HEADER HYDROLASE 17-MAR-15 4UFK TITLE MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH DIDEOXY-IMINO-LYXITOL DIL 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 DIL 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 06-NOV-24 4UFK 1 REMARK REVDAT 5 20-DEC-23 4UFK 1 HETSYN REVDAT 4 29-JUL-20 4UFK 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 10-JUN-15 4UFK 1 JRNL REVDAT 2 01-APR-15 4UFK 1 REMARK REVDAT 1 25-MAR-15 4UFK 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) : 73.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 35733 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1833 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 73.2522 - 5.6474 0.98 2655 143 0.1360 0.1698 REMARK 3 2 5.6474 - 4.4827 1.00 2642 137 0.1099 0.1323 REMARK 3 3 4.4827 - 3.9161 1.00 2630 135 0.1218 0.1652 REMARK 3 4 3.9161 - 3.5580 1.00 2592 151 0.1417 0.1913 REMARK 3 5 3.5580 - 3.3030 0.99 2614 125 0.1689 0.2162 REMARK 3 6 3.3030 - 3.1083 1.00 2584 144 0.1826 0.2248 REMARK 3 7 3.1083 - 2.9526 1.00 2619 134 0.1809 0.2167 REMARK 3 8 2.9526 - 2.8241 1.00 2629 119 0.1795 0.2163 REMARK 3 9 2.8241 - 2.7153 1.00 2592 146 0.1926 0.2614 REMARK 3 10 2.7153 - 2.6216 1.00 2587 156 0.1912 0.2142 REMARK 3 11 2.6216 - 2.5397 1.00 2592 135 0.2073 0.2200 REMARK 3 12 2.5397 - 2.4671 1.00 2599 146 0.2097 0.2690 REMARK 3 13 2.4671 - 2.4021 0.99 2565 162 0.2328 0.2922 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.47 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 5419 REMARK 3 ANGLE : 0.977 7399 REMARK 3 CHIRALITY : 0.042 795 REMARK 3 PLANARITY : 0.004 929 REMARK 3 DIHEDRAL : 11.993 1883 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): 82.5428 77.3880 43.7493 REMARK 3 T TENSOR REMARK 3 T11: 0.3022 T22: 0.4622 REMARK 3 T33: 0.2972 T12: -0.0474 REMARK 3 T13: -0.0932 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 1.7177 L22: 3.0271 REMARK 3 L33: 2.2889 L12: -0.6638 REMARK 3 L13: 0.3300 L23: -0.8074 REMARK 3 S TENSOR REMARK 3 S11: -0.0042 S12: -0.1793 S13: -0.0076 REMARK 3 S21: 0.3255 S22: 0.0494 S23: -0.3250 REMARK 3 S31: 0.0199 S32: 0.4714 S33: -0.0398 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 453:471) REMARK 3 ORIGIN FOR THE GROUP (A): 98.0987 104.7898 27.2615 REMARK 3 T TENSOR REMARK 3 T11: 0.4738 T22: 0.9105 REMARK 3 T33: 0.7334 T12: -0.3184 REMARK 3 T13: -0.0531 T23: 0.0489 REMARK 3 L TENSOR REMARK 3 L11: 0.1719 L22: 0.0315 REMARK 3 L33: 0.6694 L12: 0.1557 REMARK 3 L13: -0.3077 L23: -0.1845 REMARK 3 S TENSOR REMARK 3 S11: 0.0109 S12: 0.2738 S13: 0.1696 REMARK 3 S21: 0.1122 S22: -0.1844 S23: -0.4914 REMARK 3 S31: -0.3852 S32: 0.9242 S33: 0.1004 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 41:337) REMARK 3 ORIGIN FOR THE GROUP (A): 74.4913 99.0072 22.3481 REMARK 3 T TENSOR REMARK 3 T11: 0.2772 T22: 0.3570 REMARK 3 T33: 0.2898 T12: -0.1586 REMARK 3 T13: -0.0171 T23: 0.0160 REMARK 3 L TENSOR REMARK 3 L11: 0.8150 L22: 1.1661 REMARK 3 L33: 2.1781 L12: -0.4337 REMARK 3 L13: -0.0425 L23: -0.0655 REMARK 3 S TENSOR REMARK 3 S11: 0.0146 S12: 0.0315 S13: 0.0936 REMARK 3 S21: -0.0014 S22: 0.0045 S23: -0.2173 REMARK 3 S31: -0.2843 S32: 0.4131 S33: -0.0146 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND ((RESSEQ 25:40) OR (RESSEQ 338:452)) REMARK 3 ORIGIN FOR THE GROUP (A): 89.8262 109.9978 1.3175 REMARK 3 T TENSOR REMARK 3 T11: 0.7440 T22: 0.8281 REMARK 3 T33: 0.5569 T12: -0.3365 REMARK 3 T13: 0.1221 T23: 0.1344 REMARK 3 L TENSOR REMARK 3 L11: 2.8344 L22: 2.4564 REMARK 3 L33: 1.2754 L12: 1.1129 REMARK 3 L13: -0.3779 L23: 0.0491 REMARK 3 S TENSOR REMARK 3 S11: 0.0547 S12: 0.5046 S13: 0.5416 REMARK 3 S21: -0.4715 S22: -0.0478 S23: -0.5292 REMARK 3 S31: -0.5568 S32: 0.6193 S33: -0.0055 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 4UFK 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_1290063368. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-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 : I04-1 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 : 35733 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 73.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 1.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 60.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 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 124.41000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.82815 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.95000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 124.41000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 71.82815 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.95000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 124.41000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 71.82815 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 25.95000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 124.41000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 71.82815 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.95000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 124.41000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 71.82815 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 25.95000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 124.41000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 71.82815 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.95000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 143.65629 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 51.90000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 143.65629 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 51.90000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 143.65629 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 51.90000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 143.65629 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 51.90000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 143.65629 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 51.90000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 143.65629 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 51.90000 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 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 A2043 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 465 GLN A 419 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 ARG A 161 CZ NH1 NH2 REMARK 470 GLU A 349 CG CD OE1 OE2 REMARK 470 ARG A 420 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 424 CG CD CE NZ REMARK 470 LYS A 475 CG CD CE NZ REMARK 470 ARG A 507 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 508 CG CD OE1 OE2 REMARK 470 ARG A 663 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 665 CG CD OE1 OE2 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 175 NH2 ARG A 204 2.13 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 -70.46 -140.68 REMARK 500 ASP A 89 -1.00 73.58 REMARK 500 THR A 93 -45.12 149.54 REMARK 500 SER A 146 56.97 -99.07 REMARK 500 ILE A 179 -81.12 -107.17 REMARK 500 ASN A 212 -126.16 -149.06 REMARK 500 THR A 241 -1.59 72.61 REMARK 500 THR A 243 -157.65 -119.48 REMARK 500 PHE A 260 -101.45 70.52 REMARK 500 ASN A 264 40.37 -84.02 REMARK 500 ASN A 284 17.97 59.43 REMARK 500 SER A 296 57.72 -112.61 REMARK 500 SER A 376 23.59 -148.77 REMARK 500 GLU A 443 -167.12 -120.16 REMARK 500 ASN A 490 -15.97 67.64 REMARK 500 ARG A 555 -51.69 70.08 REMARK 500 THR A 653 -163.74 -129.28 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 NAG A 1542 REMARK 610 NAG A 2542 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 A3669 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 477 O REMARK 620 2 ASN A 479 OD1 71.4 REMARK 620 3 PHE A 511 O 92.1 90.3 REMARK 620 4 ASP A 660 OD1 79.7 151.1 92.4 REMARK 620 5 ASP A 660 OD2 128.0 160.6 89.1 48.2 REMARK 620 6 HOH A2139 O 92.0 86.3 173.5 93.2 92.3 REMARK 620 7 HOH A2141 O 159.9 88.7 91.0 119.9 71.9 83.4 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: 4UFL RELATED DB: PDB REMARK 900 MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH DEOXY-GALACTO- REMARK 900 NOEUROSTEGINE DGN 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 4UFK A 27 668 UNP P54818 GALC_MOUSE 43 684 SEQADV 4UFK HIS A 15 UNP P54818 EXPRESSION TAG SEQADV 4UFK HIS A 16 UNP P54818 EXPRESSION TAG SEQADV 4UFK HIS A 17 UNP P54818 EXPRESSION TAG SEQADV 4UFK HIS A 18 UNP P54818 EXPRESSION TAG SEQADV 4UFK HIS A 19 UNP P54818 EXPRESSION TAG SEQADV 4UFK HIS A 20 UNP P54818 EXPRESSION TAG SEQADV 4UFK ILE A 21 UNP P54818 EXPRESSION TAG SEQADV 4UFK GLU A 22 UNP P54818 EXPRESSION TAG SEQADV 4UFK GLY A 23 UNP P54818 EXPRESSION TAG SEQADV 4UFK ARG A 24 UNP P54818 EXPRESSION TAG SEQADV 4UFK GLY A 25 UNP P54818 EXPRESSION TAG SEQADV 4UFK 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 4UFK ASN A 284 ASN GLYCOSYLATION SITE MODRES 4UFK ASN A 363 ASN GLYCOSYLATION SITE MODRES 4UFK ASN A 387 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET LDU A1001 9 HET NAG A1387 14 HET NAG A1542 14 HET NAG A2542 14 HET CA A3669 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM LDU DIDEOXY-IMINO-LYXITOL 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 4 LDU C5 H11 N O3 FORMUL 8 CA CA 2+ FORMUL 9 HOH *181(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 GLY A 399 ILE A 404 5 6 HELIX 12 12 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 LEU A 421 TRP A 430 -1 O LEU A 421 N LYS A 413 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 ASN A 473 ASP A 476 0 SHEET 2 AE 2 ALA A 657 ALA A 667 1 O PHE A 662 N ASP A 476 SHEET 1 AF 7 PHE A 498 MET A 502 0 SHEET 2 AF 7 PHE A 511 GLN A 515 -1 O THR A 512 N TYR A 501 SHEET 3 AF 7 ALA A 657 ALA A 667 -1 O ALA A 657 N GLN A 515 SHEET 4 AF 7 ASN A 542 ILE A 551 -1 O ASN A 542 N ALA A 667 SHEET 5 AF 7 TRP A 612 LYS A 620 -1 O TYR A 613 N VAL A 549 SHEET 6 AF 7 PHE A 623 LEU A 628 -1 O PHE A 623 N LYS A 620 SHEET 7 AF 7 THR A 631 ARG A 638 -1 O THR A 631 N LEU A 628 SHEET 1 AG 4 PHE A 498 MET A 502 0 SHEET 2 AG 4 PHE A 511 GLN A 515 -1 O THR A 512 N TYR A 501 SHEET 3 AG 4 ALA A 657 ALA A 667 -1 O ALA A 657 N GLN A 515 SHEET 4 AG 4 ASN A 473 ASP A 476 1 O TYR A 474 N VAL A 664 SHEET 1 AH 7 ALA A 492 THR A 495 0 SHEET 2 AH 7 THR A 531 ILE A 535 -1 O ILE A 532 N GLN A 494 SHEET 3 AH 7 TRP A 646 THR A 651 -1 O ALA A 647 N ILE A 535 SHEET 4 AH 7 GLY A 558 VAL A 565 -1 O PHE A 560 N GLY A 650 SHEET 5 AH 7 THR A 576 PHE A 583 -1 O VAL A 578 N GLY A 563 SHEET 6 AH 7 SER A 587 ASP A 593 -1 O SER A 587 N PHE A 583 SHEET 7 AH 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 1.42 LINK ND2 ASN A 363 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 387 C1 NAG A1387 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 1.45 LINK O ASP A 477 CA CA A3669 1555 1555 2.43 LINK OD1 ASN A 479 CA CA A3669 1555 1555 2.38 LINK O PHE A 511 CA CA A3669 1555 1555 2.40 LINK OD1 ASP A 660 CA CA A3669 1555 1555 2.40 LINK OD2 ASP A 660 CA CA A3669 1555 1555 2.84 LINK O HOH A2139 CA CA A3669 1555 1555 2.56 LINK O HOH A2141 CA CA A3669 1555 1555 2.42 CISPEP 1 GLY A 48 GLY A 49 0 1.84 CISPEP 2 GLU A 60 PRO A 61 0 6.27 CISPEP 3 ALA A 209 SER A 210 0 -3.16 CISPEP 4 GLU A 215 PRO A 216 0 7.07 CISPEP 5 TRP A 291 ASN A 292 0 3.31 CISPEP 6 ARG A 380 PRO A 381 0 -0.35 CISPEP 7 TYR A 641 PRO A 642 0 0.20 CRYST1 248.820 248.820 77.850 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 0.004019 0.002320 0.000000 0.00000 SCALE2 0.000000 0.004641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012845 0.00000