PDB Short entry for 3LXB HEADER HYDROLASE 25-FEB-10 3LXB TITLE INTERCONVERSION OF HUMAN LYSOSOMAL ENZYME SPECIFICITIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 32-429; COMPND 5 SYNONYM: ALPHA-D-GALACTOSIDE GALACTOHYDROLASE, ALPHA-D-GALACTOSIDASE COMPND 6 A, MELIBIASE; COMPND 7 EC: 3.2.1.22; COMPND 8 ENGINEERED: YES; COMPND 9 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_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HI-FIVE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: STABLE CELL LINE; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PIB/V5-HIS-TOPO TA KEYWDS GLYCOPROTEIN, CARBOHYDRATE-BINDING PROTEIN, GLYCOSIDASE, LYSOSOMAL KEYWDS 2 ENZYME, (BETA/ALPHA)8 BARREL, ENZYME INTERCONVERSION, DISEASE KEYWDS 3 MUTATION, DISULFIDE BOND, HYDROLASE, LYSOSOME EXPDTA X-RAY DIFFRACTION AUTHOR I.B.TOMASIC,M.C.METCALF,A.I.GUCE,N.E.CLARK,S.C.GARMAN REVDAT 6 06-SEP-23 3LXB 1 REMARK REVDAT 5 13-OCT-21 3LXB 1 SEQADV HETSYN REVDAT 4 29-JUL-20 3LXB 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 08-NOV-17 3LXB 1 REMARK REVDAT 2 01-JUN-11 3LXB 1 JRNL REVDAT 1 05-MAY-10 3LXB 0 JRNL AUTH I.B.TOMASIC,M.C.METCALF,A.I.GUCE,N.E.CLARK,S.C.GARMAN JRNL TITL INTERCONVERSION OF THE SPECIFICITIES OF HUMAN LYSOSOMAL JRNL TITL 2 ENZYMES ASSOCIATED WITH FABRY AND SCHINDLER DISEASES. JRNL REF J.BIOL.CHEM. V. 285 21560 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20444686 JRNL DOI 10.1074/JBC.M110.118588 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 27799 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1352 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) : 2.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1905 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6320 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 206 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : 0.26000 REMARK 3 B33 (A**2) : -0.16000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.384 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.279 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.434 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.893 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.852 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6717 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9129 ; 1.222 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 789 ; 5.364 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 319 ;38.224 ;24.295 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1067 ;16.935 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;18.444 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 966 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5127 ; 0.005 ; 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): 3929 ; 1.890 ; 8.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6294 ; 3.204 ;12.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2788 ; 2.197 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2835 ; 3.438 ;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 : 7 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 32 A 100 2 REMARK 3 1 B 32 B 100 2 REMARK 3 2 A 106 A 117 2 REMARK 3 2 B 106 B 117 2 REMARK 3 3 A 119 A 156 2 REMARK 3 3 B 119 B 156 2 REMARK 3 4 A 163 A 206 2 REMARK 3 4 B 163 B 206 2 REMARK 3 5 A 214 A 226 2 REMARK 3 5 B 214 B 226 2 REMARK 3 6 A 233 A 244 2 REMARK 3 6 B 233 B 244 2 REMARK 3 7 A 253 A 328 2 REMARK 3 7 B 253 B 328 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1056 ; 0.040 ; 0.050 REMARK 3 MEDIUM POSITIONAL 1 A (A): 1026 ; 0.150 ; 0.500 REMARK 3 TIGHT THERMAL 1 A (A**2): 1056 ; 0.100 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1026 ; 0.110 ;10.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 4 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 329 A 344 2 REMARK 3 1 B 329 B 344 2 REMARK 3 2 A 348 A 378 2 REMARK 3 2 B 348 B 378 2 REMARK 3 3 A 384 A 392 2 REMARK 3 3 B 384 B 392 2 REMARK 3 4 A 401 A 421 2 REMARK 3 4 B 401 B 421 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 2 A (A): 308 ; 0.030 ; 0.050 REMARK 3 MEDIUM POSITIONAL 2 A (A): 298 ; 0.190 ; 0.500 REMARK 3 TIGHT THERMAL 2 A (A**2): 308 ; 0.110 ; 0.500 REMARK 3 MEDIUM THERMAL 2 A (A**2): 298 ; 0.100 ;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): 7.5790 -4.4260 20.1840 REMARK 3 T TENSOR REMARK 3 T11: 0.0755 T22: 0.0502 REMARK 3 T33: 0.0915 T12: 0.0156 REMARK 3 T13: 0.0031 T23: -0.0233 REMARK 3 L TENSOR REMARK 3 L11: 0.0949 L22: 0.2742 REMARK 3 L33: 1.3158 L12: 0.0928 REMARK 3 L13: 0.1554 L23: -0.2157 REMARK 3 S TENSOR REMARK 3 S11: 0.0274 S12: 0.0119 S13: 0.0174 REMARK 3 S21: -0.0027 S22: 0.0278 S23: 0.0082 REMARK 3 S31: 0.0022 S32: 0.0281 S33: -0.0552 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 426 REMARK 3 ORIGIN FOR THE GROUP (A): -0.8550 -19.0530 46.0900 REMARK 3 T TENSOR REMARK 3 T11: 0.1140 T22: 0.0114 REMARK 3 T33: 0.0495 T12: -0.0328 REMARK 3 T13: -0.0237 T23: 0.0093 REMARK 3 L TENSOR REMARK 3 L11: 1.8995 L22: 0.5140 REMARK 3 L33: 2.1938 L12: 0.6395 REMARK 3 L13: -0.1028 L23: 0.4993 REMARK 3 S TENSOR REMARK 3 S11: 0.1227 S12: -0.0280 S13: -0.0060 REMARK 3 S21: 0.1696 S22: -0.0464 S23: 0.0466 REMARK 3 S31: 0.3723 S32: -0.1464 S33: -0.0763 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): 21.9390 5.0110 64.9130 REMARK 3 T TENSOR REMARK 3 T11: 0.0880 T22: 0.0219 REMARK 3 T33: 0.0793 T12: 0.0117 REMARK 3 T13: -0.0238 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.5322 L22: 0.0274 REMARK 3 L33: 0.7069 L12: -0.0478 REMARK 3 L13: -0.2969 L23: -0.0589 REMARK 3 S TENSOR REMARK 3 S11: 0.0062 S12: -0.0040 S13: 0.0620 REMARK 3 S21: 0.0122 S22: 0.0227 S23: 0.0084 REMARK 3 S31: -0.0247 S32: -0.0916 S33: -0.0289 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 425 REMARK 3 ORIGIN FOR THE GROUP (A): 36.3000 12.1200 38.4080 REMARK 3 T TENSOR REMARK 3 T11: 0.0327 T22: 0.0102 REMARK 3 T33: 0.1174 T12: -0.0140 REMARK 3 T13: -0.0286 T23: 0.0178 REMARK 3 L TENSOR REMARK 3 L11: 0.2909 L22: 0.3661 REMARK 3 L33: 0.6603 L12: -0.1767 REMARK 3 L13: -0.3526 L23: -0.0230 REMARK 3 S TENSOR REMARK 3 S11: 0.0180 S12: 0.0046 S13: 0.0595 REMARK 3 S21: 0.0010 S22: 0.0033 S23: -0.0609 REMARK 3 S31: -0.0496 S32: -0.0071 S33: -0.0213 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 3LXB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000057846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-09 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 : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98010 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL CUT REMARK 200 OPTICS : TOROIDAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27897 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.17700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.61600 REMARK 200 R SYM FOR SHELL (I) : 0.61600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3HG3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, SODIUM CACODYLATE, MAGNESIUM REMARK 280 ACETATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 29.89500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 90.79900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.49800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 90.79900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.89500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.49800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 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 -139.81 59.66 REMARK 500 CYS A 52 53.59 -109.02 REMARK 500 ASP A 92 -149.74 -89.93 REMARK 500 TYR A 151 12.61 -142.91 REMARK 500 TRP A 204 -71.25 -26.23 REMARK 500 ASP A 266 -179.80 85.14 REMARK 500 ASN A 272 -123.13 -101.22 REMARK 500 LEU A 425 88.99 -67.93 REMARK 500 MET B 51 -140.31 60.86 REMARK 500 CYS B 52 52.51 -108.01 REMARK 500 ASP B 92 -146.23 -90.50 REMARK 500 PRO B 210 25.06 -70.91 REMARK 500 PHE B 211 -50.38 -141.62 REMARK 500 ASP B 266 -179.36 83.81 REMARK 500 ASN B 272 -123.03 -100.39 REMARK 500 LEU B 425 38.47 -74.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LX9 RELATED DB: PDB REMARK 900 ALPHA-GAL(SA) COMPLEX WITH GALNAC REMARK 900 RELATED ID: 3LXA RELATED DB: PDB REMARK 900 ALPHA-GAL(SA) COMPLEX WITH GALACTOSE REMARK 900 RELATED ID: 3LXC RELATED DB: PDB REMARK 900 ALPHA-GAL(SA) COMPLEX 2 WITH GLYCEROL REMARK 900 RELATED ID: 1R46 RELATED DB: PDB REMARK 900 ALPHA-GAL REMARK 900 RELATED ID: 3HG2 RELATED DB: PDB REMARK 900 ALPHA-GAL CATALYTIC MECHANISM DBREF 3LXB A 32 429 UNP P06280 AGAL_HUMAN 32 429 DBREF 3LXB B 32 429 UNP P06280 AGAL_HUMAN 32 429 SEQADV 3LXB SER A 203 UNP P06280 GLU 203 ENGINEERED MUTATION SEQADV 3LXB ALA A 206 UNP P06280 LEU 206 ENGINEERED MUTATION SEQADV 3LXB HIS A 430 UNP P06280 EXPRESSION TAG SEQADV 3LXB HIS A 431 UNP P06280 EXPRESSION TAG SEQADV 3LXB HIS A 432 UNP P06280 EXPRESSION TAG SEQADV 3LXB HIS A 433 UNP P06280 EXPRESSION TAG SEQADV 3LXB HIS A 434 UNP P06280 EXPRESSION TAG SEQADV 3LXB HIS A 435 UNP P06280 EXPRESSION TAG SEQADV 3LXB SER B 203 UNP P06280 GLU 203 ENGINEERED MUTATION SEQADV 3LXB ALA B 206 UNP P06280 LEU 206 ENGINEERED MUTATION SEQADV 3LXB HIS B 430 UNP P06280 EXPRESSION TAG SEQADV 3LXB HIS B 431 UNP P06280 EXPRESSION TAG SEQADV 3LXB HIS B 432 UNP P06280 EXPRESSION TAG SEQADV 3LXB HIS B 433 UNP P06280 EXPRESSION TAG SEQADV 3LXB HIS B 434 UNP P06280 EXPRESSION TAG SEQADV 3LXB 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 ASP 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 SER TRP PRO ALA 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 ASP 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 SER TRP PRO ALA 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 3LXB ASN A 192 ASN GLYCOSYLATION SITE MODRES 3LXB ASN B 215 ASN GLYCOSYLATION SITE MODRES 3LXB ASN B 192 ASN GLYCOSYLATION SITE MODRES 3LXB ASN B 139 ASN GLYCOSYLATION SITE MODRES 3LXB ASN A 215 ASN GLYCOSYLATION SITE MODRES 3LXB ASN A 139 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 NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET MAN E 4 11 HET NAG A 639 14 HET GOL A 802 6 HET GOL A 803 6 HET NAG B 639 14 HET NAG B 715 14 HET GOL B 801 6 HET GOL B 804 6 HET GOL B 811 6 HET GOL B 812 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM GOL GLYCEROL 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 GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAG 9(C8 H15 N O6) FORMUL 3 BMA 2(C6 H12 O6) FORMUL 3 MAN 2(C6 H12 O6) FORMUL 7 GOL 6(C3 H8 O3) FORMUL 15 HOH *131(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 GLY B 195 1 20 HELIX 22 22 SER 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 ASP A 170 1 N PHE A 169 O SER A 201 SHEET 5 A 8 LYS A 130 ASP A 136 1 N ILE A 133 O LEU A 166 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 LEU A 344 -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 ALA A 368 0 SHEET 2 C 2 ARG A 402 ILE A 407 -1 O LEU A 403 N ILE A 367 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 PHE B 169 O SER B 201 SHEET 5 D 8 LYS B 130 ASP B 136 1 N ILE B 133 O LEU B 166 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 LEU B 294 N GLY B 43 SHEET 1 E 6 TYR B 329 GLY B 334 0 SHEET 2 E 6 PHE B 337 LEU B 344 -1 O VAL B 339 N ARG B 332 SHEET 3 E 6 ALA B 348 ASN B 355 -1 O ALA B 348 N LEU B 344 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 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 LEU B 403 N ILE B 367 SSBOND 1 CYS A 52 CYS A 94 1555 1555 2.04 SSBOND 2 CYS A 56 CYS A 63 1555 1555 2.05 SSBOND 3 CYS A 142 CYS A 172 1555 1555 2.05 SSBOND 4 CYS A 202 CYS A 223 1555 1555 2.03 SSBOND 5 CYS A 378 CYS A 382 1555 1555 2.04 SSBOND 6 CYS B 52 CYS B 94 1555 1555 2.03 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 2.04 LINK ND2 ASN A 139 C1 NAG A 639 1555 1555 1.46 LINK ND2 ASN A 192 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 215 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN B 139 C1 NAG B 639 1555 1555 1.45 LINK ND2 ASN B 192 C1 NAG E 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 1.45 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 O3 BMA E 3 C1 MAN E 4 1555 1555 1.46 CISPEP 1 TRP A 209 PRO A 210 0 -0.30 CISPEP 2 ASN A 379 PRO A 380 0 1.15 CISPEP 3 LEU A 388 PRO A 389 0 3.71 CISPEP 4 ASN B 379 PRO B 380 0 7.17 CISPEP 5 LEU B 388 PRO B 389 0 3.44 CRYST1 59.790 106.996 181.598 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 0.016725 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005507 0.00000