HEADER HYDROLASE 17-MAR-15 4UFL TITLE MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH DEOXY-GALACTO-NOEUROSTEGINE TITLE 2 DGN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALACTOCEREBROSIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GALCERASE, GALACTOCEREBROSIDE BETA-GALACTOSIDASE, COMPND 5 GALACTOSYLCERAMIDASE, GALACTOSYLCERAMIDE BETA-GALACTOSIDASE; COMPND 6 EC: 3.2.1.46; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: COMPLEX WITH DGN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 T KEYWDS HYDROLASE, GLYCOSYL HYDROLASE, LYSOSOME EXPDTA X-RAY DIFFRACTION AUTHOR C.H.HILL,A.H.VIUFF,S.J.SPRATLEY,S.SALAMONE,S.H.CHRISTENSEN,R.J.READ, AUTHOR 2 N.W.MORIARTY,H.H.JENSEN,J.E.DEANE REVDAT 6 23-OCT-24 4UFL 1 REMARK REVDAT 5 20-DEC-23 4UFL 1 HETSYN REVDAT 4 29-JUL-20 4UFL 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 10-JUN-15 4UFL 1 JRNL REVDAT 2 01-APR-15 4UFL 1 REMARK REVDAT 1 25-MAR-15 4UFL 0 JRNL AUTH C.H.HILL,A.H.VIUFF,S.J.SPRATLEY,S.SALAMONE,S.H.CHRISTENSEN, JRNL AUTH 2 R.J.READ,N.W.MORIARTY,H.H.JENSEN,J.E.DEANE JRNL TITL AZASUGAR INHIBITORS AS PHARMACOLOGICAL CHAPERONES FOR KRABBE JRNL TITL 2 DISEASE. JRNL REF CHEM.SCI. V. 6 3075 2015 JRNL REFN ISSN 2041-6520 JRNL PMID 26029356 JRNL DOI 10.1039/C5SC00754B REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 34998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1785 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 73.0757 - 5.6431 0.97 2608 139 0.1521 0.1641 REMARK 3 2 5.6431 - 4.4793 0.94 2483 125 0.1355 0.1648 REMARK 3 3 4.4793 - 3.9131 0.94 2464 126 0.1428 0.1562 REMARK 3 4 3.9131 - 3.5554 0.95 2475 142 0.1630 0.2046 REMARK 3 5 3.5554 - 3.3005 0.97 2565 122 0.1859 0.2227 REMARK 3 6 3.3005 - 3.1059 0.98 2535 138 0.2068 0.2493 REMARK 3 7 3.1059 - 2.9504 0.99 2585 133 0.2020 0.2488 REMARK 3 8 2.9504 - 2.8219 0.99 2610 119 0.2027 0.2256 REMARK 3 9 2.8219 - 2.7133 1.00 2580 147 0.2097 0.2611 REMARK 3 10 2.7133 - 2.6197 1.00 2574 158 0.2131 0.2338 REMARK 3 11 2.6197 - 2.5378 1.00 2596 126 0.2351 0.2721 REMARK 3 12 2.5378 - 2.4652 1.00 2570 151 0.2368 0.2877 REMARK 3 13 2.4652 - 2.4003 0.99 2568 159 0.2442 0.2758 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 5552 REMARK 3 ANGLE : 1.266 7584 REMARK 3 CHIRALITY : 0.058 807 REMARK 3 PLANARITY : 0.006 960 REMARK 3 DIHEDRAL : 14.071 1952 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 472:668)) REMARK 3 ORIGIN FOR THE GROUP (A): 82.3184 77.3482 43.8723 REMARK 3 T TENSOR REMARK 3 T11: 0.2784 T22: 0.6302 REMARK 3 T33: 0.2726 T12: -0.0448 REMARK 3 T13: -0.0811 T23: -0.0161 REMARK 3 L TENSOR REMARK 3 L11: 2.8140 L22: 2.4723 REMARK 3 L33: 1.5693 L12: -0.0155 REMARK 3 L13: 0.6967 L23: -0.5248 REMARK 3 S TENSOR REMARK 3 S11: 0.0484 S12: -0.0793 S13: -0.0346 REMARK 3 S21: 0.2783 S22: 0.0537 S23: -0.3254 REMARK 3 S31: 0.0621 S32: 0.7788 S33: -0.1038 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 453:471)) REMARK 3 ORIGIN FOR THE GROUP (A): 97.9589 104.5548 27.2077 REMARK 3 T TENSOR REMARK 3 T11: 0.4484 T22: 1.0216 REMARK 3 T33: 0.6312 T12: -0.4540 REMARK 3 T13: 0.0288 T23: 0.0227 REMARK 3 L TENSOR REMARK 3 L11: 0.3974 L22: 0.0549 REMARK 3 L33: 0.0643 L12: 0.1356 REMARK 3 L13: 0.0231 L23: 0.0374 REMARK 3 S TENSOR REMARK 3 S11: 0.0020 S12: -0.0921 S13: 0.1384 REMARK 3 S21: 0.0437 S22: 0.0218 S23: -0.2275 REMARK 3 S31: -0.1290 S32: 0.2568 S33: 0.0183 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 25:40) OR (RESSEQ 338:452)) REMARK 3 ORIGIN FOR THE GROUP (A): 90.1278 109.3804 1.4700 REMARK 3 T TENSOR REMARK 3 T11: 0.8893 T22: 1.1652 REMARK 3 T33: 0.4858 T12: -0.7565 REMARK 3 T13: 0.1737 T23: 0.2159 REMARK 3 L TENSOR REMARK 3 L11: 1.2474 L22: 0.3137 REMARK 3 L33: 0.5041 L12: 0.2637 REMARK 3 L13: -0.3038 L23: 0.2515 REMARK 3 S TENSOR REMARK 3 S11: -0.0455 S12: 0.3347 S13: 0.3171 REMARK 3 S21: -0.3534 S22: 0.0344 S23: -0.3176 REMARK 3 S31: -0.4370 S32: 0.7509 S33: 0.0163 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 41:337)) REMARK 3 ORIGIN FOR THE GROUP (A): 74.5125 98.7881 22.3740 REMARK 3 T TENSOR REMARK 3 T11: 0.3454 T22: 0.5153 REMARK 3 T33: 0.3094 T12: -0.2802 REMARK 3 T13: -0.0005 T23: 0.0083 REMARK 3 L TENSOR REMARK 3 L11: 1.0255 L22: 0.6151 REMARK 3 L33: 0.8889 L12: 0.0853 REMARK 3 L13: 0.1934 L23: 0.2480 REMARK 3 S TENSOR REMARK 3 S11: 0.0162 S12: -0.0071 S13: 0.0336 REMARK 3 S21: -0.0316 S22: 0.0239 S23: -0.1356 REMARK 3 S31: -0.5073 S32: 0.5356 S33: -0.0309 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4UFL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1290063375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34998 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 73.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3ZR5 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE (PH 6.8), 34% PEG 8000 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 124.26500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.74443 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.88333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 124.26500 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 71.74443 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.88333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 124.26500 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 71.74443 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 25.88333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 124.26500 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 71.74443 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.88333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 124.26500 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 71.74443 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 25.88333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 124.26500 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 71.74443 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.88333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 143.48886 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 51.76667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 143.48886 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 51.76667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 143.48886 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 51.76667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 143.48886 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 51.76667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 143.48886 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 51.76667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 143.48886 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 51.76667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 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 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 A2046 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2048 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2121 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2123 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 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 HIS A 20 REMARK 465 ILE A 21 REMARK 465 GLU A 22 REMARK 465 GLY A 23 REMARK 465 ARG A 24 REMARK 465 THR A 416 REMARK 465 PRO A 417 REMARK 465 GLN A 418 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 424 CG CD CE NZ 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 O SER A 435 N SER A 437 2.05 REMARK 500 O HOH A 2144 O HOH A 2209 2.12 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 ARG A 305 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 305 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 LEU A 421 C - N - CA ANGL. DEV. = 15.1 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 PHE A 75 -68.09 -146.61 REMARK 500 ASP A 89 -6.70 77.62 REMARK 500 THR A 93 -45.82 150.90 REMARK 500 LEU A 105 -8.98 81.72 REMARK 500 SER A 146 53.50 -97.14 REMARK 500 ILE A 179 -83.99 -111.89 REMARK 500 ASN A 212 -122.90 -146.15 REMARK 500 THR A 241 -5.91 80.40 REMARK 500 THR A 243 -162.06 -113.25 REMARK 500 PHE A 260 -106.37 76.26 REMARK 500 ASN A 264 39.76 -78.93 REMARK 500 ASN A 284 16.89 59.65 REMARK 500 SER A 296 54.95 -113.17 REMARK 500 SER A 376 22.57 -147.39 REMARK 500 SER A 376 24.45 -147.39 REMARK 500 SER A 400 1.53 -57.95 REMARK 500 GLU A 443 -161.36 -112.43 REMARK 500 PRO A 465 151.81 -48.44 REMARK 500 ASN A 490 -18.87 72.96 REMARK 500 ILE A 522 97.54 -69.16 REMARK 500 ARG A 555 -53.15 69.26 REMARK 500 ARG A 555 -52.13 75.11 REMARK 500 THR A 653 -164.09 -129.99 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 CA A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 477 O REMARK 620 2 ASN A 479 OD1 73.6 REMARK 620 3 PHE A 511 O 96.3 94.3 REMARK 620 4 ASP A 660 OD2 130.1 155.5 89.5 REMARK 620 5 ASP A 660 OD1 80.5 153.1 96.0 49.6 REMARK 620 6 HOH A2171 O 86.7 84.4 176.2 90.3 86.8 REMARK 620 7 HOH A2173 O 152.7 79.2 88.3 76.7 125.9 87.9 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UFH RELATED DB: PDB REMARK 900 MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH ISO-GALACTO- FAGOMINE IGF REMARK 900 RELATED ID: 4UFI RELATED DB: PDB REMARK 900 MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH AZA-GALACTO- FAGOMINE AGF REMARK 900 RELATED ID: 4UFJ RELATED DB: PDB REMARK 900 MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH ISO-GALACTO- FAGOMINE REMARK 900 LACTAM IGL REMARK 900 RELATED ID: 4UFK RELATED DB: PDB REMARK 900 MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH DIDEOXY-IMINO- LYXITOL DIL REMARK 900 RELATED ID: 4UFM RELATED DB: PDB REMARK 900 MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH 1-DEOXY-GALACTO - REMARK 900 NOJIRIMYCIN DGJ REMARK 999 REMARK 999 SEQUENCE REMARK 999 NUMBERING IS FROM SECOND START SITE AS USED IN THE REMARK 999 LITERATURE AND IN PDB ENTRIES 3ZR5, 3ZR6, 4CCC, 4CCD, 4CCE. DBREF 4UFL A 27 668 UNP P54818 GALC_MOUSE 43 684 SEQADV 4UFL HIS A 15 UNP P54818 EXPRESSION TAG SEQADV 4UFL HIS A 16 UNP P54818 EXPRESSION TAG SEQADV 4UFL HIS A 17 UNP P54818 EXPRESSION TAG SEQADV 4UFL HIS A 18 UNP P54818 EXPRESSION TAG SEQADV 4UFL HIS A 19 UNP P54818 EXPRESSION TAG SEQADV 4UFL HIS A 20 UNP P54818 EXPRESSION TAG SEQADV 4UFL ILE A 21 UNP P54818 EXPRESSION TAG SEQADV 4UFL GLU A 22 UNP P54818 EXPRESSION TAG SEQADV 4UFL GLY A 23 UNP P54818 EXPRESSION TAG SEQADV 4UFL ARG A 24 UNP P54818 EXPRESSION TAG SEQADV 4UFL GLY A 25 UNP P54818 EXPRESSION TAG SEQADV 4UFL ALA A 26 UNP P54818 EXPRESSION TAG SEQRES 1 A 654 HIS HIS HIS HIS HIS HIS ILE GLU GLY ARG GLY ALA TYR SEQRES 2 A 654 VAL LEU ASP ASP SER ASP GLY LEU GLY ARG GLU PHE ASP SEQRES 3 A 654 GLY ILE GLY ALA VAL SER GLY GLY GLY ALA THR SER ARG SEQRES 4 A 654 LEU LEU VAL ASN TYR PRO GLU PRO TYR ARG SER GLU ILE SEQRES 5 A 654 LEU ASP TYR LEU PHE LYS PRO ASN PHE GLY ALA SER LEU SEQRES 6 A 654 HIS ILE LEU LYS VAL GLU ILE GLY GLY ASP GLY GLN THR SEQRES 7 A 654 THR ASP GLY THR GLU PRO SER HIS MET HIS TYR GLU LEU SEQRES 8 A 654 ASP GLU ASN TYR PHE ARG GLY TYR GLU TRP TRP LEU MET SEQRES 9 A 654 LYS GLU ALA LYS LYS ARG ASN PRO ASP ILE ILE LEU MET SEQRES 10 A 654 GLY LEU PRO TRP SER PHE PRO GLY TRP LEU GLY LYS GLY SEQRES 11 A 654 PHE SER TRP PRO TYR VAL ASN LEU GLN LEU THR ALA TYR SEQRES 12 A 654 TYR VAL VAL ARG TRP ILE LEU GLY ALA LYS HIS TYR HIS SEQRES 13 A 654 ASP LEU ASP ILE ASP TYR ILE GLY ILE TRP ASN GLU ARG SEQRES 14 A 654 PRO PHE ASP ALA ASN TYR ILE LYS GLU LEU ARG LYS MET SEQRES 15 A 654 LEU ASP TYR GLN GLY LEU GLN ARG VAL ARG ILE ILE ALA SEQRES 16 A 654 SER ASP ASN LEU TRP GLU PRO ILE SER SER SER LEU LEU SEQRES 17 A 654 LEU ASP GLN GLU LEU TRP LYS VAL VAL ASP VAL ILE GLY SEQRES 18 A 654 ALA HIS TYR PRO GLY THR TYR THR VAL TRP ASN ALA LYS SEQRES 19 A 654 MET SER GLY LYS LYS LEU TRP SER SER GLU ASP PHE SER SEQRES 20 A 654 THR ILE ASN SER ASN VAL GLY ALA GLY CYS TRP SER ARG SEQRES 21 A 654 ILE LEU ASN GLN ASN TYR ILE ASN GLY ASN MET THR SER SEQRES 22 A 654 THR ILE ALA TRP ASN LEU VAL ALA SER TYR TYR GLU GLU SEQRES 23 A 654 LEU PRO TYR GLY ARG SER GLY LEU MET THR ALA GLN GLU SEQRES 24 A 654 PRO TRP SER GLY HIS TYR VAL VAL ALA SER PRO ILE TRP SEQRES 25 A 654 VAL SER ALA HIS THR THR GLN PHE THR GLN PRO GLY TRP SEQRES 26 A 654 TYR TYR LEU LYS THR VAL GLY HIS LEU GLU LYS GLY GLY SEQRES 27 A 654 SER TYR VAL ALA LEU THR ASP GLY LEU GLY ASN LEU THR SEQRES 28 A 654 ILE ILE ILE GLU THR MET SER HIS GLN HIS SER MET CYS SEQRES 29 A 654 ILE ARG PRO TYR LEU PRO TYR TYR ASN VAL SER HIS GLN SEQRES 30 A 654 LEU ALA THR PHE THR LEU LYS GLY SER LEU ARG GLU ILE SEQRES 31 A 654 GLN GLU LEU GLN VAL TRP TYR THR LYS LEU GLY THR PRO SEQRES 32 A 654 GLN GLN ARG LEU HIS PHE LYS GLN LEU ASP THR LEU TRP SEQRES 33 A 654 LEU LEU ASP GLY SER GLY SER PHE THR LEU GLU LEU GLU SEQRES 34 A 654 GLU ASP GLU ILE PHE THR LEU THR THR LEU THR THR GLY SEQRES 35 A 654 ARG LYS GLY SER TYR PRO PRO PRO PRO SER SER LYS PRO SEQRES 36 A 654 PHE PRO THR ASN TYR LYS ASP ASP PHE ASN VAL GLU TYR SEQRES 37 A 654 PRO LEU PHE SER GLU ALA PRO ASN PHE ALA ASP GLN THR SEQRES 38 A 654 GLY VAL PHE GLU TYR TYR MET ASN ASN GLU ASP ARG GLU SEQRES 39 A 654 HIS ARG PHE THR LEU ARG GLN VAL LEU ASN GLN ARG PRO SEQRES 40 A 654 ILE THR TRP ALA ALA ASP ALA SER SER THR ILE SER VAL SEQRES 41 A 654 ILE GLY ASP HIS HIS TRP THR ASN MET THR VAL GLN CYS SEQRES 42 A 654 ASP VAL TYR ILE GLU THR PRO ARG SER GLY GLY VAL PHE SEQRES 43 A 654 ILE ALA GLY ARG VAL ASN LYS GLY GLY ILE LEU ILE ARG SEQRES 44 A 654 SER ALA THR GLY VAL PHE PHE TRP ILE PHE ALA ASN GLY SEQRES 45 A 654 SER TYR ARG VAL THR ALA ASP LEU GLY GLY TRP ILE THR SEQRES 46 A 654 TYR ALA SER GLY HIS ALA ASP VAL THR ALA LYS ARG TRP SEQRES 47 A 654 TYR THR LEU THR LEU GLY ILE LYS GLY TYR PHE ALA PHE SEQRES 48 A 654 GLY MET LEU ASN GLY THR ILE LEU TRP LYS ASN VAL ARG SEQRES 49 A 654 VAL LYS TYR PRO GLY HIS GLY TRP ALA ALA ILE GLY THR SEQRES 50 A 654 HIS THR PHE GLU PHE ALA GLN PHE ASP ASN PHE ARG VAL SEQRES 51 A 654 GLU ALA ALA ARG MODRES 4UFL ASN A 284 ASN GLYCOSYLATION SITE MODRES 4UFL ASN A 363 ASN GLYCOSYLATION SITE MODRES 4UFL ASN A 387 ASN GLYCOSYLATION SITE MODRES 4UFL ASN A 542 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET DZX A1001 12 HET CA A1002 1 HET NAG A1387 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM DZX DEOXY-GALACTO-NOEUROSTEGINE HETNAM CA CALCIUM 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 FORMUL 2 NAG 7(C8 H15 N O6) FORMUL 5 DZX C8 H15 N O3 FORMUL 6 CA CA 2+ FORMUL 8 HOH *223(H2 O) HELIX 1 1 PRO A 61 LYS A 72 1 12 HELIX 2 2 TYR A 113 ASN A 125 1 13 HELIX 3 3 PRO A 138 LYS A 143 5 6 HELIX 4 4 ASN A 151 ASP A 171 1 21 HELIX 5 5 ASP A 186 GLN A 200 1 15 HELIX 6 6 PRO A 216 ASP A 224 1 9 HELIX 7 7 ASP A 224 VAL A 231 1 8 HELIX 8 8 VAL A 244 GLY A 251 1 8 HELIX 9 9 SER A 265 ASN A 284 1 20 HELIX 10 10 ALA A 322 GLN A 333 1 12 HELIX 11 11 SER A 372 SER A 376 5 5 HELIX 12 12 GLY A 399 ARG A 402 5 4 HELIX 13 13 GLY A 568 SER A 574 5 7 SHEET 1 AA 3 ALA A 26 LEU A 29 0 SHEET 2 AA 3 GLN A 391 LEU A 397 1 O THR A 394 N TYR A 27 SHEET 3 AA 3 SER A 437 LEU A 442 -1 O PHE A 438 N PHE A 395 SHEET 1 AB 7 LEU A 35 GLU A 38 0 SHEET 2 AB 7 TYR A 340 LEU A 342 -1 O TYR A 341 N GLY A 36 SHEET 3 AB 7 SER A 353 THR A 358 -1 O ALA A 356 N LEU A 342 SHEET 4 AB 7 LEU A 364 GLU A 369 -1 O THR A 365 N LEU A 357 SHEET 5 AB 7 GLU A 446 THR A 451 -1 O PHE A 448 N ILE A 368 SHEET 6 AB 7 GLU A 406 LYS A 413 -1 O GLN A 408 N THR A 451 SHEET 7 AB 7 LYS A 424 TRP A 430 -1 O LYS A 424 N TYR A 411 SHEET 1 AC 4 LEU A 35 GLU A 38 0 SHEET 2 AC 4 TYR A 340 LEU A 342 -1 O TYR A 341 N GLY A 36 SHEET 3 AC 4 SER A 353 THR A 358 -1 O ALA A 356 N LEU A 342 SHEET 4 AC 4 GLY A 346 HIS A 347 1 O GLY A 346 N TYR A 354 SHEET 1 AD 9 GLY A 41 SER A 46 0 SHEET 2 AD 9 SER A 287 TRP A 291 1 O THR A 288 N GLY A 43 SHEET 3 AD 9 LYS A 253 PHE A 260 1 O SER A 256 N ILE A 289 SHEET 4 AD 9 VAL A 233 HIS A 237 1 O ILE A 234 N TRP A 255 SHEET 5 AD 9 ARG A 206 ASN A 212 1 O ALA A 209 N GLY A 235 SHEET 6 AD 9 TYR A 176 ILE A 177 1 O ILE A 177 N ILE A 208 SHEET 7 AD 9 ILE A 129 PRO A 134 1 N GLY A 132 O TYR A 176 SHEET 8 AD 9 ILE A 81 ILE A 86 1 O LEU A 82 N MET A 131 SHEET 9 AD 9 GLY A 41 SER A 46 1 O ALA A 44 N LYS A 83 SHEET 1 AE 2 VAL A 294 ALA A 295 0 SHEET 2 AE 2 MET A 309 THR A 310 1 O MET A 309 N ALA A 295 SHEET 1 AF 2 ASN A 473 ASP A 476 0 SHEET 2 AF 2 ALA A 657 ALA A 667 1 O PHE A 662 N ASP A 476 SHEET 1 AG 7 PHE A 498 MET A 502 0 SHEET 2 AG 7 PHE A 511 GLN A 515 -1 O THR A 512 N TYR A 501 SHEET 3 AG 7 ALA A 657 ALA A 667 -1 O ALA A 657 N GLN A 515 SHEET 4 AG 7 ASN A 542 ILE A 551 -1 O ASN A 542 N ALA A 667 SHEET 5 AG 7 TRP A 612 LYS A 620 -1 O TYR A 613 N VAL A 549 SHEET 6 AG 7 PHE A 623 LEU A 628 -1 O PHE A 623 N LYS A 620 SHEET 7 AG 7 THR A 631 ARG A 638 -1 O THR A 631 N LEU A 628 SHEET 1 AH 4 PHE A 498 MET A 502 0 SHEET 2 AH 4 PHE A 511 GLN A 515 -1 O THR A 512 N TYR A 501 SHEET 3 AH 4 ALA A 657 ALA A 667 -1 O ALA A 657 N GLN A 515 SHEET 4 AH 4 ASN A 473 ASP A 476 1 O TYR A 474 N VAL A 664 SHEET 1 AI 7 ALA A 492 THR A 495 0 SHEET 2 AI 7 THR A 531 ILE A 535 -1 O ILE A 532 N GLN A 494 SHEET 3 AI 7 TRP A 646 THR A 651 -1 O ALA A 647 N ILE A 535 SHEET 4 AI 7 GLY A 558 VAL A 565 -1 O PHE A 560 N GLY A 650 SHEET 5 AI 7 THR A 576 PHE A 583 -1 O VAL A 578 N GLY A 563 SHEET 6 AI 7 SER A 587 ASP A 593 -1 O SER A 587 N PHE A 583 SHEET 7 AI 7 THR A 599 HIS A 604 -1 N TYR A 600 O VAL A 590 SSBOND 1 CYS A 271 CYS A 378 1555 1555 2.03 LINK ND2 ASN A 284 C1 NAG B 1 1555 1555 1.46 LINK ND2 ASN A 363 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 387 C1 NAG A1387 1555 1555 1.46 LINK ND2 ASN A 542 C1 NAG D 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O ASP A 477 CA CA A1002 1555 1555 2.39 LINK OD1 ASN A 479 CA CA A1002 1555 1555 2.41 LINK O PHE A 511 CA CA A1002 1555 1555 2.32 LINK OD2 ASP A 660 CA CA A1002 1555 1555 2.77 LINK OD1 ASP A 660 CA CA A1002 1555 1555 2.36 LINK CA CA A1002 O HOH A2171 1555 1555 2.48 LINK CA CA A1002 O HOH A2173 1555 1555 2.56 CISPEP 1 GLY A 48 GLY A 49 0 -2.43 CISPEP 2 GLU A 60 PRO A 61 0 6.27 CISPEP 3 ALA A 209 SER A 210 0 -2.38 CISPEP 4 GLU A 215 PRO A 216 0 9.18 CISPEP 5 TRP A 291 ASN A 292 0 3.35 CISPEP 6 ARG A 380 PRO A 381 0 -1.99 CISPEP 7 ARG A 420 LEU A 421 0 26.50 CISPEP 8 TYR A 641 PRO A 642 0 0.48 CRYST1 248.530 248.530 77.650 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 0.004024 0.002323 0.000000 0.00000 SCALE2 0.000000 0.004646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012878 0.00000