SEQRES 40 A 951 TRP TRP LYS GLY LEU PHE LYS TYR ASP LYS PHE LYS GLY SEQRES 41 A 951 THR MET GLU ASN THR PHE ILE TRP ASN ASP MET ASN GLU SEQRES 42 A 951 PRO SER VAL PHE ASN GLY PRO GLU VAL THR MET PRO LYS SEQRES 43 A 951 ASP ASN LEU HIS HIS GLY ASN TRP GLU HIS ARG ASP VAL SEQRES 44 A 951 HIS ASN LEU ASN GLY MET THR PHE GLN ASN ALA THR TYR SEQRES 45 A 951 HIS ALA LEU LEU SER ARG LYS PRO GLY GLU HIS ARG ARG SEQRES 46 A 951 PRO PHE VAL LEU THR ARG ALA PHE PHE ALA GLY SER GLN SEQRES 47 A 951 ARG LEU GLY ALA MET TRP THR GLY ASP ASN THR ALA ASP SEQRES 48 A 951 TRP GLY TYR LEU LYS ALA SER ILE PRO MET VAL LEU SER SEQRES 49 A 951 GLN GLY ILE ALA GLY PHE PRO PHE ALA GLY ALA ASP VAL SEQRES 50 A 951 GLY GLY PHE PHE GLY ASN PRO ASP LYS ASP LEU LEU THR SEQRES 51 A 951 ARG TRP TYR GLN THR GLY ILE PHE TYR PRO PHE PHE ARG SEQRES 52 A 951 ALA HIS ALA HIS ILE ASP ALA ARG ARG ARG GLU PRO TYR SEQRES 53 A 951 LEU THR GLY GLU PRO TYR ASN THR ILE ILE ALA ALA ALA SEQRES 54 A 951 LEU ARG LEU ARG TYR SER LEU LEU PRO SER TRP TYR THR SEQRES 55 A 951 ALA PHE ARG HIS ALA HIS LEU ASP GLY THR PRO ILE ILE SEQRES 56 A 951 LYS PRO MET PHE TYR THR HIS PRO SER GLU GLU ALA GLY SEQRES 57 A 951 LEU PRO ILE ASP ASP GLN PHE PHE ILE GLY ASN THR GLY SEQRES 58 A 951 LEU LEU ALA LYS PRO VAL THR ASP LYS ASP ARG THR SER SEQRES 59 A 951 VAL ASP ILE TRP ILE PRO ASP SER GLU VAL TYR TYR ASP SEQRES 60 A 951 TYR PHE THR TYR ASP ILE ILE SER ALA ALA LYS SER LYS SEQRES 61 A 951 THR ALA THR LEU ASP ALA PRO LEU GLU LYS ILE PRO LEU SEQRES 62 A 951 LEU MET ARG GLY GLY HIS VAL PHE ALA ARG ARG ASP ILE SEQRES 63 A 951 PRO ARG ARG SER SER ALA LEU MET LYS TRP ASP PRO TYR SEQRES 64 A 951 THR LEU VAL VAL VAL LEU GLY ASN ASP ARG LYS ALA GLU SEQRES 65 A 951 GLY ASP LEU TYR VAL ASP ASP GLY ASP SER PHE ASP TYR SEQRES 66 A 951 GLU LYS GLY GLN TYR ILE HIS ARG ARG PHE ILE PHE ASP SEQRES 67 A 951 ALA ASN THR LEU THR SER ALA ASP TYR GLU GLY ARG ASP SEQRES 68 A 951 ASP ALA SER ILE LYS GLU GLY GLU TRP LEU LYS LYS MET SEQRES 69 A 951 ARG THR VAL ASN VAL GLU LYS ILE ILE VAL VAL GLY ALA SEQRES 70 A 951 PRO ALA ALA TRP LYS GLY LYS LYS THR VAL THR VAL GLU SEQRES 71 A 951 SER GLU GLY LYS THR TRP ALA ALA ALA ILE GLU TYR ASN SEQRES 72 A 951 PRO ALA GLU LYS SER ARG ALA ALA PHE ALA VAL VAL LYS SEQRES 73 A 951 LYS VAL GLY VAL ARG VAL GLY ALA ASP PHE LYS ILE VAL SEQRES 74 A 951 PHE GLY HET NOJ A1000 11 HETNAM NOJ 1-DEOXYNOJIRIMYCIN HETSYN NOJ MORANOLINE FORMUL 2 NOJ C6 H13 N O4 FORMUL 3 HOH *819(H2 O) HELIX 1 AA1 LYS A 38 GLN A 41 5 4 HELIX 2 AA2 SER A 42 ALA A 58 1 17 HELIX 3 AA3 PRO A 69 GLY A 72 5 4 HELIX 4 AA4 GLU A 114 LYS A 119 1 6 HELIX 5 AA5 LEU A 124 SER A 128 5 5 HELIX 6 AA6 GLU A 137 ILE A 143 1 7 HELIX 7 AA7 GLY A 168 LYS A 172 5 5 HELIX 8 AA8 THR A 385 GLY A 398 1 14 HELIX 9 AA9 GLN A 404 GLY A 409 5 6 HELIX 10 AB1 SER A 419 PHE A 433 1 15 HELIX 11 AB2 ASP A 443 THR A 447 5 5 HELIX 12 AB3 ASP A 462 ALA A 472 1 11 HELIX 13 AB4 TYR A 491 LYS A 500 1 10 HELIX 14 AB5 ASN A 528 PHE A 539 1 12 HELIX 15 AB6 GLY A 565 THR A 569 5 5 HELIX 16 AB7 HIS A 582 HIS A 586 1 5 HELIX 17 AB8 LEU A 588 LEU A 602 1 15 HELIX 18 AB9 GLY A 622 LEU A 626 5 5 HELIX 19 AC1 ASP A 637 ALA A 654 1 18 HELIX 20 AC2 ASP A 671 ILE A 683 1 13 HELIX 21 AC3 GLU A 700 THR A 704 5 5 HELIX 22 AC4 PRO A 707 LEU A 722 1 16 HELIX 23 AC5 LEU A 722 GLY A 737 1 16 HELIX 24 AC6 PRO A 743 HIS A 748 1 6 HELIX 25 AC7 GLU A 751 LEU A 755 5 5 HELIX 26 AC8 SER A 837 LYS A 841 5 5 HELIX 27 AC9 PHE A 869 GLY A 874 5 6 HELIX 28 AD1 ASP A 897 ILE A 901 5 5 HELIX 29 AD2 GLY A 904 ARG A 911 1 8 HELIX 30 AD3 PRO A 924 LYS A 928 5 5 SHEET 1 AA1 3 TYR A 65 ILE A 67 0 SHEET 2 AA1 3 GLN A 78 THR A 86 -1 O LEU A 84 N LYS A 66 SHEET 3 AA1 3 SER A 73 LYS A 75 -1 N SER A 73 O GLN A 80 SHEET 1 AA2 8 TYR A 65 ILE A 67 0 SHEET 2 AA2 8 GLN A 78 THR A 86 -1 O LEU A 84 N LYS A 66 SHEET 3 AA2 8 THR A 93 PHE A 102 -1 O LEU A 98 N ALA A 81 SHEET 4 AA2 8 ALA A 108 ILE A 112 -1 O ARG A 109 N SER A 101 SHEET 5 AA2 8 LEU A 376 PHE A 381 -1 O VAL A 378 N VAL A 110 SHEET 6 AA2 8 SER A 329 TRP A 335 -1 N GLY A 332 O PHE A 381 SHEET 7 AA2 8 PHE A 321 ARG A 326 -1 N ALA A 324 O VAL A 331 SHEET 8 AA2 8 VAL A 271 GLY A 273 -1 N PHE A 272 O GLN A 323 SHEET 1 AA3 7 LYS A 154 GLU A 158 0 SHEET 2 AA3 7 GLN A 162 TYR A 167 -1 O THR A 164 N TYR A 157 SHEET 3 AA3 7 PHE A 173 LYS A 178 -1 O ILE A 177 N MET A 163 SHEET 4 AA3 7 SER A 183 ARG A 188 -1 O LYS A 187 N GLU A 174 SHEET 5 AA3 7 ALA A 191 PHE A 196 -1 O ILE A 194 N PHE A 186 SHEET 6 AA3 7 VAL A 259 PHE A 265 -1 O SER A 264 N LYS A 195 SHEET 7 AA3 7 ASN A 203 ILE A 204 -1 N ASN A 203 O GLY A 260 SHEET 1 AA4 9 LYS A 154 GLU A 158 0 SHEET 2 AA4 9 GLN A 162 TYR A 167 -1 O THR A 164 N TYR A 157 SHEET 3 AA4 9 PHE A 173 LYS A 178 -1 O ILE A 177 N MET A 163 SHEET 4 AA4 9 SER A 183 ARG A 188 -1 O LYS A 187 N GLU A 174 SHEET 5 AA4 9 ALA A 191 PHE A 196 -1 O ILE A 194 N PHE A 186 SHEET 6 AA4 9 VAL A 259 PHE A 265 -1 O SER A 264 N LYS A 195 SHEET 7 AA4 9 ILE A 363 SER A 371 -1 O THR A 365 N PHE A 265 SHEET 8 AA4 9 THR A 341 LYS A 349 -1 N GLY A 348 O THR A 364 SHEET 9 AA4 9 TYR A 297 MET A 299 -1 N MET A 299 O THR A 341 SHEET 1 AA5 2 GLU A 243 PHE A 245 0 SHEET 2 AA5 2 ASN A 248 ASP A 250 -1 O ASP A 250 N GLU A 243 SHEET 1 AA6 8 ALA A 659 GLY A 660 0 SHEET 2 AA6 8 ALA A 628 TRP A 630 1 N MET A 629 O GLY A 660 SHEET 3 AA6 8 VAL A 614 THR A 616 1 N THR A 616 O ALA A 628 SHEET 4 AA6 8 THR A 551 ASN A 555 1 N ASN A 555 O LEU A 615 SHEET 5 AA6 8 LYS A 476 ILE A 480 1 N LEU A 477 O PHE A 552 SHEET 6 AA6 8 VAL A 439 LEU A 442 1 N LEU A 442 O VAL A 478 SHEET 7 AA6 8 HIS A 411 GLN A 412 1 N GLN A 412 O VAL A 439 SHEET 8 AA6 8 ARG A 689 ALA A 690 1 O ALA A 690 N HIS A 411 SHEET 1 AA7 3 HIS A 484 LYS A 486 0 SHEET 2 AA7 3 GLY A 519 TRP A 523 -1 O HIS A 522 N ILE A 485 SHEET 3 AA7 3 GLY A 514 CYS A 516 -1 N GLY A 514 O SER A 521 SHEET 1 AA8 2 LEU A 575 HIS A 576 0 SHEET 2 AA8 2 TRP A 580 GLU A 581 -1 O TRP A 580 N HIS A 576 SHEET 1 AA9 6 ILE A 741 LYS A 742 0 SHEET 2 AA9 6 PHE A 761 ILE A 763 -1 O PHE A 762 N LYS A 742 SHEET 3 AA9 6 LEU A 768 ALA A 770 -1 O ALA A 770 N PHE A 761 SHEET 4 AA9 6 LEU A 819 ARG A 822 -1 O LEU A 820 N LEU A 769 SHEET 5 AA9 6 TYR A 791 ASP A 793 -1 N TYR A 792 O MET A 821 SHEET 6 AA9 6 ILE A 799 SER A 801 -1 O ILE A 800 N TYR A 791 SHEET 1 AB1 2 SER A 780 ILE A 785 0 SHEET 2 AB1 2 LYS A 806 ASP A 811 -1 O LYS A 806 N ILE A 785 SHEET 1 AB212 VAL A 966 ARG A 967 0 SHEET 2 AB212 ASN A 914 VAL A 921 -1 N VAL A 915 O VAL A 966 SHEET 3 AB212 PHE A 958 VAL A 961 -1 O ALA A 959 N VAL A 920 SHEET 4 AB212 LYS A 940 ASN A 949 -1 N ASN A 949 O PHE A 958 SHEET 5 AB212 THR A 932 SER A 937 -1 N VAL A 935 O TRP A 942 SHEET 6 AB212 PHE A 972 VAL A 975 -1 O VAL A 975 N THR A 934 SHEET 7 AB212 THR A 887 ASP A 892 -1 N LEU A 888 O ILE A 974 SHEET 8 AB212 ILE A 877 ASP A 884 -1 N ARG A 880 O ALA A 891 SHEET 9 AB212 ALA A 857 VAL A 863 -1 N VAL A 863 O ILE A 877 SHEET 10 AB212 HIS A 825 ARG A 829 1 N VAL A 826 O GLU A 858 SHEET 11 AB212 TYR A 845 VAL A 850 -1 O VAL A 850 N HIS A 825 SHEET 12 AB212 ASN A 914 VAL A 921 1 O ILE A 919 N VAL A 849 CISPEP 1 ALA A 180 PRO A 181 0 -16.71 CISPEP 2 PRO A 275 SER A 276 0 6.33 CISPEP 3 GLY A 383 PRO A 384 0 22.39 CISPEP 4 TRP A 415 ASN A 416 0 2.49 CISPEP 5 GLU A 559 PRO A 560 0 7.07 CISPEP 6 GLU A 706 PRO A 707 0 7.95 SITE 1 AC1 12 ASP A 443 ILE A 444 TRP A 554 ASP A 556 SITE 2 AC1 12 ARG A 617 TRP A 630 ASP A 633 PHE A 666 SITE 3 AC1 12 HIS A 691 HOH A1123 HOH A1137 HOH A1629 CRYST1 189.523 189.523 157.784 90.00 90.00 120.00 H 3 2 18 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 0.005276 0.003046 0.000000 0.00000 SCALE2 0.000000 0.006093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006338 0.00000