HEADER HYDROLASE 21-APR-09 3H55 TITLE CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE, COMPLEX TITLE 2 WITH GALACTOSE 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, PROTEIN-LIGAND COMPLEX, DISEASE KEYWDS 3 MUTATION, DISULFIDE BOND, HYDROLASE, LYSOSOME EXPDTA X-RAY DIFFRACTION AUTHOR N.E.CLARK,S.C.GARMAN REVDAT 6 06-SEP-23 3H55 1 REMARK REVDAT 5 13-OCT-21 3H55 1 SEQADV HETSYN REVDAT 4 29-JUL-20 3H55 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 01-NOV-17 3H55 1 REMARK REVDAT 2 13-JUL-11 3H55 1 VERSN REVDAT 1 20-OCT-09 3H55 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. 1.91 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 87311 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4397 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5781 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.3790 REMARK 3 BIN FREE R VALUE SET COUNT : 296 REMARK 3 BIN FREE R VALUE : 0.3990 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 : 311 REMARK 3 SOLVENT ATOMS : 896 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 28.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.107 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.351 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6766 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9219 ; 1.084 ; 2.014 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 778 ; 5.584 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 301 ;34.702 ;24.086 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1041 ;13.307 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;17.166 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1024 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5004 ; 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): 3880 ; 2.496 ; 8.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6261 ; 3.547 ;12.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2886 ; 3.256 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2958 ; 4.619 ;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 ; 3.060 ;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 ; 0.250 ; 0.500 REMARK 3 MEDIUM THERMAL 2 B (A**2): 746 ; 2.300 ;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): 56.6082 -1.1315 10.0504 REMARK 3 T TENSOR REMARK 3 T11: 0.0389 T22: 0.0469 REMARK 3 T33: 0.0190 T12: -0.0063 REMARK 3 T13: -0.0173 T23: -0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.5104 L22: 0.1153 REMARK 3 L33: 0.1593 L12: 0.0351 REMARK 3 L13: -0.0546 L23: -0.0501 REMARK 3 S TENSOR REMARK 3 S11: 0.0078 S12: 0.0142 S13: 0.0385 REMARK 3 S21: 0.0154 S22: 0.0145 S23: 0.0112 REMARK 3 S31: 0.0081 S32: 0.0166 S33: -0.0224 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): 25.8363 3.3783 10.8286 REMARK 3 T TENSOR REMARK 3 T11: 0.0395 T22: 0.0370 REMARK 3 T33: 0.1044 T12: 0.0214 REMARK 3 T13: 0.0316 T23: 0.0490 REMARK 3 L TENSOR REMARK 3 L11: 0.7104 L22: 0.5487 REMARK 3 L33: 0.2539 L12: -0.3427 REMARK 3 L13: 0.0061 L23: -0.2262 REMARK 3 S TENSOR REMARK 3 S11: 0.0380 S12: 0.0393 S13: 0.0545 REMARK 3 S21: 0.0804 S22: 0.0773 S23: 0.1473 REMARK 3 S31: -0.0511 S32: -0.0574 S33: -0.1153 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): 21.6007 -31.5941 21.7949 REMARK 3 T TENSOR REMARK 3 T11: 0.0420 T22: 0.0509 REMARK 3 T33: 0.0517 T12: -0.0079 REMARK 3 T13: -0.0114 T23: 0.0423 REMARK 3 L TENSOR REMARK 3 L11: 0.6651 L22: 0.5064 REMARK 3 L33: 0.3566 L12: 0.0888 REMARK 3 L13: -0.2959 L23: -0.3411 REMARK 3 S TENSOR REMARK 3 S11: -0.0465 S12: 0.0243 S13: -0.0286 REMARK 3 S21: 0.0165 S22: 0.1010 S23: 0.1267 REMARK 3 S31: 0.0179 S32: -0.0381 S33: -0.0545 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): 51.3934 -37.2092 16.3471 REMARK 3 T TENSOR REMARK 3 T11: 0.0493 T22: 0.0291 REMARK 3 T33: 0.0791 T12: 0.0248 REMARK 3 T13: 0.0055 T23: 0.0269 REMARK 3 L TENSOR REMARK 3 L11: 1.0505 L22: 0.6173 REMARK 3 L33: 0.3722 L12: 0.1660 REMARK 3 L13: -0.2455 L23: -0.0456 REMARK 3 S TENSOR REMARK 3 S11: -0.0317 S12: -0.0216 S13: -0.1357 REMARK 3 S21: -0.0111 S22: -0.0374 S23: -0.1536 REMARK 3 S31: 0.0698 S32: 0.0900 S33: 0.0691 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 3H55 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_1000052704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-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) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL CUT REMARK 200 OPTICS : TOROIDAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87369 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.69800 REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3H53 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 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 76.93200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.25700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 76.93200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.25700 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: 8150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 71.0 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 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 A 599 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 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 -137.42 48.49 REMARK 500 CYS A 38 44.82 -107.26 REMARK 500 ASP A 78 -148.63 -108.19 REMARK 500 CYS A 80 16.11 82.54 REMARK 500 LYS A 149 34.64 70.85 REMARK 500 ASP A 252 -176.91 95.35 REMARK 500 ASN A 258 -144.59 -99.49 REMARK 500 SER A 283 88.09 -155.22 REMARK 500 ASP A 346 -72.99 -112.53 REMARK 500 SER A 363 -26.31 64.68 REMARK 500 ARG B 37 -136.89 49.61 REMARK 500 CYS B 38 46.56 -107.01 REMARK 500 ASP B 78 -151.50 -109.98 REMARK 500 ASP B 252 -178.18 92.16 REMARK 500 ASN B 258 -139.20 -99.17 REMARK 500 LEU B 280 76.41 -106.95 REMARK 500 SER B 283 85.59 -154.34 REMARK 500 ASP B 346 -70.29 -113.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H53 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE REMARK 900 RELATED ID: 3H54 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE, COMPLEX REMARK 900 WITH GALNAC DBREF 3H55 A 18 411 UNP P17050 NAGAB_HUMAN 18 411 DBREF 3H55 B 18 411 UNP P17050 NAGAB_HUMAN 18 411 SEQADV 3H55 GLN A 201 UNP P17050 ASN 201 ENGINEERED MUTATION SEQADV 3H55 HIS A 412 UNP P17050 EXPRESSION TAG SEQADV 3H55 HIS A 413 UNP P17050 EXPRESSION TAG SEQADV 3H55 HIS A 414 UNP P17050 EXPRESSION TAG SEQADV 3H55 HIS A 415 UNP P17050 EXPRESSION TAG SEQADV 3H55 HIS A 416 UNP P17050 EXPRESSION TAG SEQADV 3H55 HIS A 417 UNP P17050 EXPRESSION TAG SEQADV 3H55 GLN B 201 UNP P17050 ASN 201 ENGINEERED MUTATION SEQADV 3H55 HIS B 412 UNP P17050 EXPRESSION TAG SEQADV 3H55 HIS B 413 UNP P17050 EXPRESSION TAG SEQADV 3H55 HIS B 414 UNP P17050 EXPRESSION TAG SEQADV 3H55 HIS B 415 UNP P17050 EXPRESSION TAG SEQADV 3H55 HIS B 416 UNP P17050 EXPRESSION TAG SEQADV 3H55 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 3H55 ASN A 124 ASN GLYCOSYLATION SITE MODRES 3H55 ASN A 177 ASN GLYCOSYLATION SITE MODRES 3H55 ASN A 385 ASN GLYCOSYLATION SITE MODRES 3H55 ASN B 124 ASN GLYCOSYLATION SITE MODRES 3H55 ASN B 177 ASN GLYCOSYLATION SITE MODRES 3H55 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 NAG A 885 14 HET GLA A1000 12 HET GLA A1500 12 HET CIT A1100 13 HET NAG B 885 14 HET GLA B2000 12 HET GLA B2500 12 HET CIT B2100 13 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 GLA ALPHA-D-GALACTOPYRANOSE HETNAM CIT CITRIC ACID 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 GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE 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 8 GLA 4(C6 H12 O6) FORMUL 10 CIT 2(C6 H8 O7) FORMUL 15 HOH *896(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 TRP A 67 GLY A 71 5 5 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 TRP A 148 1 12 HELIX 7 7 THR A 161 THR A 179 1 19 HELIX 8 8 TRP A 189 GLY A 194 5 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 GLN A 240 1 6 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 TRP B 67 GLY B 71 5 5 HELIX 19 19 GLY B 101 LEU B 112 1 12 HELIX 20 20 LYS B 137 TRP B 148 1 12 HELIX 21 21 THR B 161 THR B 179 1 19 HELIX 22 22 TRP B 189 GLY B 194 5 6 HELIX 23 23 GLN B 201 CYS B 209 1 9 HELIX 24 24 SER B 221 HIS B 235 1 15 HELIX 25 25 HIS B 235 ALA B 243 1 9 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 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 ALA A 120 O ASP A 156 SHEET 6 A 8 TYR A 74 ASN A 76 1 N LEU A 75 O GLY A 117 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 VAL A 396 N PHE A 340 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 GLY B 117 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 2.04 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 1.44 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 1.44 LINK O6 BMA D 3 C1 MAN D 5 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 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 1.48 CISPEP 2 PRO B 197 PRO B 198 0 1.67 CRYST1 153.864 114.514 68.371 90.00 96.17 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 0.006499 0.000000 0.000703 0.00000 SCALE2 0.000000 0.008733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014711 0.00000