HEADER HYDROLASE 21-APR-09 3H53 TITLE CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-N-ACETYLGALACTOSAMINIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALPHA-GALACTOSIDASE B; COMPND 5 EC: 3.2.1.49; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NAGA; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HI-FIVE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: STABLE CELL LINE; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PIB/V5-HIS-TOPO TA KEYWDS GLYCOPROTEIN, CARBOHYDRATE-BINDING PROTEIN, GLYCOSIDASE, LYSOSOMAL KEYWDS 2 ENZYME, (BETA/ALPHA)8 BARREL, DISEASE MUTATION, DISULFIDE BOND, KEYWDS 3 HYDROLASE, LYSOSOME EXPDTA X-RAY DIFFRACTION AUTHOR N.E.CLARK,S.C.GARMAN REVDAT 6 06-SEP-23 3H53 1 REMARK REVDAT 5 13-OCT-21 3H53 1 SEQADV HETSYN REVDAT 4 29-JUL-20 3H53 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 01-NOV-17 3H53 1 REMARK REVDAT 2 13-JUL-11 3H53 1 VERSN REVDAT 1 20-OCT-09 3H53 0 JRNL AUTH N.E.CLARK,S.C.GARMAN JRNL TITL THE 1.9 A STRUCTURE OF HUMAN JRNL TITL 2 ALPHA-N-ACETYLGALACTOSAMINIDASE: THE MOLECULAR BASIS OF JRNL TITL 3 SCHINDLER AND KANZAKI DISEASES JRNL REF J.MOL.BIOL. V. 393 435 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19683538 JRNL DOI 10.1016/J.JMB.2009.08.021 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 77775 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3916 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5069 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 290 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6162 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 339 REMARK 3 SOLVENT ATOMS : 735 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 39.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.78000 REMARK 3 B22 (A**2) : -1.85000 REMARK 3 B33 (A**2) : 1.84000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.62000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.730 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6714 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9137 ; 1.048 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 778 ; 5.598 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 301 ;34.706 ;24.086 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1041 ;13.364 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;18.136 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1002 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4980 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3876 ; 2.079 ; 8.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6251 ; 2.952 ;12.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2838 ; 2.947 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2886 ; 4.299 ;12.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 18 A 310 4 REMARK 3 1 B 18 B 310 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 2305 ; 0.170 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2305 ; 2.130 ;10.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 311 A 404 4 REMARK 3 1 B 311 B 404 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 B (A): 746 ; 0.240 ; 0.500 REMARK 3 MEDIUM THERMAL 2 B (A**2): 746 ; 2.210 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 18 A 310 REMARK 3 ORIGIN FOR THE GROUP (A): 56.4433 -1.1442 9.9794 REMARK 3 T TENSOR REMARK 3 T11: 0.0377 T22: 0.0152 REMARK 3 T33: 0.0322 T12: -0.0033 REMARK 3 T13: 0.0185 T23: -0.0109 REMARK 3 L TENSOR REMARK 3 L11: 0.9469 L22: 0.5494 REMARK 3 L33: 0.3716 L12: 0.1692 REMARK 3 L13: -0.2415 L23: -0.1431 REMARK 3 S TENSOR REMARK 3 S11: 0.0497 S12: -0.0038 S13: 0.1092 REMARK 3 S21: 0.0251 S22: 0.0250 S23: -0.0338 REMARK 3 S31: -0.0385 S32: 0.0351 S33: -0.0748 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 311 A 404 REMARK 3 ORIGIN FOR THE GROUP (A): 25.7723 3.3886 10.8318 REMARK 3 T TENSOR REMARK 3 T11: 0.0473 T22: 0.0643 REMARK 3 T33: 0.1772 T12: 0.0380 REMARK 3 T13: 0.0603 T23: 0.0952 REMARK 3 L TENSOR REMARK 3 L11: 1.1474 L22: 0.9985 REMARK 3 L33: 0.4047 L12: -0.1637 REMARK 3 L13: -0.0528 L23: -0.3138 REMARK 3 S TENSOR REMARK 3 S11: 0.0699 S12: 0.1082 S13: 0.2139 REMARK 3 S21: 0.0593 S22: 0.1298 S23: 0.3061 REMARK 3 S31: -0.1077 S32: -0.1483 S33: -0.1997 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 18 B 310 REMARK 3 ORIGIN FOR THE GROUP (A): 21.7222 -31.5967 21.6606 REMARK 3 T TENSOR REMARK 3 T11: 0.0455 T22: 0.0372 REMARK 3 T33: 0.0960 T12: -0.0053 REMARK 3 T13: 0.0163 T23: 0.0469 REMARK 3 L TENSOR REMARK 3 L11: 1.0388 L22: 1.0530 REMARK 3 L33: 0.5144 L12: 0.3481 REMARK 3 L13: -0.4573 L23: -0.4317 REMARK 3 S TENSOR REMARK 3 S11: -0.0720 S12: 0.0858 S13: -0.0357 REMARK 3 S21: 0.0516 S22: 0.1612 S23: 0.2710 REMARK 3 S31: 0.0448 S32: -0.0846 S33: -0.0892 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 311 B 404 REMARK 3 ORIGIN FOR THE GROUP (A): 51.1721 -37.1320 16.1906 REMARK 3 T TENSOR REMARK 3 T11: 0.0566 T22: 0.0319 REMARK 3 T33: 0.1230 T12: 0.0368 REMARK 3 T13: 0.0285 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 1.2526 L22: 1.1062 REMARK 3 L33: 0.6482 L12: 0.3092 REMARK 3 L13: -0.3859 L23: -0.2683 REMARK 3 S TENSOR REMARK 3 S11: -0.1074 S12: -0.0439 S13: -0.3085 REMARK 3 S21: -0.0265 S22: -0.0297 S23: -0.2603 REMARK 3 S31: 0.1650 S32: 0.1351 S33: 0.1371 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 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 3H53 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052702. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : OSMIC BLUE REMARK 200 OPTICS : OSMIC BLUE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77785 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 29.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.61000 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1KTB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, CITRIC ACID, BIS-TRIS REMARK 280 PROPANE, PH 4.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 76.76600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 76.76600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.13000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 ASN A 405 REMARK 465 LEU A 406 REMARK 465 GLU A 407 REMARK 465 MET A 408 REMARK 465 SER A 409 REMARK 465 GLN A 410 REMARK 465 GLN A 411 REMARK 465 HIS A 412 REMARK 465 HIS A 413 REMARK 465 HIS A 414 REMARK 465 HIS A 415 REMARK 465 HIS A 416 REMARK 465 HIS A 417 REMARK 465 ASN B 405 REMARK 465 LEU B 406 REMARK 465 GLU B 407 REMARK 465 MET B 408 REMARK 465 SER B 409 REMARK 465 GLN B 410 REMARK 465 GLN B 411 REMARK 465 HIS B 412 REMARK 465 HIS B 413 REMARK 465 HIS B 414 REMARK 465 HIS B 415 REMARK 465 HIS B 416 REMARK 465 HIS B 417 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 ARG A 37 -135.79 51.70 REMARK 500 ASP A 78 -148.62 -112.68 REMARK 500 LYS A 149 33.71 73.23 REMARK 500 ASP A 252 -176.52 92.56 REMARK 500 ASN A 258 -144.02 -99.43 REMARK 500 LEU A 280 77.63 -102.71 REMARK 500 SER A 283 87.46 -157.29 REMARK 500 ASP A 346 -71.19 -112.58 REMARK 500 SER A 363 -20.73 65.60 REMARK 500 ARG B 37 -134.84 51.52 REMARK 500 CYS B 38 41.48 -107.41 REMARK 500 ASP B 78 -150.00 -110.50 REMARK 500 ASP B 252 -177.52 91.17 REMARK 500 ASN B 258 -139.68 -99.77 REMARK 500 LEU B 280 76.65 -106.96 REMARK 500 SER B 283 86.47 -150.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H54 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE, COMPLEX REMARK 900 WITH GALNAC REMARK 900 RELATED ID: 3H55 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE, COMPLEX REMARK 900 WITH GALACTOSE DBREF 3H53 A 18 411 UNP P17050 NAGAB_HUMAN 18 411 DBREF 3H53 B 18 411 UNP P17050 NAGAB_HUMAN 18 411 SEQADV 3H53 GLN A 201 UNP P17050 ASN 201 ENGINEERED MUTATION SEQADV 3H53 HIS A 412 UNP P17050 EXPRESSION TAG SEQADV 3H53 HIS A 413 UNP P17050 EXPRESSION TAG SEQADV 3H53 HIS A 414 UNP P17050 EXPRESSION TAG SEQADV 3H53 HIS A 415 UNP P17050 EXPRESSION TAG SEQADV 3H53 HIS A 416 UNP P17050 EXPRESSION TAG SEQADV 3H53 HIS A 417 UNP P17050 EXPRESSION TAG SEQADV 3H53 GLN B 201 UNP P17050 ASN 201 ENGINEERED MUTATION SEQADV 3H53 HIS B 412 UNP P17050 EXPRESSION TAG SEQADV 3H53 HIS B 413 UNP P17050 EXPRESSION TAG SEQADV 3H53 HIS B 414 UNP P17050 EXPRESSION TAG SEQADV 3H53 HIS B 415 UNP P17050 EXPRESSION TAG SEQADV 3H53 HIS B 416 UNP P17050 EXPRESSION TAG SEQADV 3H53 HIS B 417 UNP P17050 EXPRESSION TAG SEQRES 1 A 400 LEU ASP ASN GLY LEU LEU GLN THR PRO PRO MET GLY TRP SEQRES 2 A 400 LEU ALA TRP GLU ARG PHE ARG CYS ASN ILE ASN CYS ASP SEQRES 3 A 400 GLU ASP PRO LYS ASN CYS ILE SER GLU GLN LEU PHE MET SEQRES 4 A 400 GLU MET ALA ASP ARG MET ALA GLN ASP GLY TRP ARG ASP SEQRES 5 A 400 MET GLY TYR THR TYR LEU ASN ILE ASP ASP CYS TRP ILE SEQRES 6 A 400 GLY GLY ARG ASP ALA SER GLY ARG LEU MET PRO ASP PRO SEQRES 7 A 400 LYS ARG PHE PRO HIS GLY ILE PRO PHE LEU ALA ASP TYR SEQRES 8 A 400 VAL HIS SER LEU GLY LEU LYS LEU GLY ILE TYR ALA ASP SEQRES 9 A 400 MET GLY ASN PHE THR CYS MET GLY TYR PRO GLY THR THR SEQRES 10 A 400 LEU ASP LYS VAL VAL GLN ASP ALA GLN THR PHE ALA GLU SEQRES 11 A 400 TRP LYS VAL ASP MET LEU LYS LEU ASP GLY CYS PHE SER SEQRES 12 A 400 THR PRO GLU GLU ARG ALA GLN GLY TYR PRO LYS MET ALA SEQRES 13 A 400 ALA ALA LEU ASN ALA THR GLY ARG PRO ILE ALA PHE SER SEQRES 14 A 400 CYS SER TRP PRO ALA TYR GLU GLY GLY LEU PRO PRO ARG SEQRES 15 A 400 VAL GLN TYR SER LEU LEU ALA ASP ILE CYS ASN LEU TRP SEQRES 16 A 400 ARG ASN TYR ASP ASP ILE GLN ASP SER TRP TRP SER VAL SEQRES 17 A 400 LEU SER ILE LEU ASN TRP PHE VAL GLU HIS GLN ASP ILE SEQRES 18 A 400 LEU GLN PRO VAL ALA GLY PRO GLY HIS TRP ASN ASP PRO SEQRES 19 A 400 ASP MET LEU LEU ILE GLY ASN PHE GLY LEU SER LEU GLU SEQRES 20 A 400 GLN SER ARG ALA GLN MET ALA LEU TRP THR VAL LEU ALA SEQRES 21 A 400 ALA PRO LEU LEU MET SER THR ASP LEU ARG THR ILE SER SEQRES 22 A 400 ALA GLN ASN MET ASP ILE LEU GLN ASN PRO LEU MET ILE SEQRES 23 A 400 LYS ILE ASN GLN ASP PRO LEU GLY ILE GLN GLY ARG ARG SEQRES 24 A 400 ILE HIS LYS GLU LYS SER LEU ILE GLU VAL TYR MET ARG SEQRES 25 A 400 PRO LEU SER ASN LYS ALA SER ALA LEU VAL PHE PHE SER SEQRES 26 A 400 CYS ARG THR ASP MET PRO TYR ARG TYR HIS SER SER LEU SEQRES 27 A 400 GLY GLN LEU ASN PHE THR GLY SER VAL ILE TYR GLU ALA SEQRES 28 A 400 GLN ASP VAL TYR SER GLY ASP ILE ILE SER GLY LEU ARG SEQRES 29 A 400 ASP GLU THR ASN PHE THR VAL ILE ILE ASN PRO SER GLY SEQRES 30 A 400 VAL VAL MET TRP TYR LEU TYR PRO ILE LYS ASN LEU GLU SEQRES 31 A 400 MET SER GLN GLN HIS HIS HIS HIS HIS HIS SEQRES 1 B 400 LEU ASP ASN GLY LEU LEU GLN THR PRO PRO MET GLY TRP SEQRES 2 B 400 LEU ALA TRP GLU ARG PHE ARG CYS ASN ILE ASN CYS ASP SEQRES 3 B 400 GLU ASP PRO LYS ASN CYS ILE SER GLU GLN LEU PHE MET SEQRES 4 B 400 GLU MET ALA ASP ARG MET ALA GLN ASP GLY TRP ARG ASP SEQRES 5 B 400 MET GLY TYR THR TYR LEU ASN ILE ASP ASP CYS TRP ILE SEQRES 6 B 400 GLY GLY ARG ASP ALA SER GLY ARG LEU MET PRO ASP PRO SEQRES 7 B 400 LYS ARG PHE PRO HIS GLY ILE PRO PHE LEU ALA ASP TYR SEQRES 8 B 400 VAL HIS SER LEU GLY LEU LYS LEU GLY ILE TYR ALA ASP SEQRES 9 B 400 MET GLY ASN PHE THR CYS MET GLY TYR PRO GLY THR THR SEQRES 10 B 400 LEU ASP LYS VAL VAL GLN ASP ALA GLN THR PHE ALA GLU SEQRES 11 B 400 TRP LYS VAL ASP MET LEU LYS LEU ASP GLY CYS PHE SER SEQRES 12 B 400 THR PRO GLU GLU ARG ALA GLN GLY TYR PRO LYS MET ALA SEQRES 13 B 400 ALA ALA LEU ASN ALA THR GLY ARG PRO ILE ALA PHE SER SEQRES 14 B 400 CYS SER TRP PRO ALA TYR GLU GLY GLY LEU PRO PRO ARG SEQRES 15 B 400 VAL GLN TYR SER LEU LEU ALA ASP ILE CYS ASN LEU TRP SEQRES 16 B 400 ARG ASN TYR ASP ASP ILE GLN ASP SER TRP TRP SER VAL SEQRES 17 B 400 LEU SER ILE LEU ASN TRP PHE VAL GLU HIS GLN ASP ILE SEQRES 18 B 400 LEU GLN PRO VAL ALA GLY PRO GLY HIS TRP ASN ASP PRO SEQRES 19 B 400 ASP MET LEU LEU ILE GLY ASN PHE GLY LEU SER LEU GLU SEQRES 20 B 400 GLN SER ARG ALA GLN MET ALA LEU TRP THR VAL LEU ALA SEQRES 21 B 400 ALA PRO LEU LEU MET SER THR ASP LEU ARG THR ILE SER SEQRES 22 B 400 ALA GLN ASN MET ASP ILE LEU GLN ASN PRO LEU MET ILE SEQRES 23 B 400 LYS ILE ASN GLN ASP PRO LEU GLY ILE GLN GLY ARG ARG SEQRES 24 B 400 ILE HIS LYS GLU LYS SER LEU ILE GLU VAL TYR MET ARG SEQRES 25 B 400 PRO LEU SER ASN LYS ALA SER ALA LEU VAL PHE PHE SER SEQRES 26 B 400 CYS ARG THR ASP MET PRO TYR ARG TYR HIS SER SER LEU SEQRES 27 B 400 GLY GLN LEU ASN PHE THR GLY SER VAL ILE TYR GLU ALA SEQRES 28 B 400 GLN ASP VAL TYR SER GLY ASP ILE ILE SER GLY LEU ARG SEQRES 29 B 400 ASP GLU THR ASN PHE THR VAL ILE ILE ASN PRO SER GLY SEQRES 30 B 400 VAL VAL MET TRP TYR LEU TYR PRO ILE LYS ASN LEU GLU SEQRES 31 B 400 MET SER GLN GLN HIS HIS HIS HIS HIS HIS MODRES 3H53 ASN A 124 ASN GLYCOSYLATION SITE MODRES 3H53 ASN A 177 ASN GLYCOSYLATION SITE MODRES 3H53 ASN A 385 ASN GLYCOSYLATION SITE MODRES 3H53 ASN B 124 ASN GLYCOSYLATION SITE MODRES 3H53 ASN B 177 ASN GLYCOSYLATION SITE MODRES 3H53 ASN B 385 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET FUC C 4 10 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET MAN D 4 11 HET MAN D 5 11 HET NAG E 1 14 HET NAG E 2 14 HET FUC E 3 10 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET MAN F 4 11 HET MAN F 5 11 HET GOL A1024 6 HET GOL A1039 6 HET GOL A1108 6 HET GOL A1113 6 HET GOL A1165 6 HET GOL A1200 6 HET GOL A1201 6 HET GOL A1328 6 HET GOL A1030 6 HET GOL A1210 6 HET NAG A 885 14 HET GOL A1001 6 HET GOL B1024 6 HET GOL B1108 6 HET GOL B1113 6 HET GOL B1200 6 HET GOL B1328 6 HET NAG B 885 14 HET GOL B1001 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM GOL GLYCEROL 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 FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAG 10(C8 H15 N O6) FORMUL 3 BMA 3(C6 H12 O6) FORMUL 3 FUC 2(C6 H12 O5) FORMUL 4 MAN 4(C6 H12 O6) FORMUL 7 GOL 17(C3 H8 O3) FORMUL 26 HOH *735(H2 O) HELIX 1 1 ALA A 32 ARG A 37 1 6 HELIX 2 2 SER A 51 ASP A 65 1 15 HELIX 3 3 GLY A 66 GLY A 71 1 6 HELIX 4 4 GLY A 101 LEU A 112 1 12 HELIX 5 5 THR A 134 ASP A 136 5 3 HELIX 6 6 LYS A 137 LYS A 149 1 13 HELIX 7 7 THR A 161 THR A 179 1 19 HELIX 8 8 SER A 188 GLU A 193 1 6 HELIX 9 9 GLN A 201 CYS A 209 1 9 HELIX 10 10 SER A 221 HIS A 235 1 15 HELIX 11 11 HIS A 235 ALA A 243 1 9 HELIX 12 12 SER A 262 LEU A 276 1 15 HELIX 13 13 SER A 290 GLN A 298 1 9 HELIX 14 14 ASN A 299 GLN A 307 1 9 HELIX 15 15 GLY A 356 ASN A 359 5 4 HELIX 16 16 ALA B 32 ARG B 37 1 6 HELIX 17 17 SER B 51 ASP B 65 1 15 HELIX 18 18 GLY B 101 LEU B 112 1 12 HELIX 19 19 LYS B 137 TRP B 148 1 12 HELIX 20 20 THR B 161 GLY B 180 1 20 HELIX 21 21 SER B 188 GLU B 193 1 6 HELIX 22 22 GLN B 201 CYS B 209 1 9 HELIX 23 23 SER B 221 HIS B 235 1 15 HELIX 24 24 HIS B 235 GLN B 240 1 6 HELIX 25 25 PRO B 241 ALA B 243 5 3 HELIX 26 26 SER B 262 LEU B 276 1 15 HELIX 27 27 SER B 290 GLN B 298 1 9 HELIX 28 28 ASN B 299 GLN B 307 1 9 HELIX 29 29 SER B 354 ASN B 359 5 6 SHEET 1 A 8 TRP A 248 ASP A 250 0 SHEET 2 A 8 LEU A 211 ARG A 213 1 N TRP A 212 O ASP A 250 SHEET 3 A 8 ALA A 184 CYS A 187 1 N CYS A 187 O LEU A 211 SHEET 4 A 8 MET A 152 ASP A 156 1 N LEU A 153 O SER A 186 SHEET 5 A 8 LYS A 115 ASP A 121 1 N ILE A 118 O MET A 152 SHEET 6 A 8 TYR A 74 ASN A 76 1 N LEU A 75 O LYS A 115 SHEET 7 A 8 MET A 28 LEU A 31 1 N TRP A 30 O ASN A 76 SHEET 8 A 8 LEU A 280 MET A 282 1 O MET A 282 N LEU A 31 SHEET 1 B 2 ILE A 82 ARG A 85 0 SHEET 2 B 2 LEU A 91 PRO A 93 -1 O MET A 92 N GLY A 83 SHEET 1 C 6 ARG A 315 LYS A 319 0 SHEET 2 C 6 ILE A 324 PRO A 330 -1 O VAL A 326 N ILE A 317 SHEET 3 C 6 SER A 336 SER A 342 -1 O PHE A 341 N GLU A 325 SHEET 4 C 6 VAL A 395 PRO A 402 -1 O LEU A 400 N SER A 336 SHEET 5 C 6 TYR A 366 ASP A 370 -1 N GLN A 369 O TYR A 399 SHEET 6 C 6 ILE A 376 LEU A 380 -1 O ILE A 377 N ALA A 368 SHEET 1 D 2 TYR A 349 SER A 354 0 SHEET 2 D 2 ASN A 385 ILE A 390 -1 O VAL A 388 N TYR A 351 SHEET 1 E 8 TRP B 248 ASP B 250 0 SHEET 2 E 8 LEU B 211 ARG B 213 1 N TRP B 212 O ASP B 250 SHEET 3 E 8 ALA B 184 CYS B 187 1 N CYS B 187 O LEU B 211 SHEET 4 E 8 MET B 152 ASP B 156 1 N LEU B 153 O SER B 186 SHEET 5 E 8 LYS B 115 ASP B 121 1 N ALA B 120 O ASP B 156 SHEET 6 E 8 TYR B 74 ASN B 76 1 N LEU B 75 O LYS B 115 SHEET 7 E 8 MET B 28 LEU B 31 1 N TRP B 30 O ASN B 76 SHEET 8 E 8 LEU B 280 MET B 282 1 O MET B 282 N LEU B 31 SHEET 1 F 2 ILE B 82 ARG B 85 0 SHEET 2 F 2 LEU B 91 PRO B 93 -1 O MET B 92 N GLY B 83 SHEET 1 G 6 ARG B 315 LYS B 319 0 SHEET 2 G 6 ILE B 324 PRO B 330 -1 O MET B 328 N ARG B 315 SHEET 3 G 6 SER B 336 SER B 342 -1 O PHE B 341 N GLU B 325 SHEET 4 G 6 VAL B 395 PRO B 402 -1 O VAL B 396 N PHE B 340 SHEET 5 G 6 TYR B 366 ASP B 370 -1 N GLU B 367 O TYR B 401 SHEET 6 G 6 ILE B 376 LEU B 380 -1 O LEU B 380 N TYR B 366 SHEET 1 H 2 TYR B 349 SER B 353 0 SHEET 2 H 2 PHE B 386 ILE B 390 -1 O VAL B 388 N TYR B 351 SSBOND 1 CYS A 38 CYS A 80 1555 1555 2.04 SSBOND 2 CYS A 42 CYS A 49 1555 1555 2.04 SSBOND 3 CYS A 127 CYS A 158 1555 1555 2.04 SSBOND 4 CYS A 187 CYS A 209 1555 1555 2.04 SSBOND 5 CYS B 38 CYS B 80 1555 1555 2.03 SSBOND 6 CYS B 42 CYS B 49 1555 1555 2.04 SSBOND 7 CYS B 127 CYS B 158 1555 1555 2.04 SSBOND 8 CYS B 187 CYS B 209 1555 1555 2.04 LINK ND2 ASN A 124 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 177 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN A 385 C1 NAG A 885 1555 1555 1.45 LINK ND2 ASN B 124 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN B 177 C1 NAG F 1 1555 1555 1.44 LINK ND2 ASN B 385 C1 NAG B 885 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O6 NAG C 1 C1 FUC C 4 1555 1555 1.45 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.44 LINK O3 BMA D 3 C1 MAN D 4 1555 1555 1.45 LINK O6 BMA D 3 C1 MAN D 5 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 LINK O6 NAG E 1 C1 FUC E 3 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.44 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.44 LINK O3 BMA F 3 C1 MAN F 4 1555 1555 1.45 LINK O6 BMA F 3 C1 MAN F 5 1555 1555 1.44 CISPEP 1 PRO A 197 PRO A 198 0 1.87 CISPEP 2 PRO B 197 PRO B 198 0 1.80 CRYST1 153.532 114.260 68.408 90.00 96.11 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006513 0.000000 0.000697 0.00000 SCALE2 0.000000 0.008752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014702 0.00000