HEADER HYDROLASE 02-APR-09 3GXN TITLE CRYSTAL STRUCTURE OF APO ALPHA-GALACTOSIDASE A AT PH 4.5 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 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: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS HYDROLASE, DISEASE MUTATION, DISULFIDE BOND, GLYCOPROTEIN, KEYWDS 2 GLYCOSIDASE, LYSOSOME, RNA EDITING EXPDTA X-RAY DIFFRACTION AUTHOR R.L.LIEBERMAN REVDAT 4 29-JUL-20 3GXN 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 13-JUL-11 3GXN 1 VERSN REVDAT 2 16-JUN-09 3GXN 1 JRNL REVDAT 1 05-MAY-09 3GXN 0 JRNL AUTH R.L.LIEBERMAN,J.A.D'AQUINO,D.RINGE,G.A.PETSKO JRNL TITL EFFECTS OF PH AND IMINOSUGAR PHARMACOLOGICAL CHAPERONES ON JRNL TITL 2 LYSOSOMAL GLYCOSIDASE STRUCTURE AND STABILITY. JRNL REF BIOCHEMISTRY V. 48 4816 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19374450 JRNL DOI 10.1021/BI9002265 REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 3.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.1 REMARK 3 NUMBER OF REFLECTIONS : 18676 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) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 971 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) : 3.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 813 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 57.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.3420 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6244 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 121.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.48000 REMARK 3 B22 (A**2) : 4.48000 REMARK 3 B33 (A**2) : -6.72000 REMARK 3 B12 (A**2) : 2.24000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.573 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.440 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 53.739 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6490 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8824 ; 1.844 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 778 ; 7.568 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 318 ;39.224 ;24.277 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1048 ;23.591 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;23.071 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 914 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5020 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3207 ; 0.253 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4323 ; 0.328 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 249 ; 0.163 ; 0.200 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): 71 ; 0.484 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.370 ; 0.200 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): 3978 ; 0.388 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6208 ; 0.630 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2978 ; 1.033 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2616 ; 1.606 ; 4.500 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 : 1 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 421 1 REMARK 3 1 B 32 B 421 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 3122 ; 0.070 ; 0.050 REMARK 3 TIGHT THERMAL 1 A (A**2): 3122 ; 0.120 ; 0.500 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): 36.4863 -12.4214 -1.4811 REMARK 3 T TENSOR REMARK 3 T11: -0.2191 T22: -0.0938 REMARK 3 T33: -0.3320 T12: 0.0565 REMARK 3 T13: 0.0396 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 1.8682 L22: 3.1188 REMARK 3 L33: 2.1248 L12: -0.7498 REMARK 3 L13: -0.2358 L23: -0.3083 REMARK 3 S TENSOR REMARK 3 S11: 0.1079 S12: -0.0963 S13: 0.2881 REMARK 3 S21: -0.1716 S22: -0.0325 S23: 0.3587 REMARK 3 S31: -0.4476 S32: -0.2553 S33: -0.0754 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 : B 32 B 328 REMARK 3 ORIGIN FOR THE GROUP (A): 45.6226 -49.5679 28.3092 REMARK 3 T TENSOR REMARK 3 T11: -0.2356 T22: 0.1025 REMARK 3 T33: -0.3276 T12: 0.0179 REMARK 3 T13: -0.0098 T23: 0.0949 REMARK 3 L TENSOR REMARK 3 L11: 2.1231 L22: 3.3373 REMARK 3 L33: 2.7986 L12: -0.6442 REMARK 3 L13: -0.8191 L23: -0.0351 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: -0.2315 S13: -0.5837 REMARK 3 S21: 0.1304 S22: -0.0858 S23: 0.0797 REMARK 3 S31: 0.5925 S32: 0.0345 S33: 0.0857 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 : A 329 A 414 REMARK 3 ORIGIN FOR THE GROUP (A): 52.8687 -38.2427 -5.3803 REMARK 3 T TENSOR REMARK 3 T11: -0.2582 T22: -0.0762 REMARK 3 T33: -0.4391 T12: 0.1332 REMARK 3 T13: 0.0289 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 1.5936 L22: 2.1340 REMARK 3 L33: 4.3364 L12: -0.1676 REMARK 3 L13: -0.5537 L23: 0.2100 REMARK 3 S TENSOR REMARK 3 S11: 0.0739 S12: 0.1173 S13: -0.2312 REMARK 3 S21: -0.2819 S22: -0.1049 S23: -0.1935 REMARK 3 S31: 0.5403 S32: 0.2538 S33: 0.0310 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 414 REMARK 3 ORIGIN FOR THE GROUP (A): 36.6410 -20.6913 34.4399 REMARK 3 T TENSOR REMARK 3 T11: -0.0788 T22: 0.1521 REMARK 3 T33: -0.3060 T12: 0.0122 REMARK 3 T13: 0.1312 T23: -0.0710 REMARK 3 L TENSOR REMARK 3 L11: 1.6365 L22: 2.2473 REMARK 3 L33: 2.9280 L12: -0.0640 REMARK 3 L13: -1.1988 L23: -1.6014 REMARK 3 S TENSOR REMARK 3 S11: 0.3564 S12: -0.5075 S13: 0.6555 REMARK 3 S21: 0.5757 S22: -0.0513 S23: 0.1970 REMARK 3 S31: -1.0879 S32: -0.1813 S33: -0.3051 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: NULL REMARK 4 REMARK 4 3GXN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18676 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.010 REMARK 200 RESOLUTION RANGE LOW (A) : 78.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 145.01600 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 72.50800 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 72.50800 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 145.01600 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: 3490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 GLN A 422 REMARK 465 MET A 423 REMARK 465 SER A 424 REMARK 465 LEU A 425 REMARK 465 LYS A 426 REMARK 465 ASP A 427 REMARK 465 LEU A 428 REMARK 465 LEU A 429 REMARK 465 GLN B 422 REMARK 465 MET B 423 REMARK 465 SER B 424 REMARK 465 LEU B 425 REMARK 465 LYS B 426 REMARK 465 ASP B 427 REMARK 465 LEU B 428 REMARK 465 LEU B 429 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CB PRO B 210 O5 NAG C 1 4545 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 382 CB CYS A 382 SG -0.119 REMARK 500 CYS B 382 CB CYS B 382 SG -0.124 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 286 CA - CB - CG ANGL. DEV. = -15.2 DEGREES REMARK 500 ARG A 332 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 LEU B 286 CA - CB - CG ANGL. DEV. = -14.9 DEGREES 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 MET A 51 -145.61 47.02 REMARK 500 CYS A 52 50.95 -108.66 REMARK 500 GLN A 57 -81.12 -64.25 REMARK 500 PRO A 60 -7.11 -56.90 REMARK 500 ASP A 92 -154.17 -102.74 REMARK 500 ALA A 121 -70.41 -53.55 REMARK 500 ASN A 122 -58.87 -20.07 REMARK 500 TYR A 173 70.04 58.32 REMARK 500 ASP A 175 -65.46 -26.12 REMARK 500 PRO A 210 45.28 -91.92 REMARK 500 GLN A 212 141.95 157.12 REMARK 500 ALA A 230 -179.37 -30.75 REMARK 500 ASP A 266 177.69 99.24 REMARK 500 ASN A 272 -124.62 -97.94 REMARK 500 LEU A 372 -98.34 -79.89 REMARK 500 LYS A 374 -1.14 72.27 REMARK 500 CYS A 378 20.71 88.25 REMARK 500 LEU A 388 131.52 -175.14 REMARK 500 VAL A 390 -50.53 -123.80 REMARK 500 LYS A 391 64.76 84.24 REMARK 500 THR A 410 4.92 54.09 REMARK 500 MET B 51 -144.43 50.48 REMARK 500 CYS B 52 51.64 -108.86 REMARK 500 GLN B 57 -82.05 -63.31 REMARK 500 ASP B 92 -158.11 -102.29 REMARK 500 ASP B 101 -167.52 -78.30 REMARK 500 TYR B 173 75.91 55.38 REMARK 500 ASP B 175 -74.31 -26.14 REMARK 500 PRO B 210 42.97 -95.93 REMARK 500 GLN B 212 150.18 160.70 REMARK 500 ALA B 230 177.09 -49.61 REMARK 500 ASN B 249 20.12 -144.83 REMARK 500 ASP B 266 -176.76 103.05 REMARK 500 ASN B 272 -122.51 -98.44 REMARK 500 ALA B 291 51.89 37.02 REMARK 500 GLU B 358 32.59 -85.35 REMARK 500 LEU B 372 -100.55 -85.62 REMARK 500 CYS B 378 22.37 87.59 REMARK 500 LYS B 391 61.70 83.69 REMARK 500 THR B 410 -5.73 62.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG C 1 REMARK 610 NAG D 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GXP RELATED DB: PDB REMARK 900 STRUCTURE OF ACID-ALPHA-GALACTOSIDASE A COMPLEXED WITH GALACTOSE AT REMARK 900 PH 4.5 REMARK 900 RELATED ID: 3GXT RELATED DB: PDB REMARK 900 STRUCTURE OF ALPHA-GALACTOSIDASE A AT PH 4.5 COMPLEXED WITH 1- REMARK 900 DEOXYGALACTONIJIRIMYCIN DBREF 3GXN A 32 429 UNP P06280 AGAL_HUMAN 32 429 DBREF 3GXN B 32 429 UNP P06280 AGAL_HUMAN 32 429 SEQRES 1 A 398 LEU ASP ASN GLY LEU ALA ARG THR PRO THR MET GLY TRP SEQRES 2 A 398 LEU HIS TRP GLU ARG PHE MET CYS ASN LEU ASP CYS GLN SEQRES 3 A 398 GLU GLU PRO ASP SER CYS ILE SER GLU LYS LEU PHE MET SEQRES 4 A 398 GLU MET ALA GLU LEU MET VAL SER GLU GLY TRP LYS ASP SEQRES 5 A 398 ALA GLY TYR GLU TYR LEU CYS ILE ASP ASP CYS TRP MET SEQRES 6 A 398 ALA PRO GLN ARG ASP SER GLU GLY ARG LEU GLN ALA ASP SEQRES 7 A 398 PRO GLN ARG PHE PRO HIS GLY ILE ARG GLN LEU ALA ASN SEQRES 8 A 398 TYR VAL HIS SER LYS GLY LEU LYS LEU GLY ILE TYR ALA SEQRES 9 A 398 ASP VAL GLY ASN LYS THR CYS ALA GLY PHE PRO GLY SER SEQRES 10 A 398 PHE GLY TYR TYR ASP ILE ASP ALA GLN THR PHE ALA ASP SEQRES 11 A 398 TRP GLY VAL ASP LEU LEU LYS PHE ASP GLY CYS TYR CYS SEQRES 12 A 398 ASP SER LEU GLU ASN LEU ALA ASP GLY TYR LYS HIS MET SEQRES 13 A 398 SER LEU ALA LEU ASN ARG THR GLY ARG SER ILE VAL TYR SEQRES 14 A 398 SER CYS GLU TRP PRO LEU TYR MET TRP PRO PHE GLN LYS SEQRES 15 A 398 PRO ASN TYR THR GLU ILE ARG GLN TYR CYS ASN HIS TRP SEQRES 16 A 398 ARG ASN PHE ALA ASP ILE ASP ASP SER TRP LYS SER ILE SEQRES 17 A 398 LYS SER ILE LEU ASP TRP THR SER PHE ASN GLN GLU ARG SEQRES 18 A 398 ILE VAL ASP VAL ALA GLY PRO GLY GLY TRP ASN ASP PRO SEQRES 19 A 398 ASP MET LEU VAL ILE GLY ASN PHE GLY LEU SER TRP ASN SEQRES 20 A 398 GLN GLN VAL THR GLN MET ALA LEU TRP ALA ILE MET ALA SEQRES 21 A 398 ALA PRO LEU PHE MET SER ASN ASP LEU ARG HIS ILE SER SEQRES 22 A 398 PRO GLN ALA LYS ALA LEU LEU GLN ASP LYS ASP VAL ILE SEQRES 23 A 398 ALA ILE ASN GLN ASP PRO LEU GLY LYS GLN GLY TYR GLN SEQRES 24 A 398 LEU ARG GLN GLY ASP ASN PHE GLU VAL TRP GLU ARG PRO SEQRES 25 A 398 LEU SER GLY LEU ALA TRP ALA VAL ALA MET ILE ASN ARG SEQRES 26 A 398 GLN GLU ILE GLY GLY PRO ARG SER TYR THR ILE ALA VAL SEQRES 27 A 398 ALA SER LEU GLY LYS GLY VAL ALA CYS ASN PRO ALA CYS SEQRES 28 A 398 PHE ILE THR GLN LEU LEU PRO VAL LYS ARG LYS LEU GLY SEQRES 29 A 398 PHE TYR GLU TRP THR SER ARG LEU ARG SER HIS ILE ASN SEQRES 30 A 398 PRO THR GLY THR VAL LEU LEU GLN LEU GLU ASN THR MET SEQRES 31 A 398 GLN MET SER LEU LYS ASP LEU LEU SEQRES 1 B 398 LEU ASP ASN GLY LEU ALA ARG THR PRO THR MET GLY TRP SEQRES 2 B 398 LEU HIS TRP GLU ARG PHE MET CYS ASN LEU ASP CYS GLN SEQRES 3 B 398 GLU GLU PRO ASP SER CYS ILE SER GLU LYS LEU PHE MET SEQRES 4 B 398 GLU MET ALA GLU LEU MET VAL SER GLU GLY TRP LYS ASP SEQRES 5 B 398 ALA GLY TYR GLU TYR LEU CYS ILE ASP ASP CYS TRP MET SEQRES 6 B 398 ALA PRO GLN ARG ASP SER GLU GLY ARG LEU GLN ALA ASP SEQRES 7 B 398 PRO GLN ARG PHE PRO HIS GLY ILE ARG GLN LEU ALA ASN SEQRES 8 B 398 TYR VAL HIS SER LYS GLY LEU LYS LEU GLY ILE TYR ALA SEQRES 9 B 398 ASP VAL GLY ASN LYS THR CYS ALA GLY PHE PRO GLY SER SEQRES 10 B 398 PHE GLY TYR TYR ASP ILE ASP ALA GLN THR PHE ALA ASP SEQRES 11 B 398 TRP GLY VAL ASP LEU LEU LYS PHE ASP GLY CYS TYR CYS SEQRES 12 B 398 ASP SER LEU GLU ASN LEU ALA ASP GLY TYR LYS HIS MET SEQRES 13 B 398 SER LEU ALA LEU ASN ARG THR GLY ARG SER ILE VAL TYR SEQRES 14 B 398 SER CYS GLU TRP PRO LEU TYR MET TRP PRO PHE GLN LYS SEQRES 15 B 398 PRO ASN TYR THR GLU ILE ARG GLN TYR CYS ASN HIS TRP SEQRES 16 B 398 ARG ASN PHE ALA ASP ILE ASP ASP SER TRP LYS SER ILE SEQRES 17 B 398 LYS SER ILE LEU ASP TRP THR SER PHE ASN GLN GLU ARG SEQRES 18 B 398 ILE VAL ASP VAL ALA GLY PRO GLY GLY TRP ASN ASP PRO SEQRES 19 B 398 ASP MET LEU VAL ILE GLY ASN PHE GLY LEU SER TRP ASN SEQRES 20 B 398 GLN GLN VAL THR GLN MET ALA LEU TRP ALA ILE MET ALA SEQRES 21 B 398 ALA PRO LEU PHE MET SER ASN ASP LEU ARG HIS ILE SER SEQRES 22 B 398 PRO GLN ALA LYS ALA LEU LEU GLN ASP LYS ASP VAL ILE SEQRES 23 B 398 ALA ILE ASN GLN ASP PRO LEU GLY LYS GLN GLY TYR GLN SEQRES 24 B 398 LEU ARG GLN GLY ASP ASN PHE GLU VAL TRP GLU ARG PRO SEQRES 25 B 398 LEU SER GLY LEU ALA TRP ALA VAL ALA MET ILE ASN ARG SEQRES 26 B 398 GLN GLU ILE GLY GLY PRO ARG SER TYR THR ILE ALA VAL SEQRES 27 B 398 ALA SER LEU GLY LYS GLY VAL ALA CYS ASN PRO ALA CYS SEQRES 28 B 398 PHE ILE THR GLN LEU LEU PRO VAL LYS ARG LYS LEU GLY SEQRES 29 B 398 PHE TYR GLU TRP THR SER ARG LEU ARG SER HIS ILE ASN SEQRES 30 B 398 PRO THR GLY THR VAL LEU LEU GLN LEU GLU ASN THR MET SEQRES 31 B 398 GLN MET SER LEU LYS ASP LEU LEU HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET SO4 A 1 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 5 SO4 O4 S 2- 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 GLY A 116 LYS A 127 1 12 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 GLU A 203 TRP A 209 1 7 HELIX 8 8 ASN A 215 CYS A 223 1 9 HELIX 9 9 SER A 235 PHE A 248 1 14 HELIX 10 10 ASN A 249 ASP A 255 1 7 HELIX 11 11 SER A 276 MET A 290 1 15 HELIX 12 12 SER A 304 ASP A 313 1 10 HELIX 13 13 ASP A 313 GLN A 321 1 9 HELIX 14 14 ALA A 370 LEU A 372 5 3 HELIX 15 15 HIS B 46 MET B 51 1 6 HELIX 16 16 SER B 65 GLU B 79 1 15 HELIX 17 17 GLY B 80 GLY B 85 1 6 HELIX 18 18 HIS B 115 LYS B 127 1 13 HELIX 19 19 TYR B 151 GLY B 163 1 13 HELIX 20 20 SER B 176 THR B 194 1 19 HELIX 21 21 GLU B 203 TRP B 209 1 7 HELIX 22 22 ASN B 215 GLN B 221 1 7 HELIX 23 23 SER B 235 PHE B 248 1 14 HELIX 24 24 ASN B 249 ASP B 255 1 7 HELIX 25 25 SER B 276 MET B 290 1 15 HELIX 26 26 SER B 304 GLN B 312 1 9 HELIX 27 27 ASP B 313 GLN B 321 1 9 HELIX 28 28 ALA B 370 LEU B 372 5 3 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 ASP 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 ASP 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 TYR A 88 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 LEU A 331 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 415 N VAL A 351 SHEET 5 B 6 ALA A 381 LEU A 388 -1 N LEU A 387 O LEU A 414 SHEET 6 B 6 LYS A 393 GLU A 398 -1 O TYR A 397 N CYS A 382 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 HIS B 225 SHEET 4 D 8 LEU B 166 ASP B 170 1 N LEU B 167 O VAL B 199 SHEET 5 D 8 LYS B 130 ASP B 136 1 N ALA B 135 O ASP 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 TYR B 88 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 TRP B 349 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 415 N VAL B 351 SHEET 5 E 6 ALA B 381 LEU B 388 -1 N PHE B 383 O GLU B 418 SHEET 6 E 6 LYS B 393 GLU B 398 -1 O TYR B 397 N CYS B 382 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 2.05 SSBOND 2 CYS A 56 CYS A 63 1555 1555 2.05 SSBOND 3 CYS A 142 CYS A 172 1555 1555 2.08 SSBOND 4 CYS A 202 CYS A 223 1555 1555 2.02 SSBOND 5 CYS A 378 CYS A 382 1555 1555 2.04 SSBOND 6 CYS B 52 CYS B 94 1555 1555 2.07 SSBOND 7 CYS B 56 CYS B 63 1555 1555 2.06 SSBOND 8 CYS B 142 CYS B 172 1555 1555 2.05 SSBOND 9 CYS B 202 CYS B 223 1555 1555 2.03 SSBOND 10 CYS B 378 CYS B 382 1555 1555 2.05 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.43 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.45 CISPEP 1 TRP A 209 PRO A 210 0 -3.32 CISPEP 2 ASN A 379 PRO A 380 0 2.65 CISPEP 3 LEU A 388 PRO A 389 0 14.21 CISPEP 4 TRP B 209 PRO B 210 0 -1.34 CISPEP 5 ASN B 379 PRO B 380 0 0.92 CISPEP 6 LEU B 388 PRO B 389 0 10.71 CRYST1 90.375 90.375 217.524 90.00 90.00 120.00 P 32 2 1 12 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 0.011065 0.006388 0.000000 0.00000 SCALE2 0.000000 0.012777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004597 0.00000