HEADER HYDROLASE 02-APR-09 3GXT TITLE CRYSTAL STRUCTURE OF ALPHA-GALACTOSIDASE A AT PH 4.5 COMPLEXED WITH 1- TITLE 2 DEOXYGALACTONIJIRIMYCIN CAVEAT 3GXT MAN E 2 HAS WRONG CHIRALITY AT ATOM C1 NAG G 1 HAS WRONG CAVEAT 2 3GXT CHIRALITY AT ATOM C1 MAN G 3 HAS WRONG CHIRALITY AT ATOM C1 CAVEAT 3 3GXT MAN H 3 HAS WRONG CHIRALITY AT ATOM C1 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 3GXT 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 13-JUL-11 3GXT 1 VERSN REVDAT 2 16-JUN-09 3GXT 1 JRNL REVDAT 1 26-MAY-09 3GXT 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. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 26233 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1400 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1848 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.4110 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.4170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6253 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 256 REMARK 3 SOLVENT ATOMS : 64 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) : 57.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.22000 REMARK 3 B12 (A**2) : -0.07000 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): 0.424 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.419 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 44.702 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.854 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6701 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9127 ; 1.950 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 779 ; 9.413 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 319 ;38.935 ;24.295 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1050 ;21.561 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;18.923 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 978 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5056 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3325 ; 0.262 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4441 ; 0.331 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 310 ; 0.208 ; 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 ; 0.349 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.200 ; 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): 3967 ; 0.412 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6216 ; 0.668 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3187 ; 1.207 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2911 ; 1.775 ; 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 418 1 REMARK 3 1 B 32 B 418 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 3099 ; 0.07 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 3099 ; 0.12 ; 0.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 418 REMARK 3 ORIGIN FOR THE GROUP (A): -9.0681 51.9893 110.9311 REMARK 3 T TENSOR REMARK 3 T11: -0.2711 T22: -0.1957 REMARK 3 T33: -0.2393 T12: 0.1813 REMARK 3 T13: -0.0343 T23: -0.0288 REMARK 3 L TENSOR REMARK 3 L11: 3.5773 L22: 0.9339 REMARK 3 L33: 2.0658 L12: 0.1886 REMARK 3 L13: -0.1640 L23: -0.0213 REMARK 3 S TENSOR REMARK 3 S11: 0.1258 S12: -0.1349 S13: 0.1468 REMARK 3 S21: -0.0486 S22: -0.1060 S23: 0.1275 REMARK 3 S31: 0.2283 S32: -0.2600 S33: -0.0199 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 418 REMARK 3 ORIGIN FOR THE GROUP (A): 13.6926 61.7165 78.4978 REMARK 3 T TENSOR REMARK 3 T11: -0.1329 T22: -0.2570 REMARK 3 T33: -0.2093 T12: 0.1830 REMARK 3 T13: 0.0150 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 3.2610 L22: 1.2289 REMARK 3 L33: 3.2424 L12: 0.1154 REMARK 3 L13: 0.3133 L23: -0.4227 REMARK 3 S TENSOR REMARK 3 S11: -0.0333 S12: 0.2070 S13: 0.3223 REMARK 3 S21: -0.1575 S22: -0.0291 S23: -0.0963 REMARK 3 S31: -0.1836 S32: 0.3534 S33: 0.0624 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3GXT 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_1000052440. 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 : XSCALE REMARK 200 DATA SCALING SOFTWARE : SCALA, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27633 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 77.600 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 (%): 55.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 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 144.42667 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 72.21333 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 72.21333 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 144.42667 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: 7450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 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 IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 175 O7 NAG C 1 1.94 REMARK 500 OD1 ASP B 335 O HOH B 440 2.07 REMARK 500 N GLN B 306 O HOH B 444 2.08 REMARK 500 O4 SO4 A 2 O HOH A 12 2.11 REMARK 500 O3 MAN G 4 O HOH B 438 2.16 REMARK 500 ND2 ASN B 215 O5 NAG H 1 2.19 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 PRO A 265 C - N - CA ANGL. DEV. = 9.8 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 ASP A 33 63.53 -68.46 REMARK 500 MET A 51 -149.87 43.34 REMARK 500 CYS A 52 41.41 -103.03 REMARK 500 ASN A 53 98.95 -65.32 REMARK 500 ASP A 92 -158.64 -109.00 REMARK 500 CYS A 94 36.54 79.59 REMARK 500 PRO A 98 -57.27 -16.39 REMARK 500 ASP A 101 -176.38 -67.42 REMARK 500 GLU A 103 -117.09 -9.57 REMARK 500 PRO A 146 136.86 -29.29 REMARK 500 TRP A 209 -65.48 -23.31 REMARK 500 ALA A 230 148.20 -29.01 REMARK 500 ASP A 231 157.94 -45.43 REMARK 500 ASP A 234 53.28 -98.10 REMARK 500 LYS A 237 -72.05 -54.31 REMARK 500 ASN A 249 57.91 -118.42 REMARK 500 PRO A 259 116.91 -22.57 REMARK 500 ASP A 266 -179.66 75.39 REMARK 500 ASN A 272 -142.49 -77.54 REMARK 500 GLN A 306 -67.47 -22.66 REMARK 500 LYS A 314 -71.60 -53.35 REMARK 500 ALA A 318 -62.57 -28.29 REMARK 500 ASP A 335 35.04 71.50 REMARK 500 LYS A 374 0.59 59.92 REMARK 500 CYS A 378 4.96 94.45 REMARK 500 GLU A 398 153.23 -38.37 REMARK 500 SER A 405 140.58 -172.41 REMARK 500 THR A 420 -72.21 -30.39 REMARK 500 ASP B 33 63.54 -65.98 REMARK 500 MET B 51 -148.70 33.44 REMARK 500 CYS B 52 46.57 -100.41 REMARK 500 ASP B 61 3.27 -69.63 REMARK 500 ILE B 64 91.65 -64.07 REMARK 500 ASP B 92 -163.31 -114.12 REMARK 500 CYS B 94 45.91 77.71 REMARK 500 PRO B 98 -54.35 -16.85 REMARK 500 ASP B 101 179.60 -59.82 REMARK 500 SER B 102 62.12 -109.42 REMARK 500 GLU B 103 -93.54 -93.68 REMARK 500 PRO B 146 132.38 -36.03 REMARK 500 THR B 194 -39.35 -39.44 REMARK 500 ALA B 230 163.35 -49.35 REMARK 500 ASP B 233 -169.92 -113.05 REMARK 500 ASP B 234 49.65 -99.94 REMARK 500 ASN B 249 57.03 -116.43 REMARK 500 PRO B 259 118.50 -18.64 REMARK 500 ASP B 266 172.90 72.87 REMARK 500 ASN B 272 -136.88 -85.62 REMARK 500 GLN B 306 -71.34 -17.24 REMARK 500 ALA B 318 -65.07 -21.59 REMARK 500 REMARK 500 THIS ENTRY HAS 57 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 102 GLU A 103 31.40 REMARK 500 GLU A 103 GLY A 104 -39.66 REMARK 500 GLY A 104 ARG A 105 -145.96 REMARK 500 TRP A 209 PRO A 210 -136.25 REMARK 500 SER B 102 GLU B 103 122.53 REMARK 500 THR B 420 MET B 421 42.26 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 MAN E 1 REMARK 610 NAG H 1 REMARK 610 NAG B 639 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GXN RELATED DB: PDB REMARK 900 STRUCTURE OF APO ALPHA-GALACTOSIDASE A AT PH 4.5 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 DBREF 3GXT A 32 429 UNP P06280 AGAL_HUMAN 32 429 DBREF 3GXT 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 MODRES 3GXT ASN A 139 ASN GLYCOSYLATION SITE MODRES 3GXT ASN A 192 ASN GLYCOSYLATION SITE MODRES 3GXT ASN A 215 ASN GLYCOSYLATION SITE MODRES 3GXT ASN B 192 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET MAN E 1 11 HET MAN E 2 11 HET NAG F 1 14 HET NAG F 2 14 HET NAG G 1 14 HET NAG G 2 14 HET MAN G 3 11 HET MAN G 4 11 HET NAG H 1 14 HET NAG H 2 14 HET MAN H 3 11 HET SO4 A 1 5 HET SO4 A 2 5 HET SO4 A 5 5 HET NOJ A 430 11 HET NAG B 639 14 HET SO4 B 3 5 HET SO4 B 4 5 HET NOJ B 1 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM SO4 SULFATE ION HETNAM NOJ 1-DEOXYNOJIRIMYCIN HETSYN NOJ MORANOLINE FORMUL 3 NAG 11(C8 H15 N O6) FORMUL 5 MAN 5(C6 H12 O6) FORMUL 9 SO4 5(O4 S 2-) FORMUL 12 NOJ 2(C6 H13 N O4) FORMUL 17 HOH *64(H2 O) HELIX 1 1 HIS A 46 MET A 51 1 6 HELIX 2 2 GLU A 59 CYS A 63 5 5 HELIX 3 3 SER A 65 GLU A 79 1 15 HELIX 4 4 GLY A 80 GLY A 85 1 6 HELIX 5 5 HIS A 115 LYS A 127 1 13 HELIX 6 6 TYR A 151 GLY A 163 1 13 HELIX 7 7 SER A 176 GLY A 195 1 20 HELIX 8 8 GLU A 203 TRP A 209 1 7 HELIX 9 9 ASN A 215 GLN A 221 1 7 HELIX 10 10 SER A 235 ASN A 249 1 15 HELIX 11 11 ASN A 249 VAL A 254 1 6 HELIX 12 12 SER A 276 ALA A 291 1 16 HELIX 13 13 SER A 304 GLN A 312 1 9 HELIX 14 14 ASP A 313 GLN A 321 1 9 HELIX 15 15 ALA A 370 VAL A 376 5 7 HELIX 16 16 HIS B 46 MET B 51 1 6 HELIX 17 17 GLU B 59 CYS B 63 5 5 HELIX 18 18 SER B 65 GLU B 79 1 15 HELIX 19 19 GLY B 80 GLY B 85 1 6 HELIX 20 20 HIS B 115 LYS B 127 1 13 HELIX 21 21 TYR B 151 GLY B 163 1 13 HELIX 22 22 SER B 176 GLY B 195 1 20 HELIX 23 23 GLU B 203 TRP B 209 1 7 HELIX 24 24 ASN B 215 GLN B 221 1 7 HELIX 25 25 SER B 235 ASN B 249 1 15 HELIX 26 26 ASN B 249 VAL B 254 1 6 HELIX 27 27 SER B 276 MET B 290 1 15 HELIX 28 28 SER B 304 GLN B 312 1 9 HELIX 29 29 ASP B 313 GLN B 321 1 9 HELIX 30 30 ALA B 370 VAL B 376 5 7 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 ARG A 227 SHEET 4 A 8 LEU A 166 ASP A 170 1 N PHE A 169 O SER A 201 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 GLY A 132 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 ALA A 348 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 ARG A 392 GLU A 398 -1 O ARG A 392 N GLN A 386 SHEET 1 C 2 ARG A 363 SER A 364 0 SHEET 2 C 2 HIS A 406 ILE A 407 -1 O ILE A 407 N ARG A 363 SHEET 1 D 2 ILE A 367 ALA A 368 0 SHEET 2 D 2 ARG A 402 LEU A 403 -1 O LEU A 403 N ILE A 367 SHEET 1 E 8 TRP B 262 ASP B 264 0 SHEET 2 E 8 HIS B 225 ARG B 227 1 N TRP B 226 O ASP B 264 SHEET 3 E 8 VAL B 199 CYS B 202 1 N CYS B 202 O HIS B 225 SHEET 4 E 8 LEU B 166 ASP B 170 1 N PHE B 169 O SER B 201 SHEET 5 E 8 LYS B 130 ASP B 136 1 N ALA B 135 O ASP B 170 SHEET 6 E 8 TYR B 88 CYS B 90 1 N LEU B 89 O GLY B 132 SHEET 7 E 8 MET B 42 LEU B 45 1 N TRP B 44 O CYS B 90 SHEET 8 E 8 LEU B 294 MET B 296 1 O MET B 296 N LEU B 45 SHEET 1 F 6 TYR B 329 GLY B 334 0 SHEET 2 F 6 PHE B 337 PRO B 343 -1 O VAL B 339 N ARG B 332 SHEET 3 F 6 TRP B 349 ASN B 355 -1 O ALA B 352 N TRP B 340 SHEET 4 F 6 THR B 412 ASN B 419 -1 O LEU B 415 N VAL B 351 SHEET 5 F 6 ALA B 381 LEU B 388 -1 N LEU B 387 O LEU B 414 SHEET 6 F 6 ARG B 392 GLU B 398 -1 O ARG B 392 N GLN B 386 SHEET 1 G 2 ARG B 363 ALA B 368 0 SHEET 2 G 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 2.07 SSBOND 2 CYS A 56 CYS A 63 1555 1555 2.08 SSBOND 3 CYS A 142 CYS A 172 1555 1555 2.12 SSBOND 4 CYS A 202 CYS A 223 1555 1555 2.08 SSBOND 5 CYS A 378 CYS A 382 1555 1555 2.05 SSBOND 6 CYS B 52 CYS B 94 1555 1555 2.07 SSBOND 7 CYS B 56 CYS B 63 1555 1555 2.09 SSBOND 8 CYS B 142 CYS B 172 1555 1555 2.06 SSBOND 9 CYS B 202 CYS B 223 1555 1555 2.05 SSBOND 10 CYS B 378 CYS B 382 1555 1555 2.06 LINK ND2 ASN A 139 C1 NAG C 1 1555 1555 1.47 LINK ND2 ASN A 192 C1 NAG D 1 1555 1555 1.46 LINK ND2 ASN A 215 C1 NAG F 1 1555 1555 1.47 LINK ND2 ASN B 192 C1 NAG G 1 1555 1555 1.43 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.45 LINK O3 MAN E 1 C1 MAN E 2 1555 1555 1.47 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.47 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.43 LINK O4 NAG G 2 C1 MAN G 3 1555 1555 1.43 LINK O3 MAN G 3 C1 MAN G 4 1555 1555 1.43 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.46 LINK O4 NAG H 2 C1 MAN H 3 1555 1555 1.46 CISPEP 1 ASN A 379 PRO A 380 0 6.12 CISPEP 2 LEU A 388 PRO A 389 0 5.03 CISPEP 3 THR A 420 MET A 421 0 -13.23 CISPEP 4 ASN B 379 PRO B 380 0 5.72 CISPEP 5 LEU B 388 PRO B 389 0 0.94 CRYST1 89.610 89.610 216.640 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 0.011159 0.006443 0.000000 0.00000 SCALE2 0.000000 0.012886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004616 0.00000