PDB Short entry for 3ZR6 HEADER HYDROLASE 14-JUN-11 3ZR6 TITLE STRUCTURE OF GALACTOCEREBROSIDASE FROM MOUSE IN COMPLEX WITH GALACTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALACTOCEREBROSIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 40-684; COMPND 5 SYNONYM: GALCERASE, GALACTOCEREBROSIDE BETA-GALACTOSIDASE, COMPND 6 GALACTOSYLCERAMIDASE, GALACTOSYLCERAMIDE BETA-GALACTOSIDASE; COMPND 7 EC: 3.2.1.46; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: FRAGMENT CORRESPONDS TO RESIDUES 25-668 BASED ON COMPND 10 NUMBERING STARTING AT SECOND UNIPROT INITIATION SITE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: 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; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSECTAG2B KEYWDS HYDROLASE, GALC, GLYCOSYL HYDROLASE, KRABBE DISEASE, TIM BARREL, KEYWDS 2 LECTIN DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR J.E.DEANE,S.C.GRAHAM,N.N.KIM,P.E.STEIN,R.MCNAIR,M.B.CACHON-GONZALEZ, AUTHOR 2 T.M.COX,R.J.READ REVDAT 4 20-DEC-23 3ZR6 1 HETSYN REVDAT 3 29-JUL-20 3ZR6 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 03-APR-19 3ZR6 1 SOURCE REVDAT 1 28-SEP-11 3ZR6 0 JRNL AUTH J.E.DEANE,S.C.GRAHAM,N.N.KIM,P.E.STEIN,R.MCNAIR, JRNL AUTH 2 M.B.CACHON-GONZALEZ,T.M.COX,R.J.READ JRNL TITL INSIGHTS INTO KRABBE DISEASE FROM STRUCTURES OF JRNL TITL 2 GALACTOCEREBROSIDASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 15169 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21876145 JRNL DOI 10.1073/PNAS.1105639108 REMARK 2 REMARK 2 RESOLUTION. 2.44 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) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 66636 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3369 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 62.9743 - 7.0352 0.99 2652 125 0.1352 0.1463 REMARK 3 2 7.0352 - 5.5851 0.98 2602 156 0.1619 0.2025 REMARK 3 3 5.5851 - 4.8794 0.98 2608 135 0.1405 0.1675 REMARK 3 4 4.8794 - 4.4334 0.99 2613 127 0.1133 0.1722 REMARK 3 5 4.4334 - 4.1157 0.99 2655 115 0.1226 0.1546 REMARK 3 6 4.1157 - 3.8731 0.99 2595 158 0.1360 0.1965 REMARK 3 7 3.8731 - 3.6792 0.99 2620 154 0.1561 0.2017 REMARK 3 8 3.6792 - 3.5190 0.99 2646 135 0.1770 0.2448 REMARK 3 9 3.5190 - 3.3836 1.00 2669 111 0.1905 0.2722 REMARK 3 10 3.3836 - 3.2668 1.00 2619 147 0.1962 0.2285 REMARK 3 11 3.2668 - 3.1647 1.00 2637 172 0.1966 0.2374 REMARK 3 12 3.1647 - 3.0742 1.00 2661 121 0.1944 0.2491 REMARK 3 13 3.0742 - 2.9933 1.00 2650 116 0.2010 0.2179 REMARK 3 14 2.9933 - 2.9202 1.00 2662 149 0.1982 0.2223 REMARK 3 15 2.9202 - 2.8539 1.00 2656 119 0.2175 0.3070 REMARK 3 16 2.8539 - 2.7931 1.00 2647 148 0.2345 0.2719 REMARK 3 17 2.7931 - 2.7372 1.00 2641 146 0.2442 0.3453 REMARK 3 18 2.7372 - 2.6856 1.00 2581 152 0.2241 0.2889 REMARK 3 19 2.6856 - 2.6376 1.00 2683 155 0.2433 0.2426 REMARK 3 20 2.6376 - 2.5929 1.00 2639 141 0.2508 0.2681 REMARK 3 21 2.5929 - 2.5511 1.00 2650 132 0.2810 0.2870 REMARK 3 22 2.5511 - 2.5118 1.00 2610 149 0.3045 0.3739 REMARK 3 23 2.5118 - 2.4749 1.00 2668 154 0.3183 0.3506 REMARK 3 24 2.4749 - 2.4400 0.99 2603 152 0.3283 0.3843 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 34.07 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.730 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.98290 REMARK 3 B22 (A**2) : 3.98290 REMARK 3 B33 (A**2) : -7.96570 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 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 : 0.010 5414 REMARK 3 ANGLE : 1.330 7390 REMARK 3 CHIRALITY : 0.081 793 REMARK 3 PLANARITY : 0.006 925 REMARK 3 DIHEDRAL : 16.562 1910 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 25:40 OR RESSEQ 338:452) REMARK 3 ORIGIN FOR THE GROUP (A): 90.3814 109.9912 1.5876 REMARK 3 T TENSOR REMARK 3 T11: 0.6230 T22: 0.7617 REMARK 3 T33: 0.4314 T12: -0.2407 REMARK 3 T13: 0.1876 T23: 0.1720 REMARK 3 L TENSOR REMARK 3 L11: 0.8326 L22: 0.2998 REMARK 3 L33: 0.2266 L12: 0.0300 REMARK 3 L13: -0.2937 L23: 0.1049 REMARK 3 S TENSOR REMARK 3 S11: 0.1346 S12: 0.3282 S13: 0.3442 REMARK 3 S21: -0.3227 S22: -0.0518 S23: -0.3023 REMARK 3 S31: -0.2899 S32: 0.2368 S33: 0.0279 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESSEQ 41:337 REMARK 3 ORIGIN FOR THE GROUP (A): 74.8015 99.4384 22.2689 REMARK 3 T TENSOR REMARK 3 T11: 0.2743 T22: 0.3616 REMARK 3 T33: 0.1933 T12: -0.1759 REMARK 3 T13: 0.0073 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.9378 L22: 0.6827 REMARK 3 L33: 0.4927 L12: -0.1754 REMARK 3 L13: 0.2346 L23: 0.0587 REMARK 3 S TENSOR REMARK 3 S11: 0.0986 S12: 0.1439 S13: 0.0728 REMARK 3 S21: -0.0401 S22: -0.0503 S23: -0.0971 REMARK 3 S31: -0.2216 S32: 0.3024 S33: -0.0270 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESSEQ 453:471 REMARK 3 ORIGIN FOR THE GROUP (A): 98.3001 104.9396 27.1342 REMARK 3 T TENSOR REMARK 3 T11: 0.4468 T22: 0.8549 REMARK 3 T33: 0.5554 T12: -0.3235 REMARK 3 T13: -0.0113 T23: 0.0732 REMARK 3 L TENSOR REMARK 3 L11: 0.8858 L22: 0.2588 REMARK 3 L33: 0.3426 L12: 0.2467 REMARK 3 L13: -0.1295 L23: 0.2120 REMARK 3 S TENSOR REMARK 3 S11: 0.0980 S12: 0.1335 S13: 0.1323 REMARK 3 S21: -0.0343 S22: 0.0963 S23: -0.1216 REMARK 3 S31: -0.0994 S32: 0.0935 S33: -0.0925 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESSEQ 472:668 REMARK 3 ORIGIN FOR THE GROUP (A): 82.7120 77.9529 43.5122 REMARK 3 T TENSOR REMARK 3 T11: 0.3103 T22: 0.5290 REMARK 3 T33: 0.3029 T12: -0.1039 REMARK 3 T13: -0.1357 T23: 0.0577 REMARK 3 L TENSOR REMARK 3 L11: 1.1666 L22: 1.1014 REMARK 3 L33: 1.0002 L12: -0.0959 REMARK 3 L13: 0.4514 L23: -0.2934 REMARK 3 S TENSOR REMARK 3 S11: 0.1792 S12: -0.3462 S13: -0.2104 REMARK 3 S21: 0.2879 S22: -0.0329 S23: -0.1552 REMARK 3 S31: 0.0834 S32: 0.3911 S33: -0.1432 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 3ZR6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1290048700. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-10 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 : I03 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 : 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 : 34204 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 72.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.75000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3ZR5 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE, PH 6.8, 34% (W/V) POLYETHYLENE GLYCOL 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 124.77400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.03830 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.81867 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 124.77400 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 72.03830 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.81867 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 124.77400 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 72.03830 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 25.81867 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 124.77400 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 72.03830 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.81867 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 124.77400 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 72.03830 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 25.81867 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 124.77400 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 72.03830 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.81867 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 144.07660 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 51.63733 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 144.07660 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 51.63733 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 144.07660 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 51.63733 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 144.07660 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 51.63733 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 144.07660 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 51.63733 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 144.07660 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 51.63733 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 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 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 ILE A 19 REMARK 465 GLU A 20 REMARK 465 GLY A 21 REMARK 465 HIS A 22 REMARK 465 ILE A 23 REMARK 465 GLY 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 350 CG CD CE NZ REMARK 470 LYS A 398 CG CD CE NZ REMARK 470 ARG A 402 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 420 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 508 CG CD OE1 OE2 REMARK 470 ARG A 611 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 640 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 N LYS A 343 O HOH A 4001 2.12 REMARK 500 NZ LYS A 248 OD1 ASN A 284 2.19 REMARK 500 ND2 ASN A 363 C2 NAG B 1 2.19 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 -73.03 -147.37 REMARK 500 ASP A 89 -3.19 68.20 REMARK 500 THR A 93 -42.59 150.02 REMARK 500 LEU A 105 -2.80 83.74 REMARK 500 ILE A 179 -82.11 -110.62 REMARK 500 ASN A 181 113.20 -39.64 REMARK 500 ASN A 212 -122.56 -141.33 REMARK 500 THR A 241 -8.20 83.70 REMARK 500 THR A 243 -158.27 -110.58 REMARK 500 PHE A 260 -105.67 79.81 REMARK 500 ASN A 264 37.84 -75.63 REMARK 500 SER A 306 45.97 -105.07 REMARK 500 ALA A 311 77.37 -151.14 REMARK 500 SER A 376 24.12 -146.15 REMARK 500 SER A 400 15.10 -66.71 REMARK 500 GLU A 403 15.16 -68.59 REMARK 500 GLU A 443 -168.11 -125.72 REMARK 500 PRO A 465 153.13 -47.91 REMARK 500 ASN A 490 -14.58 69.99 REMARK 500 THR A 541 -41.85 -130.75 REMARK 500 ARG A 555 -53.90 73.72 REMARK 500 ASN A 636 48.94 37.68 REMARK 500 THR A 653 -164.76 -129.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 N-ACETYL-D-GLUCOSAMINE (NAG): THE LAST 3 NUMBERS MATCH THE REMARK 600 ASN RESIDUE THEY ARE LINKED TO. THE GLYCANS ARE THEN REMARK 600 NUMBERED ACCORDING TO THEIR POSITION DISTANT FROM THE REMARK 600 ATTACHED ASN. 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 A 709 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 477 O REMARK 620 2 ASN A 479 OD1 61.8 REMARK 620 3 PHE A 511 O 75.8 89.8 REMARK 620 4 ASP A 660 OD1 70.5 131.8 84.8 REMARK 620 5 ASP A 660 OD2 114.3 174.0 84.7 45.3 REMARK 620 6 HOH A4005 O 81.3 84.1 156.5 82.6 100.1 REMARK 620 7 HOH A4024 O 144.8 101.6 138.0 114.0 84.1 65.5 REMARK 620 N 1 2 3 4 5 6 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: DSSP OUTPUT MODIFIED BY AUTHOR 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: 3ZR5 RELATED DB: PDB REMARK 900 STRUCTURE OF GALACTOCEREBROSIDASE FROM MOUSE REMARK 999 REMARK 999 SEQUENCE REMARK 999 TWO DIFFERENT START SITES ARE PRESENT IN MOUSE GALC, WE REMARK 999 HAVE USED THE SECOND START SITE (TO MATCH THE LITERATURE) REMARK 999 WHICH IS M17 IN THE UNIPROT ENTRY. THE FULL CONSTRUCT REMARK 999 CONTAINED A SECRETION TAG (THAT WAS CLEAVED A HIS TAG AND A REMARK 999 FACTOR XA SITE WHICH WERE NOT. DBREF 3ZR6 A 24 668 UNP P54818 GALC_MOUSE 40 684 SEQADV 3ZR6 HIS A 13 UNP P54818 EXPRESSION TAG SEQADV 3ZR6 HIS A 14 UNP P54818 EXPRESSION TAG SEQADV 3ZR6 HIS A 15 UNP P54818 EXPRESSION TAG SEQADV 3ZR6 HIS A 16 UNP P54818 EXPRESSION TAG SEQADV 3ZR6 HIS A 17 UNP P54818 EXPRESSION TAG SEQADV 3ZR6 HIS A 18 UNP P54818 EXPRESSION TAG SEQADV 3ZR6 ILE A 19 UNP P54818 EXPRESSION TAG SEQADV 3ZR6 GLU A 20 UNP P54818 EXPRESSION TAG SEQADV 3ZR6 GLY A 21 UNP P54818 EXPRESSION TAG SEQADV 3ZR6 HIS A 22 UNP P54818 EXPRESSION TAG SEQADV 3ZR6 ILE A 23 UNP P54818 EXPRESSION TAG SEQRES 1 A 656 HIS HIS HIS HIS HIS HIS ILE GLU GLY HIS ILE GLY GLY SEQRES 2 A 656 ALA TYR VAL LEU ASP ASP SER ASP GLY LEU GLY ARG GLU SEQRES 3 A 656 PHE ASP GLY ILE GLY ALA VAL SER GLY GLY GLY ALA THR SEQRES 4 A 656 SER ARG LEU LEU VAL ASN TYR PRO GLU PRO TYR ARG SER SEQRES 5 A 656 GLU ILE LEU ASP TYR LEU PHE LYS PRO ASN PHE GLY ALA SEQRES 6 A 656 SER LEU HIS ILE LEU LYS VAL GLU ILE GLY GLY ASP GLY SEQRES 7 A 656 GLN THR THR ASP GLY THR GLU PRO SER HIS MET HIS TYR SEQRES 8 A 656 GLU LEU ASP GLU ASN TYR PHE ARG GLY TYR GLU TRP TRP SEQRES 9 A 656 LEU MET LYS GLU ALA LYS LYS ARG ASN PRO ASP ILE ILE SEQRES 10 A 656 LEU MET GLY LEU PRO TRP SER PHE PRO GLY TRP LEU GLY SEQRES 11 A 656 LYS GLY PHE SER TRP PRO TYR VAL ASN LEU GLN LEU THR SEQRES 12 A 656 ALA TYR TYR VAL VAL ARG TRP ILE LEU GLY ALA LYS HIS SEQRES 13 A 656 TYR HIS ASP LEU ASP ILE ASP TYR ILE GLY ILE TRP ASN SEQRES 14 A 656 GLU ARG PRO PHE ASP ALA ASN TYR ILE LYS GLU LEU ARG SEQRES 15 A 656 LYS MET LEU ASP TYR GLN GLY LEU GLN ARG VAL ARG ILE SEQRES 16 A 656 ILE ALA SER ASP ASN LEU TRP GLU PRO ILE SER SER SER SEQRES 17 A 656 LEU LEU LEU ASP GLN GLU LEU TRP LYS VAL VAL ASP VAL SEQRES 18 A 656 ILE GLY ALA HIS TYR PRO GLY THR TYR THR VAL TRP ASN SEQRES 19 A 656 ALA LYS MET SER GLY LYS LYS LEU TRP SER SER GLU ASP SEQRES 20 A 656 PHE SER THR ILE ASN SER ASN VAL GLY ALA GLY CYS TRP SEQRES 21 A 656 SER ARG ILE LEU ASN GLN ASN TYR ILE ASN GLY ASN MET SEQRES 22 A 656 THR SER THR ILE ALA TRP ASN LEU VAL ALA SER TYR TYR SEQRES 23 A 656 GLU GLU LEU PRO TYR GLY ARG SER GLY LEU MET THR ALA SEQRES 24 A 656 GLN GLU PRO TRP SER GLY HIS TYR VAL VAL ALA SER PRO SEQRES 25 A 656 ILE TRP VAL SER ALA HIS THR THR GLN PHE THR GLN PRO SEQRES 26 A 656 GLY TRP TYR TYR LEU LYS THR VAL GLY HIS LEU GLU LYS SEQRES 27 A 656 GLY GLY SER TYR VAL ALA LEU THR ASP GLY LEU GLY ASN SEQRES 28 A 656 LEU THR ILE ILE ILE GLU THR MET SER HIS GLN HIS SER SEQRES 29 A 656 MET CYS ILE ARG PRO TYR LEU PRO TYR TYR ASN VAL SER SEQRES 30 A 656 HIS GLN LEU ALA THR PHE THR LEU LYS GLY SER LEU ARG SEQRES 31 A 656 GLU ILE GLN GLU LEU GLN VAL TRP TYR THR LYS LEU GLY SEQRES 32 A 656 THR PRO GLN GLN ARG LEU HIS PHE LYS GLN LEU ASP THR SEQRES 33 A 656 LEU TRP LEU LEU ASP GLY SER GLY SER PHE THR LEU GLU SEQRES 34 A 656 LEU GLU GLU ASP GLU ILE PHE THR LEU THR THR LEU THR SEQRES 35 A 656 THR GLY ARG LYS GLY SER TYR PRO PRO PRO PRO SER SER SEQRES 36 A 656 LYS PRO PHE PRO THR ASN TYR LYS ASP ASP PHE ASN VAL SEQRES 37 A 656 GLU TYR PRO LEU PHE SER GLU ALA PRO ASN PHE ALA ASP SEQRES 38 A 656 GLN THR GLY VAL PHE GLU TYR TYR MET ASN ASN GLU ASP SEQRES 39 A 656 ARG GLU HIS ARG PHE THR LEU ARG GLN VAL LEU ASN GLN SEQRES 40 A 656 ARG PRO ILE THR TRP ALA ALA ASP ALA SER SER THR ILE SEQRES 41 A 656 SER VAL ILE GLY ASP HIS HIS TRP THR ASN MET THR VAL SEQRES 42 A 656 GLN CYS ASP VAL TYR ILE GLU THR PRO ARG SER GLY GLY SEQRES 43 A 656 VAL PHE ILE ALA GLY ARG VAL ASN LYS GLY GLY ILE LEU SEQRES 44 A 656 ILE ARG SER ALA THR GLY VAL PHE PHE TRP ILE PHE ALA SEQRES 45 A 656 ASN GLY SER TYR ARG VAL THR ALA ASP LEU GLY GLY TRP SEQRES 46 A 656 ILE THR TYR ALA SER GLY HIS ALA ASP VAL THR ALA LYS SEQRES 47 A 656 ARG TRP TYR THR LEU THR LEU GLY ILE LYS GLY TYR PHE SEQRES 48 A 656 ALA PHE GLY MET LEU ASN GLY THR ILE LEU TRP LYS ASN SEQRES 49 A 656 VAL ARG VAL LYS TYR PRO GLY HIS GLY TRP ALA ALA ILE SEQRES 50 A 656 GLY THR HIS THR PHE GLU PHE ALA GLN PHE ASP ASN PHE SEQRES 51 A 656 ARG VAL GLU ALA ALA ARG MODRES 3ZR6 ASN A 284 ASN GLYCOSYLATION SITE MODRES 3ZR6 ASN A 363 ASN GLYCOSYLATION SITE MODRES 3ZR6 ASN A 387 ASN GLYCOSYLATION SITE MODRES 3ZR6 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 BMA C 3 11 HET NAG A 701 14 HET NAG A 704 14 HET GAL A 708 12 HET CA A 709 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 2 NAG 6(C8 H15 N O6) FORMUL 3 BMA C6 H12 O6 FORMUL 6 GAL C6 H12 O6 FORMUL 7 CA CA 2+ FORMUL 8 HOH *139(H2 O) HELIX 1 AA1 PRO A 61 LYS A 72 1 12 HELIX 2 AA2 TYR A 113 ASN A 125 1 13 HELIX 3 AA3 PRO A 138 LYS A 143 5 6 HELIX 4 AA4 ASN A 151 ASP A 171 1 21 HELIX 5 AA5 ASP A 186 GLN A 200 1 15 HELIX 6 AA6 PRO A 216 ASP A 224 1 9 HELIX 7 AA7 ASP A 224 VAL A 231 1 8 HELIX 8 AA8 VAL A 244 GLY A 251 1 8 HELIX 9 AA9 SER A 265 ASN A 284 1 20 HELIX 10 AB1 ALA A 322 GLN A 333 1 12 HELIX 11 AB2 SER A 372 SER A 376 5 5 HELIX 12 AB3 GLY A 399 ARG A 402 5 4 HELIX 13 AB4 GLY A 568 SER A 574 5 7 SHEET 1 AA1 3 ALA A 26 LEU A 29 0 SHEET 2 AA1 3 GLN A 391 LEU A 397 1 O THR A 394 N TYR A 27 SHEET 3 AA1 3 SER A 437 LEU A 442 -1 O PHE A 438 N PHE A 395 SHEET 1 AA2 4 LEU A 35 GLU A 38 0 SHEET 2 AA2 4 TYR A 340 LEU A 342 -1 O TYR A 341 N ARG A 37 SHEET 3 AA2 4 SER A 353 THR A 358 -1 O THR A 358 N TYR A 340 SHEET 4 AA2 4 GLY A 346 HIS A 347 -1 N GLY A 346 O TYR A 354 SHEET 1 AA3 7 LEU A 35 GLU A 38 0 SHEET 2 AA3 7 TYR A 340 LEU A 342 -1 O TYR A 341 N ARG A 37 SHEET 3 AA3 7 SER A 353 THR A 358 -1 O THR A 358 N TYR A 340 SHEET 4 AA3 7 LEU A 364 GLU A 369 -1 O THR A 365 N LEU A 357 SHEET 5 AA3 7 GLU A 446 THR A 451 -1 O LEU A 450 N ILE A 366 SHEET 6 AA3 7 GLU A 406 LYS A 413 -1 N GLN A 408 O THR A 451 SHEET 7 AA3 7 LEU A 421 TRP A 430 -1 O LEU A 426 N VAL A 409 SHEET 1 AA4 9 GLY A 41 SER A 46 0 SHEET 2 AA4 9 ILE A 81 ILE A 86 1 O LYS A 83 N SER A 46 SHEET 3 AA4 9 ILE A 129 PRO A 134 1 O ILE A 129 N LEU A 82 SHEET 4 AA4 9 TYR A 176 ILE A 177 1 O TYR A 176 N GLY A 132 SHEET 5 AA4 9 ARG A 206 ASN A 212 1 O ARG A 206 N ILE A 177 SHEET 6 AA4 9 VAL A 233 HIS A 237 1 O HIS A 237 N ASN A 212 SHEET 7 AA4 9 LYS A 253 PHE A 260 1 O LYS A 253 N ILE A 234 SHEET 8 AA4 9 SER A 287 TRP A 291 1 O TRP A 291 N ASP A 259 SHEET 9 AA4 9 GLY A 41 SER A 46 1 N VAL A 45 O ALA A 290 SHEET 1 AA5 4 ASN A 473 ASP A 476 0 SHEET 2 AA5 4 ALA A 657 ALA A 667 -1 O PHE A 662 N ASP A 476 SHEET 3 AA5 4 PHE A 511 GLN A 515 -1 N LEU A 513 O PHE A 659 SHEET 4 AA5 4 PHE A 498 MET A 502 -1 N GLU A 499 O ARG A 514 SHEET 1 AA6 6 ASN A 473 ASP A 476 0 SHEET 2 AA6 6 ALA A 657 ALA A 667 -1 O PHE A 662 N ASP A 476 SHEET 3 AA6 6 ASN A 542 ILE A 551 -1 N ASN A 542 O ALA A 667 SHEET 4 AA6 6 TYR A 613 LYS A 620 -1 O LEU A 615 N CYS A 547 SHEET 5 AA6 6 PHE A 623 LEU A 628 -1 O PHE A 623 N LYS A 620 SHEET 6 AA6 6 THR A 631 ARG A 638 -1 O LEU A 633 N GLY A 626 SHEET 1 AA7 7 ALA A 492 THR A 495 0 SHEET 2 AA7 7 THR A 531 ILE A 535 -1 O VAL A 534 N ALA A 492 SHEET 3 AA7 7 TRP A 646 THR A 651 -1 O ILE A 649 N SER A 533 SHEET 4 AA7 7 GLY A 558 VAL A 565 -1 N VAL A 565 O TRP A 646 SHEET 5 AA7 7 THR A 576 PHE A 583 -1 O PHE A 580 N ILE A 561 SHEET 6 AA7 7 SER A 587 ASP A 593 -1 O THR A 591 N PHE A 579 SHEET 7 AA7 7 THR A 599 HIS A 604 -1 O TYR A 600 N VAL A 590 SSBOND 1 CYS A 271 CYS A 378 1555 1555 2.03 LINK ND2 ASN A 284 C1 NAG A 701 1555 1555 1.44 LINK ND2 ASN A 363 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN A 387 C1 NAG A 704 1555 1555 1.47 LINK ND2 ASN A 542 C1 NAG C 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 1.45 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.47 LINK O ASP A 477 CA CA A 709 1555 1555 3.04 LINK OD1 ASN A 479 CA CA A 709 1555 1555 2.67 LINK O PHE A 511 CA CA A 709 1555 1555 2.54 LINK OD1 ASP A 660 CA CA A 709 1555 1555 2.67 LINK OD2 ASP A 660 CA CA A 709 1555 1555 2.96 LINK CA CA A 709 O HOH A4005 1555 1555 2.99 LINK CA CA A 709 O HOH A4024 1555 1555 2.63 CISPEP 1 GLY A 48 GLY A 49 0 -0.52 CISPEP 2 GLU A 60 PRO A 61 0 3.42 CISPEP 3 ALA A 209 SER A 210 0 -5.97 CISPEP 4 GLU A 215 PRO A 216 0 10.49 CISPEP 5 TRP A 291 ASN A 292 0 5.34 CISPEP 6 ARG A 380 PRO A 381 0 -8.30 CISPEP 7 TYR A 641 PRO A 642 0 1.03 CRYST1 249.548 249.548 77.456 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 0.004007 0.002314 0.000000 0.00000 SCALE2 0.000000 0.004627 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012911 0.00000