HEADER HYDROLASE 13-MAY-09 3HG3 TITLE HUMAN ALPHA-GALACTOSIDASE CATALYTIC MECHANISM 2. SUBSTRATE BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALPHA-D-GALACTOSIDE GALACTOHYDROLASE, ALPHA-D-GALACTOSIDASE COMPND 5 A, MELIBIASE; COMPND 6 EC: 3.2.1.22; COMPND 7 ENGINEERED: YES; COMPND 8 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: GLA; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HI-FIVE; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: STABLE CELL LINE; SOURCE 11 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 A.I.GUCE,N.E.CLARK,S.C.GARMAN REVDAT 7 03-APR-24 3HG3 1 REMARK REVDAT 6 13-OCT-21 3HG3 1 SEQADV HETSYN REVDAT 5 29-JUL-20 3HG3 1 COMPND REMARK SEQADV HETNAM REVDAT 5 2 1 LINK SITE ATOM REVDAT 4 01-NOV-17 3HG3 1 REMARK REVDAT 3 13-JUL-11 3HG3 1 VERSN REVDAT 2 23-FEB-10 3HG3 1 JRNL REVDAT 1 24-NOV-09 3HG3 0 JRNL AUTH A.I.GUCE,N.E.CLARK,E.N.SALGADO,D.R.IVANEN,A.A.KULMINSKAYA, JRNL AUTH 2 H.BRUMER,S.C.GARMAN JRNL TITL CATALYTIC MECHANISM OF HUMAN ALPHA-GALACTOSIDASE. JRNL REF J.BIOL.CHEM. V. 285 3625 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 19940122 JRNL DOI 10.1074/JBC.M109.060145 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 90229 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4521 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5373 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 281 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6309 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 269 REMARK 3 SOLVENT ATOMS : 893 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 37.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.21000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.142 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6846 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9308 ; 1.058 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 795 ; 5.598 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 325 ;36.574 ;24.277 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1085 ;13.050 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;10.362 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1001 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5138 ; 0.003 ; 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): 3953 ; 1.904 ; 8.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6352 ; 2.872 ;12.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2893 ; 2.888 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2955 ; 4.304 ;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 32 A 328 4 REMARK 3 1 B 32 B 328 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 2339 ; 0.430 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2339 ; 1.400 ;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 329 A 421 4 REMARK 3 1 B 329 B 421 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 B (A): 733 ; 0.330 ; 0.500 REMARK 3 MEDIUM THERMAL 2 B (A**2): 733 ; 1.540 ;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 32 A 328 REMARK 3 ORIGIN FOR THE GROUP (A): 7.3790 -4.2200 20.0630 REMARK 3 T TENSOR REMARK 3 T11: 0.0335 T22: 0.0499 REMARK 3 T33: 0.0344 T12: 0.0188 REMARK 3 T13: -0.0240 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 0.9245 L22: 0.9217 REMARK 3 L33: 2.7376 L12: 0.0517 REMARK 3 L13: -0.0708 L23: -0.3037 REMARK 3 S TENSOR REMARK 3 S11: 0.0469 S12: 0.1468 S13: 0.0156 REMARK 3 S21: -0.1259 S22: -0.0151 S23: 0.0436 REMARK 3 S31: 0.0688 S32: 0.1043 S33: -0.0318 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 329 A 421 REMARK 3 ORIGIN FOR THE GROUP (A): -0.8010 -17.5660 46.5550 REMARK 3 T TENSOR REMARK 3 T11: 0.1853 T22: 0.0972 REMARK 3 T33: 0.0907 T12: -0.0763 REMARK 3 T13: -0.0077 T23: 0.0316 REMARK 3 L TENSOR REMARK 3 L11: 2.2219 L22: 2.1894 REMARK 3 L33: 2.5794 L12: 1.2079 REMARK 3 L13: 1.0868 L23: 0.7333 REMARK 3 S TENSOR REMARK 3 S11: 0.2350 S12: -0.2720 S13: -0.1905 REMARK 3 S21: 0.3016 S22: -0.1608 S23: 0.1360 REMARK 3 S31: 0.5709 S32: -0.2825 S33: -0.0741 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 32 B 328 REMARK 3 ORIGIN FOR THE GROUP (A): 21.9590 5.3720 64.7190 REMARK 3 T TENSOR REMARK 3 T11: 0.0750 T22: 0.0525 REMARK 3 T33: 0.0505 T12: 0.0418 REMARK 3 T13: -0.0432 T23: -0.0301 REMARK 3 L TENSOR REMARK 3 L11: 1.2990 L22: 0.7422 REMARK 3 L33: 2.4838 L12: 0.0121 REMARK 3 L13: -0.3505 L23: -0.2515 REMARK 3 S TENSOR REMARK 3 S11: -0.0270 S12: -0.1626 S13: 0.0931 REMARK 3 S21: 0.1676 S22: 0.0795 S23: -0.0419 REMARK 3 S31: -0.0598 S32: -0.1571 S33: -0.0525 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 329 B 421 REMARK 3 ORIGIN FOR THE GROUP (A): 35.5280 12.2650 37.9170 REMARK 3 T TENSOR REMARK 3 T11: 0.0592 T22: 0.0601 REMARK 3 T33: 0.1194 T12: -0.0121 REMARK 3 T13: -0.0192 T23: 0.0175 REMARK 3 L TENSOR REMARK 3 L11: 2.8540 L22: 1.3348 REMARK 3 L33: 1.5447 L12: 0.8655 REMARK 3 L13: -0.4487 L23: -0.0660 REMARK 3 S TENSOR REMARK 3 S11: -0.0239 S12: 0.3223 S13: 0.1977 REMARK 3 S21: -0.0696 S22: 0.0647 S23: -0.1454 REMARK 3 S31: -0.1665 S32: 0.0809 S33: -0.0408 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 3HG3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000053090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0085 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90308 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 30.1670 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 (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : 0.75500 REMARK 200 R SYM FOR SHELL (I) : 0.75500 REMARK 200 FOR SHELL : 3.100 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: HUMAN ALPHA-GALACTOSIDASE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, MAGNESIUM ACETATE, SODIUM REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.77400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 90.86050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.05300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 90.86050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.77400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.05300 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G 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 ASP A 427 REMARK 465 LEU A 428 REMARK 465 LEU A 429 REMARK 465 HIS A 430 REMARK 465 HIS A 431 REMARK 465 HIS A 432 REMARK 465 HIS A 433 REMARK 465 HIS A 434 REMARK 465 HIS A 435 REMARK 465 LYS B 426 REMARK 465 ASP B 427 REMARK 465 LEU B 428 REMARK 465 LEU B 429 REMARK 465 HIS B 430 REMARK 465 HIS B 431 REMARK 465 HIS B 432 REMARK 465 HIS B 433 REMARK 465 HIS B 434 REMARK 465 HIS B 435 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 MET A 51 -135.14 57.49 REMARK 500 CYS A 52 51.69 -112.78 REMARK 500 ASP A 92 -153.99 -98.84 REMARK 500 CYS A 94 32.48 76.53 REMARK 500 ASP A 266 -178.41 85.15 REMARK 500 ASN A 272 -129.01 -102.60 REMARK 500 GLU A 358 43.83 -98.49 REMARK 500 LYS A 374 17.42 58.03 REMARK 500 MET B 51 -137.57 55.82 REMARK 500 CYS B 52 51.23 -110.93 REMARK 500 ASP B 92 -151.98 -98.96 REMARK 500 ASP B 266 -177.64 87.93 REMARK 500 ASN B 272 -129.33 -100.58 REMARK 500 GLU B 358 41.19 -99.73 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 2PE A 821 REMARK 610 2PE A 822 REMARK 610 2PE A 823 REMARK 610 2PE A 824 REMARK 610 2PE A 825 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HG2 RELATED DB: PDB REMARK 900 HUMAN ALPHA-GALACTOSIDASE MECHANISM 1. EMPTY ACTIVE SITE REMARK 900 RELATED ID: 3HG4 RELATED DB: PDB REMARK 900 HUMAN ALPHA-GALACTOSIDASE MECHANISM 3. COVALENT INTERMEDIATE REMARK 900 RELATED ID: 3HG5 RELATED DB: PDB REMARK 900 HUMAN ALPHA-GALACTOSIDASE MECHANISM 4. PRODUCT BOUND REMARK 900 RELATED ID: 1R46 RELATED DB: PDB REMARK 900 RELATED ID: 1R47 RELATED DB: PDB DBREF 3HG3 A 32 429 UNP P06280 AGAL_HUMAN 32 429 DBREF 3HG3 B 32 429 UNP P06280 AGAL_HUMAN 32 429 SEQADV 3HG3 ALA A 170 UNP P06280 ASP 170 ENGINEERED MUTATION SEQADV 3HG3 HIS A 430 UNP P06280 EXPRESSION TAG SEQADV 3HG3 HIS A 431 UNP P06280 EXPRESSION TAG SEQADV 3HG3 HIS A 432 UNP P06280 EXPRESSION TAG SEQADV 3HG3 HIS A 433 UNP P06280 EXPRESSION TAG SEQADV 3HG3 HIS A 434 UNP P06280 EXPRESSION TAG SEQADV 3HG3 HIS A 435 UNP P06280 EXPRESSION TAG SEQADV 3HG3 ALA B 170 UNP P06280 ASP 170 ENGINEERED MUTATION SEQADV 3HG3 HIS B 430 UNP P06280 EXPRESSION TAG SEQADV 3HG3 HIS B 431 UNP P06280 EXPRESSION TAG SEQADV 3HG3 HIS B 432 UNP P06280 EXPRESSION TAG SEQADV 3HG3 HIS B 433 UNP P06280 EXPRESSION TAG SEQADV 3HG3 HIS B 434 UNP P06280 EXPRESSION TAG SEQADV 3HG3 HIS B 435 UNP P06280 EXPRESSION TAG SEQRES 1 A 404 LEU ASP ASN GLY LEU ALA ARG THR PRO THR MET GLY TRP SEQRES 2 A 404 LEU HIS TRP GLU ARG PHE MET CYS ASN LEU ASP CYS GLN SEQRES 3 A 404 GLU GLU PRO ASP SER CYS ILE SER GLU LYS LEU PHE MET SEQRES 4 A 404 GLU MET ALA GLU LEU MET VAL SER GLU GLY TRP LYS ASP SEQRES 5 A 404 ALA GLY TYR GLU TYR LEU CYS ILE ASP ASP CYS TRP MET SEQRES 6 A 404 ALA PRO GLN ARG ASP SER GLU GLY ARG LEU GLN ALA ASP SEQRES 7 A 404 PRO GLN ARG PHE PRO HIS GLY ILE ARG GLN LEU ALA ASN SEQRES 8 A 404 TYR VAL HIS SER LYS GLY LEU LYS LEU GLY ILE TYR ALA SEQRES 9 A 404 ASP VAL GLY ASN LYS THR CYS ALA GLY PHE PRO GLY SER SEQRES 10 A 404 PHE GLY TYR TYR ASP ILE ASP ALA GLN THR PHE ALA ASP SEQRES 11 A 404 TRP GLY VAL ASP LEU LEU LYS PHE ALA GLY CYS TYR CYS SEQRES 12 A 404 ASP SER LEU GLU ASN LEU ALA ASP GLY TYR LYS HIS MET SEQRES 13 A 404 SER LEU ALA LEU ASN ARG THR GLY ARG SER ILE VAL TYR SEQRES 14 A 404 SER CYS GLU TRP PRO LEU TYR MET TRP PRO PHE GLN LYS SEQRES 15 A 404 PRO ASN TYR THR GLU ILE ARG GLN TYR CYS ASN HIS TRP SEQRES 16 A 404 ARG ASN PHE ALA ASP ILE ASP ASP SER TRP LYS SER ILE SEQRES 17 A 404 LYS SER ILE LEU ASP TRP THR SER PHE ASN GLN GLU ARG SEQRES 18 A 404 ILE VAL ASP VAL ALA GLY PRO GLY GLY TRP ASN ASP PRO SEQRES 19 A 404 ASP MET LEU VAL ILE GLY ASN PHE GLY LEU SER TRP ASN SEQRES 20 A 404 GLN GLN VAL THR GLN MET ALA LEU TRP ALA ILE MET ALA SEQRES 21 A 404 ALA PRO LEU PHE MET SER ASN ASP LEU ARG HIS ILE SER SEQRES 22 A 404 PRO GLN ALA LYS ALA LEU LEU GLN ASP LYS ASP VAL ILE SEQRES 23 A 404 ALA ILE ASN GLN ASP PRO LEU GLY LYS GLN GLY TYR GLN SEQRES 24 A 404 LEU ARG GLN GLY ASP ASN PHE GLU VAL TRP GLU ARG PRO SEQRES 25 A 404 LEU SER GLY LEU ALA TRP ALA VAL ALA MET ILE ASN ARG SEQRES 26 A 404 GLN GLU ILE GLY GLY PRO ARG SER TYR THR ILE ALA VAL SEQRES 27 A 404 ALA SER LEU GLY LYS GLY VAL ALA CYS ASN PRO ALA CYS SEQRES 28 A 404 PHE ILE THR GLN LEU LEU PRO VAL LYS ARG LYS LEU GLY SEQRES 29 A 404 PHE TYR GLU TRP THR SER ARG LEU ARG SER HIS ILE ASN SEQRES 30 A 404 PRO THR GLY THR VAL LEU LEU GLN LEU GLU ASN THR MET SEQRES 31 A 404 GLN MET SER LEU LYS ASP LEU LEU HIS HIS HIS HIS HIS SEQRES 32 A 404 HIS SEQRES 1 B 404 LEU ASP ASN GLY LEU ALA ARG THR PRO THR MET GLY TRP SEQRES 2 B 404 LEU HIS TRP GLU ARG PHE MET CYS ASN LEU ASP CYS GLN SEQRES 3 B 404 GLU GLU PRO ASP SER CYS ILE SER GLU LYS LEU PHE MET SEQRES 4 B 404 GLU MET ALA GLU LEU MET VAL SER GLU GLY TRP LYS ASP SEQRES 5 B 404 ALA GLY TYR GLU TYR LEU CYS ILE ASP ASP CYS TRP MET SEQRES 6 B 404 ALA PRO GLN ARG ASP SER GLU GLY ARG LEU GLN ALA ASP SEQRES 7 B 404 PRO GLN ARG PHE PRO HIS GLY ILE ARG GLN LEU ALA ASN SEQRES 8 B 404 TYR VAL HIS SER LYS GLY LEU LYS LEU GLY ILE TYR ALA SEQRES 9 B 404 ASP VAL GLY ASN LYS THR CYS ALA GLY PHE PRO GLY SER SEQRES 10 B 404 PHE GLY TYR TYR ASP ILE ASP ALA GLN THR PHE ALA ASP SEQRES 11 B 404 TRP GLY VAL ASP LEU LEU LYS PHE ALA GLY CYS TYR CYS SEQRES 12 B 404 ASP SER LEU GLU ASN LEU ALA ASP GLY TYR LYS HIS MET SEQRES 13 B 404 SER LEU ALA LEU ASN ARG THR GLY ARG SER ILE VAL TYR SEQRES 14 B 404 SER CYS GLU TRP PRO LEU TYR MET TRP PRO PHE GLN LYS SEQRES 15 B 404 PRO ASN TYR THR GLU ILE ARG GLN TYR CYS ASN HIS TRP SEQRES 16 B 404 ARG ASN PHE ALA ASP ILE ASP ASP SER TRP LYS SER ILE SEQRES 17 B 404 LYS SER ILE LEU ASP TRP THR SER PHE ASN GLN GLU ARG SEQRES 18 B 404 ILE VAL ASP VAL ALA GLY PRO GLY GLY TRP ASN ASP PRO SEQRES 19 B 404 ASP MET LEU VAL ILE GLY ASN PHE GLY LEU SER TRP ASN SEQRES 20 B 404 GLN GLN VAL THR GLN MET ALA LEU TRP ALA ILE MET ALA SEQRES 21 B 404 ALA PRO LEU PHE MET SER ASN ASP LEU ARG HIS ILE SER SEQRES 22 B 404 PRO GLN ALA LYS ALA LEU LEU GLN ASP LYS ASP VAL ILE SEQRES 23 B 404 ALA ILE ASN GLN ASP PRO LEU GLY LYS GLN GLY TYR GLN SEQRES 24 B 404 LEU ARG GLN GLY ASP ASN PHE GLU VAL TRP GLU ARG PRO SEQRES 25 B 404 LEU SER GLY LEU ALA TRP ALA VAL ALA MET ILE ASN ARG SEQRES 26 B 404 GLN GLU ILE GLY GLY PRO ARG SER TYR THR ILE ALA VAL SEQRES 27 B 404 ALA SER LEU GLY LYS GLY VAL ALA CYS ASN PRO ALA CYS SEQRES 28 B 404 PHE ILE THR GLN LEU LEU PRO VAL LYS ARG LYS LEU GLY SEQRES 29 B 404 PHE TYR GLU TRP THR SER ARG LEU ARG SER HIS ILE ASN SEQRES 30 B 404 PRO THR GLY THR VAL LEU LEU GLN LEU GLU ASN THR MET SEQRES 31 B 404 GLN MET SER LEU LYS ASP LEU LEU HIS HIS HIS HIS HIS SEQRES 32 B 404 HIS MODRES 3HG3 ASN A 139 ASN GLYCOSYLATION SITE MODRES 3HG3 ASN A 192 ASN GLYCOSYLATION SITE MODRES 3HG3 ASN A 215 ASN GLYCOSYLATION SITE MODRES 3HG3 ASN B 139 ASN GLYCOSYLATION SITE MODRES 3HG3 ASN B 192 ASN GLYCOSYLATION SITE MODRES 3HG3 ASN B 215 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET NAG D 1 14 HET NAG D 2 14 HET GLC E 1 12 HET GLA E 2 11 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET MAN F 4 11 HET GLC G 1 12 HET GLA G 2 11 HET NAG A 639 14 HET 2PE A 821 19 HET 2PE A 822 7 HET 2PE A 823 7 HET 2PE A 824 7 HET 2PE A 825 13 HET NAG B 639 14 HET NAG B 715 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM 2PE NONAETHYLENE GLYCOL 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 MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE FORMUL 3 NAG 9(C8 H15 N O6) FORMUL 3 BMA 2(C6 H12 O6) FORMUL 3 MAN 2(C6 H12 O6) FORMUL 5 GLC 2(C6 H12 O6) FORMUL 5 GLA 2(C6 H12 O6) FORMUL 9 2PE 5(C18 H38 O10) FORMUL 16 HOH *893(H2 O) HELIX 1 1 HIS A 46 MET A 51 1 6 HELIX 2 2 SER A 65 GLU A 79 1 15 HELIX 3 3 GLY A 80 GLY A 85 1 6 HELIX 4 4 HIS A 115 LYS A 127 1 13 HELIX 5 5 TYR A 151 GLY A 163 1 13 HELIX 6 6 SER A 176 THR A 194 1 19 HELIX 7 7 TRP A 204 TRP A 209 5 6 HELIX 8 8 ASN A 215 CYS A 223 1 9 HELIX 9 9 SER A 235 ASN A 249 1 15 HELIX 10 10 ASN A 249 VAL A 254 1 6 HELIX 11 11 SER A 276 MET A 290 1 15 HELIX 12 12 SER A 304 GLN A 312 1 9 HELIX 13 13 ASP A 313 GLN A 321 1 9 HELIX 14 14 ALA A 370 VAL A 376 5 7 HELIX 15 15 THR A 420 LEU A 425 1 6 HELIX 16 16 HIS B 46 MET B 51 1 6 HELIX 17 17 SER B 65 GLU B 79 1 15 HELIX 18 18 GLY B 80 GLY B 85 1 6 HELIX 19 19 HIS B 115 LYS B 127 1 13 HELIX 20 20 TYR B 151 GLY B 163 1 13 HELIX 21 21 SER B 176 THR B 194 1 19 HELIX 22 22 GLU B 203 TRP B 209 1 7 HELIX 23 23 ASN B 215 CYS B 223 1 9 HELIX 24 24 SER B 235 ASN B 249 1 15 HELIX 25 25 ASN B 249 VAL B 254 1 6 HELIX 26 26 SER B 276 MET B 290 1 15 HELIX 27 27 SER B 304 GLN B 312 1 9 HELIX 28 28 ASP B 313 GLN B 321 1 9 HELIX 29 29 ALA B 370 VAL B 376 5 7 HELIX 30 30 THR B 420 LEU B 425 1 6 SHEET 1 A 8 TRP A 262 ASP A 264 0 SHEET 2 A 8 HIS A 225 ARG A 227 1 N TRP A 226 O ASP A 264 SHEET 3 A 8 VAL A 199 CYS A 202 1 N CYS A 202 O HIS A 225 SHEET 4 A 8 LEU A 166 ALA A 170 1 N LEU A 167 O VAL A 199 SHEET 5 A 8 LYS A 130 ASP A 136 1 N ALA A 135 O ALA A 170 SHEET 6 A 8 TYR A 88 CYS A 90 1 N LEU A 89 O LYS A 130 SHEET 7 A 8 MET A 42 LEU A 45 1 N TRP A 44 O CYS A 90 SHEET 8 A 8 LEU A 294 MET A 296 1 O MET A 296 N LEU A 45 SHEET 1 B 6 TYR A 329 GLY A 334 0 SHEET 2 B 6 PHE A 337 PRO A 343 -1 O VAL A 339 N ARG A 332 SHEET 3 B 6 TRP A 349 ASN A 355 -1 O ALA A 352 N TRP A 340 SHEET 4 B 6 THR A 412 ASN A 419 -1 O LEU A 417 N TRP A 349 SHEET 5 B 6 ALA A 381 LEU A 388 -1 N LEU A 387 O LEU A 414 SHEET 6 B 6 ARG A 392 GLU A 398 -1 O ARG A 392 N GLN A 386 SHEET 1 C 2 ARG A 363 ALA A 368 0 SHEET 2 C 2 ARG A 402 ILE A 407 -1 O SER A 405 N TYR A 365 SHEET 1 D 8 TRP B 262 ASP B 264 0 SHEET 2 D 8 HIS B 225 ARG B 227 1 N TRP B 226 O ASP B 264 SHEET 3 D 8 VAL B 199 CYS B 202 1 N CYS B 202 O ARG B 227 SHEET 4 D 8 LEU B 166 ALA B 170 1 N LEU B 167 O SER B 201 SHEET 5 D 8 LYS B 130 ASP B 136 1 N ALA B 135 O ALA B 170 SHEET 6 D 8 TYR B 88 CYS B 90 1 N LEU B 89 O LYS B 130 SHEET 7 D 8 MET B 42 LEU B 45 1 N TRP B 44 O CYS B 90 SHEET 8 D 8 LEU B 294 MET B 296 1 O MET B 296 N LEU B 45 SHEET 1 E 6 TYR B 329 GLY B 334 0 SHEET 2 E 6 PHE B 337 PRO B 343 -1 O VAL B 339 N LEU B 331 SHEET 3 E 6 ALA B 348 ASN B 355 -1 O ALA B 352 N TRP B 340 SHEET 4 E 6 THR B 412 ASN B 419 -1 O LEU B 417 N TRP B 349 SHEET 5 E 6 ALA B 381 LEU B 388 -1 N LEU B 387 O LEU B 414 SHEET 6 E 6 ARG B 392 GLU B 398 -1 O ARG B 392 N GLN B 386 SHEET 1 F 2 ARG B 363 ALA B 368 0 SHEET 2 F 2 ARG B 402 ILE B 407 -1 O SER B 405 N TYR B 365 SSBOND 1 CYS A 52 CYS A 94 1555 1555 2.04 SSBOND 2 CYS A 56 CYS A 63 1555 1555 2.04 SSBOND 3 CYS A 142 CYS A 172 1555 1555 2.03 SSBOND 4 CYS A 202 CYS A 223 1555 1555 2.04 SSBOND 5 CYS A 378 CYS A 382 1555 1555 2.04 SSBOND 6 CYS B 52 CYS B 94 1555 1555 2.04 SSBOND 7 CYS B 56 CYS B 63 1555 1555 2.04 SSBOND 8 CYS B 142 CYS B 172 1555 1555 2.04 SSBOND 9 CYS B 202 CYS B 223 1555 1555 2.04 SSBOND 10 CYS B 378 CYS B 382 1555 1555 2.05 LINK ND2 ASN A 139 C1 NAG A 639 1555 1555 1.45 LINK ND2 ASN A 192 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 215 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN B 139 C1 NAG B 639 1555 1555 1.44 LINK ND2 ASN B 192 C1 NAG F 1 1555 1555 1.44 LINK ND2 ASN B 215 C1 NAG B 715 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 LINK O3 BMA C 3 C1 MAN C 4 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O6 GLC E 1 C1 GLA E 2 1555 1555 1.44 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 1.46 LINK O6 GLC G 1 C1 GLA G 2 1555 1555 1.44 CISPEP 1 TRP A 209 PRO A 210 0 -0.19 CISPEP 2 ASN A 379 PRO A 380 0 1.90 CISPEP 3 LEU A 388 PRO A 389 0 0.89 CISPEP 4 ASN B 379 PRO B 380 0 3.14 CISPEP 5 LEU B 388 PRO B 389 0 3.13 CRYST1 59.548 106.106 181.721 90.00 90.00 90.00 P 21 21 21 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 0.016793 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005503 0.00000