HEADER HYDROLASE 30-NOV-18 6IBM TITLE CRYSTAL STRUCTURE OF HUMAN ALPHA-GALACTOSIDASE A IN COMPLEX WITH TITLE 2 ALPHA-GALACTOSE CONFIGURED CYCLOSULFATE ME776 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALPHA-D-GALACTOSIDASE A,ALPHA-D-GALACTOSIDE COMPND 5 GALACTOHYDROLASE,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, GLYCOSIDASE, GALACTOSE, CARBOHYDRATE EXPDTA X-RAY DIFFRACTION AUTHOR R.J.ROWLAND,L.WU,G.J.DAVIES REVDAT 4 06-NOV-24 6IBM 1 REMARK REVDAT 3 24-JAN-24 6IBM 1 HETSYN LINK REVDAT 2 29-JUL-20 6IBM 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE ATOM REVDAT 1 09-OCT-19 6IBM 0 JRNL AUTH M.ARTOLA,C.HEDBERG,R.J.ROWLAND,L.WU,L.RAICH,M.J.FERRAZ, JRNL AUTH 2 K.KYTIDOU,G.A.MAREL,J.D.C.CODEE,C.ROVIRA,J.M.F.G.AERTS, JRNL AUTH 3 G.J.DAVIES,H.S.OVERKLEEFT JRNL TITL ALPHA-D-GAL-CYCLOPHELLITOL CYCLOSULFAMIDATE IS A MICHAELIS JRNL TITL 2 COMPLEX ANALOG THAT STABILIZES THERAPEUTIC LYSOSOMAL JRNL TITL 3 ALPHA-GALACTOSIDASE A IN FABRY DISEASE JRNL REF CHEM SCI 2019 JRNL REFN ESSN 2041-6539 JRNL DOI 10.1039/C9SC03342D REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 78.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 60057 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3072 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4347 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE SET COUNT : 225 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6242 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 409 REMARK 3 SOLVENT ATOMS : 272 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.64000 REMARK 3 B22 (A**2) : 1.64000 REMARK 3 B33 (A**2) : -5.31000 REMARK 3 B12 (A**2) : 0.82000 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): 0.176 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.147 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.953 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6854 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6002 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9317 ; 1.568 ; 1.703 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13984 ; 1.296 ; 1.625 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 861 ; 7.501 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 357 ;35.049 ;22.773 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1086 ;14.980 ;15.193 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;16.481 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 896 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7452 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1452 ; 0.002 ; 0.020 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): 3145 ; 3.897 ; 5.593 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3143 ; 3.893 ; 5.591 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3928 ; 5.105 ; 8.379 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3929 ; 5.105 ; 8.381 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3709 ; 4.860 ; 6.333 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3710 ; 4.859 ; 6.334 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5390 ; 6.646 ; 9.352 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7770 ; 7.909 ;66.443 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7770 ; 7.908 ;66.442 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 REMARK 4 REMARK 4 6IBM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97951 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63220 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 78.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 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 : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1R46 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000 (50%), SODIUM ACETATE (PH REMARK 280 4.6) AND LITHIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 144.00000 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 72.00000 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 72.00000 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 144.00000 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: 11890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 29.0 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 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 731 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 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 67 CE NZ REMARK 470 LYS A 237 CE NZ REMARK 470 LYS A 314 NZ REMARK 470 MET A 421 CG SD CE REMARK 470 LYS B 67 CE NZ REMARK 470 LYS B 314 CD CE NZ REMARK 470 ARG B 404 CG CD NE CZ NH1 NH2 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 ASP A 170 CG ASP A 170 OD2 0.192 REMARK 500 ASP B 170 CG ASP B 170 OD2 0.201 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 ARG A 220 CG - CD - NE ANGL. DEV. = -13.8 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 MET A 51 -141.70 58.81 REMARK 500 MET A 51 -140.53 50.97 REMARK 500 CYS A 52 55.58 -108.78 REMARK 500 CYS A 52 55.58 -107.04 REMARK 500 ASP A 92 -155.54 -99.83 REMARK 500 SER A 197 101.84 -57.96 REMARK 500 ASP A 266 -178.00 85.85 REMARK 500 ASN A 272 -136.33 -99.74 REMARK 500 GLU A 358 48.51 -99.28 REMARK 500 MET B 51 -136.31 54.48 REMARK 500 ASP B 92 -158.24 -99.79 REMARK 500 CYS B 94 31.31 81.00 REMARK 500 ASP B 101 -179.45 -66.17 REMARK 500 ARG B 193 -8.68 -58.69 REMARK 500 PHE B 211 -65.17 -120.56 REMARK 500 ASP B 266 -178.83 88.35 REMARK 500 ASN B 272 -134.78 -93.23 REMARK 500 GLU B 358 41.20 -103.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 755 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 756 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH A 757 DISTANCE = 7.22 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6IBK RELATED DB: PDB REMARK 900 6IBK CONTAINS SAME PROTEIN COMPLEXED WITH GALACTOSE CONFIGURED REMARK 900 CYCLOSULFATE ME763 DBREF 6IBM A 32 429 UNP P06280 AGAL_HUMAN 32 429 DBREF 6IBM 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 BMA C 3 11 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 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 MAN F 6 11 HET NAG G 1 14 HET NAG G 2 14 HET NAG H 1 14 HET NAG H 2 14 HET BMA H 3 11 HET PEG A 509 7 HET PEG A 510 7 HET ACT A 511 4 HET ACT A 512 4 HET ACT A 513 4 HET SO4 A 514 5 HET SO4 A 515 5 HET SO4 A 516 5 HET HF8 A 517 16 HET EDO A 518 4 HET EDO A 519 4 HET EDO A 520 4 HET EDO A 521 4 HET EDO A 522 4 HET EDO A 523 4 HET EDO A 524 4 HET EDO A 525 4 HET EDO A 526 4 HET ACT B 512 4 HET SO4 B 513 5 HET SO4 B 514 5 HET SO4 B 515 5 HET HF8 B 516 16 HET EDO B 517 4 HET EDO B 518 4 HET EDO B 519 4 HET EDO B 520 4 HET EDO B 521 4 HET EDO B 522 4 HET EDO B 523 4 HET EDO B 524 4 HET EDO B 525 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETNAM HF8 [(1~{S},2~{R},3~{S},4~{S},5~{R},6~{S})-2- HETNAM 2 HF8 (HYDROXYMETHYL)-3,4,5,6-TETRAKIS(OXIDANYL)CYCLOHEXYL] HETNAM 3 HF8 HYDROGEN SULFATE HETNAM EDO 1,2-ETHANEDIOL 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 EDO ETHYLENE GLYCOL FORMUL 3 NAG 12(C8 H15 N O6) FORMUL 3 BMA 4(C6 H12 O6) FORMUL 6 MAN 3(C6 H12 O6) FORMUL 9 PEG 2(C4 H10 O3) FORMUL 11 ACT 4(C2 H3 O2 1-) FORMUL 14 SO4 6(O4 S 2-) FORMUL 17 HF8 2(C7 H14 O9 S) FORMUL 18 EDO 18(C2 H6 O2) FORMUL 41 HOH *272(H2 O) HELIX 1 AA1 HIS A 46 MET A 51 1 6 HELIX 2 AA2 SER A 65 GLU A 79 1 15 HELIX 3 AA3 GLY A 80 GLY A 85 1 6 HELIX 4 AA4 HIS A 115 LYS A 127 1 13 HELIX 5 AA5 TYR A 151 TRP A 162 1 12 HELIX 6 AA6 SER A 176 THR A 194 1 19 HELIX 7 AA7 GLU A 203 TRP A 209 1 7 HELIX 8 AA8 ASN A 215 CYS A 223 1 9 HELIX 9 AA9 SER A 235 ASN A 249 1 15 HELIX 10 AB1 ASN A 249 VAL A 254 1 6 HELIX 11 AB2 SER A 276 MET A 290 1 15 HELIX 12 AB3 SER A 304 GLN A 312 1 9 HELIX 13 AB4 ASP A 313 GLN A 321 1 9 HELIX 14 AB5 SER A 345 LEU A 347 5 3 HELIX 15 AB6 ALA A 370 VAL A 376 5 7 HELIX 16 AB7 HIS B 46 MET B 51 1 6 HELIX 17 AB8 SER B 65 GLU B 79 1 15 HELIX 18 AB9 TRP B 81 GLY B 85 5 5 HELIX 19 AC1 HIS B 115 LYS B 127 1 13 HELIX 20 AC2 TYR B 151 GLY B 163 1 13 HELIX 21 AC3 SER B 176 ARG B 193 1 18 HELIX 22 AC4 GLU B 203 TRP B 209 1 7 HELIX 23 AC5 ASN B 215 CYS B 223 1 9 HELIX 24 AC6 SER B 235 ASN B 249 1 15 HELIX 25 AC7 ASN B 249 VAL B 254 1 6 HELIX 26 AC8 SER B 276 MET B 290 1 15 HELIX 27 AC9 SER B 304 GLN B 312 1 9 HELIX 28 AD1 ASP B 313 GLN B 321 1 9 HELIX 29 AD2 ALA B 370 VAL B 376 5 7 SHEET 1 AA1 8 TRP A 262 ASP A 264 0 SHEET 2 AA1 8 HIS A 225 ARG A 227 1 N TRP A 226 O ASP A 264 SHEET 3 AA1 8 VAL A 199 CYS A 202 1 N CYS A 202 O HIS A 225 SHEET 4 AA1 8 LEU A 166 ASP A 170 1 N LEU A 167 O SER A 201 SHEET 5 AA1 8 LYS A 130 ASP A 136 1 N ILE A 133 O LYS A 168 SHEET 6 AA1 8 TYR A 88 CYS A 90 1 N LEU A 89 O LYS A 130 SHEET 7 AA1 8 MET A 42 LEU A 45 1 N TRP A 44 O CYS A 90 SHEET 8 AA1 8 LEU A 294 MET A 296 1 O LEU A 294 N GLY A 43 SHEET 1 AA2 6 TYR A 329 GLY A 334 0 SHEET 2 AA2 6 PHE A 337 PRO A 343 -1 O VAL A 339 N LEU A 331 SHEET 3 AA2 6 TRP A 349 ASN A 355 -1 O ALA A 352 N TRP A 340 SHEET 4 AA2 6 THR A 412 ASN A 419 -1 O LEU A 415 N VAL A 351 SHEET 5 AA2 6 ALA A 381 LEU A 388 -1 N LEU A 387 O LEU A 414 SHEET 6 AA2 6 ARG A 392 GLU A 398 -1 O TYR A 397 N CYS A 382 SHEET 1 AA3 2 ARG A 363 ALA A 368 0 SHEET 2 AA3 2 ARG A 402 ILE A 407 -1 O SER A 405 N TYR A 365 SHEET 1 AA4 8 TRP B 262 ASP B 264 0 SHEET 2 AA4 8 HIS B 225 ARG B 227 1 N TRP B 226 O ASP B 264 SHEET 3 AA4 8 VAL B 199 CYS B 202 1 N CYS B 202 O HIS B 225 SHEET 4 AA4 8 LEU B 166 ASP B 170 1 N LEU B 167 O SER B 201 SHEET 5 AA4 8 LYS B 130 ASP B 136 1 N ALA B 135 O ASP B 170 SHEET 6 AA4 8 TYR B 88 CYS B 90 1 N LEU B 89 O LYS B 130 SHEET 7 AA4 8 MET B 42 LEU B 45 1 N TRP B 44 O CYS B 90 SHEET 8 AA4 8 LEU B 294 MET B 296 1 O MET B 296 N LEU B 45 SHEET 1 AA5 6 TYR B 329 GLY B 334 0 SHEET 2 AA5 6 PHE B 337 LEU B 344 -1 O VAL B 339 N LEU B 331 SHEET 3 AA5 6 ALA B 348 ASN B 355 -1 O ALA B 348 N LEU B 344 SHEET 4 AA5 6 THR B 412 THR B 420 -1 O LEU B 417 N TRP B 349 SHEET 5 AA5 6 ALA B 381 LEU B 388 -1 N LEU B 387 O LEU B 414 SHEET 6 AA5 6 ARG B 392 GLU B 398 -1 O TYR B 397 N CYS B 382 SHEET 1 AA6 2 ARG B 363 ALA B 368 0 SHEET 2 AA6 2 ARG B 402 ILE B 407 -1 O LEU B 403 N ILE B 367 SSBOND 1 CYS A 52 CYS A 94 1555 1555 2.00 SSBOND 2 CYS A 56 CYS A 63 1555 1555 2.10 SSBOND 3 CYS A 142 CYS A 172 1555 1555 2.09 SSBOND 4 CYS A 202 CYS A 223 1555 1555 2.08 SSBOND 5 CYS A 378 CYS A 382 1555 1555 2.10 SSBOND 6 CYS B 52 CYS B 94 1555 1555 2.06 SSBOND 7 CYS B 56 CYS B 63 1555 1555 2.09 SSBOND 8 CYS B 142 CYS B 172 1555 1555 2.07 SSBOND 9 CYS B 202 CYS B 223 1555 1555 2.06 SSBOND 10 CYS B 378 CYS B 382 1555 1555 2.08 LINK ND2 ASN A 139 C1 NAG E 1 1555 1555 1.44 LINK OD2 ASP A 170 C5 HF8 A 517 1555 1555 1.43 LINK ND2 ASN A 192 C1 NAG C 1 1555 1555 1.41 LINK ND2 ASN A 215 C1 NAG D 1 1555 1555 1.42 LINK ND2 ASN B 139 C1 NAG H 1 1555 1555 1.43 LINK OD2 ASP B 170 C5 HF8 B 516 1555 1555 1.43 LINK ND2 ASN B 192 C1 NAG F 1 1555 1555 1.43 LINK ND2 ASN B 215 C1 NAG G 1 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.42 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.43 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.44 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.43 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.42 LINK O3 BMA F 3 C1 MAN F 4 1555 1555 1.44 LINK O6 BMA F 3 C1 MAN F 6 1555 1555 1.45 LINK O2 MAN F 4 C1 MAN F 5 1555 1555 1.44 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.45 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.45 LINK O4 NAG H 2 C1 BMA H 3 1555 1555 1.45 CISPEP 1 ASN A 379 PRO A 380 0 1.51 CISPEP 2 LEU A 388 PRO A 389 0 1.91 CISPEP 3 ASN B 379 PRO B 380 0 2.44 CISPEP 4 LEU B 388 PRO B 389 0 1.84 CRYST1 90.340 90.340 216.000 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 0.011069 0.006391 0.000000 0.00000 SCALE2 0.000000 0.012782 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004630 0.00000