HEADER HYDROLASE 09-FEB-12 4DO6 TITLE PHARMACOLOGICAL CHAPERONES FOR HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-N-ACETYLGALACTOSAMINIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALPHA-GALACTOSIDASE B; COMPND 5 EC: 3.2.1.49; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: NAGA; SOURCE 5 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HI-FIVE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PIB/V5-HIS-TOPO TA KEYWDS BETA/ALPHA)8 BARREL, GLYCOSIDASE, CARBOHYDRATE-BINDING PROTEIN, KEYWDS 2 GLYCOPROTEIN, LYSOSOME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.E.CLARK,S.C.GARMAN REVDAT 6 30-OCT-24 4DO6 1 REMARK REVDAT 5 13-SEP-23 4DO6 1 HETSYN REVDAT 4 29-JUL-20 4DO6 1 CAVEAT COMPND REMARK SEQADV REVDAT 4 2 1 HETNAM LINK SITE ATOM REVDAT 3 15-NOV-17 4DO6 1 REMARK REVDAT 2 21-NOV-12 4DO6 1 JRNL REVDAT 1 10-OCT-12 4DO6 0 JRNL AUTH N.E.CLARK,M.C.METCALF,D.BEST,G.W.FLEET,S.C.GARMAN JRNL TITL PHARMACOLOGICAL CHAPERONES FOR HUMAN JRNL TITL 2 ALPHA-N-ACETYLGALACTOSAMINIDASE JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 17400 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 23045655 JRNL DOI 10.1073/PNAS.1203924109 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 145693 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 7382 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7021 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.3500 REMARK 3 BIN FREE R VALUE SET COUNT : 359 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6287 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 294 REMARK 3 SOLVENT ATOMS : 786 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.20000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.067 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.032 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6847 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4591 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9353 ; 1.244 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11113 ; 0.854 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 802 ; 6.106 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 313 ;34.508 ;24.121 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1068 ;12.095 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;18.122 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1039 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7436 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1356 ; 0.001 ; 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): 3970 ; 2.593 ;12.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1598 ; 1.038 ;12.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6409 ; 4.054 ;16.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2877 ; 5.806 ;20.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2942 ; 8.566 ;24.000 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 : NULL 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 18 A 310 REMARK 3 ORIGIN FOR THE GROUP (A): 56.3047 -1.2059 10.1753 REMARK 3 T TENSOR REMARK 3 T11: 0.0500 T22: 0.0302 REMARK 3 T33: 0.0114 T12: -0.0047 REMARK 3 T13: 0.0009 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 1.0935 L22: 0.2458 REMARK 3 L33: 0.4182 L12: 0.0456 REMARK 3 L13: -0.1369 L23: -0.0853 REMARK 3 S TENSOR REMARK 3 S11: 0.0265 S12: 0.0037 S13: 0.0887 REMARK 3 S21: 0.0259 S22: 0.0208 S23: 0.0113 REMARK 3 S31: -0.0335 S32: 0.0477 S33: -0.0473 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 311 A 404 REMARK 3 ORIGIN FOR THE GROUP (A): 25.7022 3.2041 10.8671 REMARK 3 T TENSOR REMARK 3 T11: 0.0504 T22: 0.0626 REMARK 3 T33: 0.1342 T12: 0.0349 REMARK 3 T13: 0.0355 T23: 0.0585 REMARK 3 L TENSOR REMARK 3 L11: 1.4073 L22: 1.4424 REMARK 3 L33: 0.7668 L12: -0.1776 REMARK 3 L13: -0.3220 L23: -0.4192 REMARK 3 S TENSOR REMARK 3 S11: 0.0668 S12: 0.0509 S13: 0.1424 REMARK 3 S21: 0.1140 S22: 0.1113 S23: 0.3632 REMARK 3 S31: -0.1198 S32: -0.1633 S33: -0.1781 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 18 B 310 REMARK 3 ORIGIN FOR THE GROUP (A): 21.3708 -31.4322 21.8454 REMARK 3 T TENSOR REMARK 3 T11: 0.0514 T22: 0.0568 REMARK 3 T33: 0.0895 T12: -0.0132 REMARK 3 T13: -0.0156 T23: 0.0572 REMARK 3 L TENSOR REMARK 3 L11: 1.2454 L22: 1.2771 REMARK 3 L33: 0.7764 L12: 0.4679 REMARK 3 L13: -0.5546 L23: -0.5398 REMARK 3 S TENSOR REMARK 3 S11: -0.0291 S12: 0.0746 S13: 0.0398 REMARK 3 S21: 0.0560 S22: 0.1528 S23: 0.2786 REMARK 3 S31: 0.0019 S32: -0.1254 S33: -0.1237 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 311 B 404 REMARK 3 ORIGIN FOR THE GROUP (A): 51.1557 -36.9640 16.8231 REMARK 3 T TENSOR REMARK 3 T11: 0.0653 T22: 0.0483 REMARK 3 T33: 0.1605 T12: 0.0219 REMARK 3 T13: -0.0080 T23: 0.0365 REMARK 3 L TENSOR REMARK 3 L11: 1.9876 L22: 1.4820 REMARK 3 L33: 0.8943 L12: -0.0618 REMARK 3 L13: -0.4573 L23: -0.1537 REMARK 3 S TENSOR REMARK 3 S11: -0.0656 S12: -0.0873 S13: -0.3017 REMARK 3 S21: -0.0013 S22: -0.0579 S23: -0.3839 REMARK 3 S31: 0.1269 S32: 0.1674 S33: 0.1235 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4DO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : PT COATED 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 : 145750 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 94.7 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.65300 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3H53 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8-16% PEG3350, 70MM CITRIC ACID, 30MM REMARK 280 BIS-TRIS PROPANE, PH 3.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 76.65450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.15200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 76.65450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.15200 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: 1970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 LEU A 406 REMARK 465 GLU A 407 REMARK 465 MET A 408 REMARK 465 SER A 409 REMARK 465 GLN A 410 REMARK 465 GLN A 411 REMARK 465 HIS A 412 REMARK 465 HIS A 413 REMARK 465 HIS A 414 REMARK 465 HIS A 415 REMARK 465 HIS A 416 REMARK 465 HIS A 417 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 ARG A 37 -134.55 51.48 REMARK 500 CYS A 38 42.92 -108.75 REMARK 500 ASP A 78 -147.43 -111.37 REMARK 500 CYS A 80 16.56 82.31 REMARK 500 LYS A 149 34.19 71.10 REMARK 500 ASP A 252 -178.39 91.69 REMARK 500 ASN A 258 -142.48 -99.46 REMARK 500 LEU A 280 79.47 -109.34 REMARK 500 SER A 283 88.85 -156.73 REMARK 500 ASP A 346 -67.81 -107.00 REMARK 500 SER A 363 -1.10 70.67 REMARK 500 ARG B 37 -137.17 53.18 REMARK 500 CYS B 38 47.67 -108.42 REMARK 500 ASP B 78 -150.14 -113.79 REMARK 500 ASP B 252 -176.54 91.36 REMARK 500 ASN B 258 -143.54 -99.86 REMARK 500 LEU B 280 79.32 -108.27 REMARK 500 SER B 283 88.06 -156.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 2PE B 510 REMARK 610 2PE B 513 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H53 RELATED DB: PDB REMARK 900 COMPLEX WITH GLYCEROL REMARK 900 RELATED ID: 3H54 RELATED DB: PDB REMARK 900 COMPLEX WITH GALNAC REMARK 900 RELATED ID: 3H55 RELATED DB: PDB REMARK 900 COMPLEX WITH GALACTOSE REMARK 900 RELATED ID: 3IGU RELATED DB: PDB REMARK 900 COVALENT COMPLEX REMARK 900 RELATED ID: 4DO4 RELATED DB: PDB REMARK 900 COMPLEX WITH DGJNAC REMARK 900 RELATED ID: 4DO5 RELATED DB: PDB REMARK 900 COMPLEX WITH DGJ DBREF 4DO6 A 18 411 UNP P17050 NAGAB_HUMAN 18 411 DBREF 4DO6 B 18 411 UNP P17050 NAGAB_HUMAN 18 411 SEQADV 4DO6 GLN A 201 UNP P17050 ASN 201 ENGINEERED MUTATION SEQADV 4DO6 HIS A 412 UNP P17050 EXPRESSION TAG SEQADV 4DO6 HIS A 413 UNP P17050 EXPRESSION TAG SEQADV 4DO6 HIS A 414 UNP P17050 EXPRESSION TAG SEQADV 4DO6 HIS A 415 UNP P17050 EXPRESSION TAG SEQADV 4DO6 HIS A 416 UNP P17050 EXPRESSION TAG SEQADV 4DO6 HIS A 417 UNP P17050 EXPRESSION TAG SEQADV 4DO6 GLN B 201 UNP P17050 ASN 201 ENGINEERED MUTATION SEQADV 4DO6 HIS B 412 UNP P17050 EXPRESSION TAG SEQADV 4DO6 HIS B 413 UNP P17050 EXPRESSION TAG SEQADV 4DO6 HIS B 414 UNP P17050 EXPRESSION TAG SEQADV 4DO6 HIS B 415 UNP P17050 EXPRESSION TAG SEQADV 4DO6 HIS B 416 UNP P17050 EXPRESSION TAG SEQADV 4DO6 HIS B 417 UNP P17050 EXPRESSION TAG SEQRES 1 A 400 LEU ASP ASN GLY LEU LEU GLN THR PRO PRO MET GLY TRP SEQRES 2 A 400 LEU ALA TRP GLU ARG PHE ARG CYS ASN ILE ASN CYS ASP SEQRES 3 A 400 GLU ASP PRO LYS ASN CYS ILE SER GLU GLN LEU PHE MET SEQRES 4 A 400 GLU MET ALA ASP ARG MET ALA GLN ASP GLY TRP ARG ASP SEQRES 5 A 400 MET GLY TYR THR TYR LEU ASN ILE ASP ASP CYS TRP ILE SEQRES 6 A 400 GLY GLY ARG ASP ALA SER GLY ARG LEU MET PRO ASP PRO SEQRES 7 A 400 LYS ARG PHE PRO HIS GLY ILE PRO PHE LEU ALA ASP TYR SEQRES 8 A 400 VAL HIS SER LEU GLY LEU LYS LEU GLY ILE TYR ALA ASP SEQRES 9 A 400 MET GLY ASN PHE THR CYS MET GLY TYR PRO GLY THR THR SEQRES 10 A 400 LEU ASP LYS VAL VAL GLN ASP ALA GLN THR PHE ALA GLU SEQRES 11 A 400 TRP LYS VAL ASP MET LEU LYS LEU ASP GLY CYS PHE SER SEQRES 12 A 400 THR PRO GLU GLU ARG ALA GLN GLY TYR PRO LYS MET ALA SEQRES 13 A 400 ALA ALA LEU ASN ALA THR GLY ARG PRO ILE ALA PHE SER SEQRES 14 A 400 CYS SER TRP PRO ALA TYR GLU GLY GLY LEU PRO PRO ARG SEQRES 15 A 400 VAL GLN TYR SER LEU LEU ALA ASP ILE CYS ASN LEU TRP SEQRES 16 A 400 ARG ASN TYR ASP ASP ILE GLN ASP SER TRP TRP SER VAL SEQRES 17 A 400 LEU SER ILE LEU ASN TRP PHE VAL GLU HIS GLN ASP ILE SEQRES 18 A 400 LEU GLN PRO VAL ALA GLY PRO GLY HIS TRP ASN ASP PRO SEQRES 19 A 400 ASP MET LEU LEU ILE GLY ASN PHE GLY LEU SER LEU GLU SEQRES 20 A 400 GLN SER ARG ALA GLN MET ALA LEU TRP THR VAL LEU ALA SEQRES 21 A 400 ALA PRO LEU LEU MET SER THR ASP LEU ARG THR ILE SER SEQRES 22 A 400 ALA GLN ASN MET ASP ILE LEU GLN ASN PRO LEU MET ILE SEQRES 23 A 400 LYS ILE ASN GLN ASP PRO LEU GLY ILE GLN GLY ARG ARG SEQRES 24 A 400 ILE HIS LYS GLU LYS SER LEU ILE GLU VAL TYR MET ARG SEQRES 25 A 400 PRO LEU SER ASN LYS ALA SER ALA LEU VAL PHE PHE SER SEQRES 26 A 400 CYS ARG THR ASP MET PRO TYR ARG TYR HIS SER SER LEU SEQRES 27 A 400 GLY GLN LEU ASN PHE THR GLY SER VAL ILE TYR GLU ALA SEQRES 28 A 400 GLN ASP VAL TYR SER GLY ASP ILE ILE SER GLY LEU ARG SEQRES 29 A 400 ASP GLU THR ASN PHE THR VAL ILE ILE ASN PRO SER GLY SEQRES 30 A 400 VAL VAL MET TRP TYR LEU TYR PRO ILE LYS ASN LEU GLU SEQRES 31 A 400 MET SER GLN GLN HIS HIS HIS HIS HIS HIS SEQRES 1 B 400 LEU ASP ASN GLY LEU LEU GLN THR PRO PRO MET GLY TRP SEQRES 2 B 400 LEU ALA TRP GLU ARG PHE ARG CYS ASN ILE ASN CYS ASP SEQRES 3 B 400 GLU ASP PRO LYS ASN CYS ILE SER GLU GLN LEU PHE MET SEQRES 4 B 400 GLU MET ALA ASP ARG MET ALA GLN ASP GLY TRP ARG ASP SEQRES 5 B 400 MET GLY TYR THR TYR LEU ASN ILE ASP ASP CYS TRP ILE SEQRES 6 B 400 GLY GLY ARG ASP ALA SER GLY ARG LEU MET PRO ASP PRO SEQRES 7 B 400 LYS ARG PHE PRO HIS GLY ILE PRO PHE LEU ALA ASP TYR SEQRES 8 B 400 VAL HIS SER LEU GLY LEU LYS LEU GLY ILE TYR ALA ASP SEQRES 9 B 400 MET GLY ASN PHE THR CYS MET GLY TYR PRO GLY THR THR SEQRES 10 B 400 LEU ASP LYS VAL VAL GLN ASP ALA GLN THR PHE ALA GLU SEQRES 11 B 400 TRP LYS VAL ASP MET LEU LYS LEU ASP GLY CYS PHE SER SEQRES 12 B 400 THR PRO GLU GLU ARG ALA GLN GLY TYR PRO LYS MET ALA SEQRES 13 B 400 ALA ALA LEU ASN ALA THR GLY ARG PRO ILE ALA PHE SER SEQRES 14 B 400 CYS SER TRP PRO ALA TYR GLU GLY GLY LEU PRO PRO ARG SEQRES 15 B 400 VAL GLN TYR SER LEU LEU ALA ASP ILE CYS ASN LEU TRP SEQRES 16 B 400 ARG ASN TYR ASP ASP ILE GLN ASP SER TRP TRP SER VAL SEQRES 17 B 400 LEU SER ILE LEU ASN TRP PHE VAL GLU HIS GLN ASP ILE SEQRES 18 B 400 LEU GLN PRO VAL ALA GLY PRO GLY HIS TRP ASN ASP PRO SEQRES 19 B 400 ASP MET LEU LEU ILE GLY ASN PHE GLY LEU SER LEU GLU SEQRES 20 B 400 GLN SER ARG ALA GLN MET ALA LEU TRP THR VAL LEU ALA SEQRES 21 B 400 ALA PRO LEU LEU MET SER THR ASP LEU ARG THR ILE SER SEQRES 22 B 400 ALA GLN ASN MET ASP ILE LEU GLN ASN PRO LEU MET ILE SEQRES 23 B 400 LYS ILE ASN GLN ASP PRO LEU GLY ILE GLN GLY ARG ARG SEQRES 24 B 400 ILE HIS LYS GLU LYS SER LEU ILE GLU VAL TYR MET ARG SEQRES 25 B 400 PRO LEU SER ASN LYS ALA SER ALA LEU VAL PHE PHE SER SEQRES 26 B 400 CYS ARG THR ASP MET PRO TYR ARG TYR HIS SER SER LEU SEQRES 27 B 400 GLY GLN LEU ASN PHE THR GLY SER VAL ILE TYR GLU ALA SEQRES 28 B 400 GLN ASP VAL TYR SER GLY ASP ILE ILE SER GLY LEU ARG SEQRES 29 B 400 ASP GLU THR ASN PHE THR VAL ILE ILE ASN PRO SER GLY SEQRES 30 B 400 VAL VAL MET TRP TYR LEU TYR PRO ILE LYS ASN LEU GLU SEQRES 31 B 400 MET SER GLN GLN HIS HIS HIS HIS HIS HIS MODRES 4DO6 ASN A 177 ASN GLYCOSYLATION SITE MODRES 4DO6 ASN B 177 ASN GLYCOSYLATION SITE MODRES 4DO6 ASN A 385 ASN GLYCOSYLATION SITE MODRES 4DO6 ASN A 124 ASN GLYCOSYLATION SITE MODRES 4DO6 ASN B 124 ASN GLYCOSYLATION SITE MODRES 4DO6 ASN B 385 ASN GLYCOSYLATION SITE 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 BMA D 3 11 HET MAN D 4 11 HET MAN D 5 11 HET NAG E 1 14 HET NAG E 2 14 HET FUC E 3 10 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 NAG A 509 14 HET CIT A 510 13 HET GLC A 511 12 HET GLC A 512 12 HET NAG B 509 14 HET 2PE B 510 3 HET BGC B 511 12 HET GLC B 512 12 HET 2PE B 513 3 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM CIT CITRIC ACID HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM 2PE NONAETHYLENE GLYCOL HETNAM BGC BETA-D-GLUCOPYRANOSE 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 FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 3 NAG 10(C8 H15 N O6) FORMUL 3 BMA 3(C6 H12 O6) FORMUL 4 MAN 4(C6 H12 O6) FORMUL 5 FUC C6 H12 O5 FORMUL 8 CIT C6 H8 O7 FORMUL 9 GLC 3(C6 H12 O6) FORMUL 12 2PE 2(C18 H38 O10) FORMUL 13 BGC C6 H12 O6 FORMUL 16 HOH *786(H2 O) HELIX 1 1 ALA A 32 ARG A 37 1 6 HELIX 2 2 SER A 51 ASP A 65 1 15 HELIX 3 3 GLY A 66 GLY A 71 1 6 HELIX 4 4 GLY A 101 LEU A 112 1 12 HELIX 5 5 THR A 134 ASP A 136 5 3 HELIX 6 6 LYS A 137 TRP A 148 1 12 HELIX 7 7 THR A 161 THR A 179 1 19 HELIX 8 8 SER A 188 GLU A 193 1 6 HELIX 9 9 GLN A 201 CYS A 209 1 9 HELIX 10 10 SER A 221 HIS A 235 1 15 HELIX 11 11 HIS A 235 GLN A 240 1 6 HELIX 12 12 PRO A 241 ALA A 243 5 3 HELIX 13 13 SER A 262 LEU A 276 1 15 HELIX 14 14 SER A 290 GLN A 298 1 9 HELIX 15 15 ASN A 299 GLN A 307 1 9 HELIX 16 16 SER A 332 LYS A 334 5 3 HELIX 17 17 LEU A 355 ASN A 359 5 5 HELIX 18 18 ALA B 32 ARG B 37 1 6 HELIX 19 19 SER B 51 ASP B 65 1 15 HELIX 20 20 GLY B 66 GLY B 71 1 6 HELIX 21 21 GLY B 101 LEU B 112 1 12 HELIX 22 22 THR B 134 ASP B 136 5 3 HELIX 23 23 LYS B 137 LYS B 149 1 13 HELIX 24 24 THR B 161 THR B 179 1 19 HELIX 25 25 TRP B 189 GLY B 194 5 6 HELIX 26 26 GLN B 201 CYS B 209 1 9 HELIX 27 27 SER B 221 HIS B 235 1 15 HELIX 28 28 HIS B 235 GLN B 240 1 6 HELIX 29 29 PRO B 241 ALA B 243 5 3 HELIX 30 30 SER B 262 LEU B 276 1 15 HELIX 31 31 SER B 290 GLN B 298 1 9 HELIX 32 32 ASN B 299 GLN B 307 1 9 HELIX 33 33 SER B 332 LYS B 334 5 3 HELIX 34 34 SER B 354 ASN B 359 5 6 HELIX 35 35 ILE B 403 GLN B 411 1 9 SHEET 1 A 8 TRP A 248 ASP A 250 0 SHEET 2 A 8 LEU A 211 ARG A 213 1 N TRP A 212 O ASP A 250 SHEET 3 A 8 ALA A 184 CYS A 187 1 N CYS A 187 O LEU A 211 SHEET 4 A 8 MET A 152 ASP A 156 1 N LEU A 153 O SER A 186 SHEET 5 A 8 LYS A 115 ASP A 121 1 N ALA A 120 O ASP A 156 SHEET 6 A 8 TYR A 74 ASN A 76 1 N LEU A 75 O LYS A 115 SHEET 7 A 8 MET A 28 LEU A 31 1 N TRP A 30 O ASN A 76 SHEET 8 A 8 LEU A 280 MET A 282 1 O MET A 282 N GLY A 29 SHEET 1 B 2 ILE A 82 ARG A 85 0 SHEET 2 B 2 LEU A 91 PRO A 93 -1 O MET A 92 N GLY A 83 SHEET 1 C 6 ARG A 315 LYS A 319 0 SHEET 2 C 6 ILE A 324 PRO A 330 -1 O VAL A 326 N ILE A 317 SHEET 3 C 6 SER A 336 SER A 342 -1 O PHE A 341 N GLU A 325 SHEET 4 C 6 VAL A 395 PRO A 402 -1 O VAL A 396 N PHE A 340 SHEET 5 C 6 TYR A 366 ASP A 370 -1 N GLN A 369 O TYR A 399 SHEET 6 C 6 ILE A 376 LEU A 380 -1 O ILE A 377 N ALA A 368 SHEET 1 D 2 TYR A 349 SER A 353 0 SHEET 2 D 2 PHE A 386 ILE A 390 -1 O VAL A 388 N TYR A 351 SHEET 1 E 8 TRP B 248 ASP B 250 0 SHEET 2 E 8 LEU B 211 ARG B 213 1 N TRP B 212 O ASP B 250 SHEET 3 E 8 ALA B 184 CYS B 187 1 N CYS B 187 O LEU B 211 SHEET 4 E 8 MET B 152 ASP B 156 1 N LEU B 153 O SER B 186 SHEET 5 E 8 LYS B 115 ASP B 121 1 N ALA B 120 O ASP B 156 SHEET 6 E 8 TYR B 74 ASN B 76 1 N LEU B 75 O LYS B 115 SHEET 7 E 8 MET B 28 LEU B 31 1 N TRP B 30 O ASN B 76 SHEET 8 E 8 LEU B 280 MET B 282 1 O MET B 282 N LEU B 31 SHEET 1 F 2 ILE B 82 ARG B 85 0 SHEET 2 F 2 LEU B 91 PRO B 93 -1 O MET B 92 N GLY B 83 SHEET 1 G 6 ARG B 315 LYS B 319 0 SHEET 2 G 6 ILE B 324 PRO B 330 -1 O VAL B 326 N ILE B 317 SHEET 3 G 6 SER B 336 SER B 342 -1 O PHE B 341 N GLU B 325 SHEET 4 G 6 VAL B 395 PRO B 402 -1 O VAL B 396 N PHE B 340 SHEET 5 G 6 TYR B 366 ASP B 370 -1 N GLN B 369 O TYR B 399 SHEET 6 G 6 ILE B 376 LEU B 380 -1 O LEU B 380 N TYR B 366 SHEET 1 H 2 TYR B 349 SER B 353 0 SHEET 2 H 2 PHE B 386 ILE B 390 -1 O VAL B 388 N TYR B 351 SSBOND 1 CYS A 38 CYS A 80 1555 1555 2.09 SSBOND 2 CYS A 42 CYS A 49 1555 1555 2.07 SSBOND 3 CYS A 127 CYS A 158 1555 1555 2.08 SSBOND 4 CYS A 187 CYS A 209 1555 1555 2.04 SSBOND 5 CYS B 38 CYS B 80 1555 1555 2.05 SSBOND 6 CYS B 42 CYS B 49 1555 1555 2.05 SSBOND 7 CYS B 127 CYS B 158 1555 1555 2.05 SSBOND 8 CYS B 187 CYS B 209 1555 1555 2.03 LINK ND2 ASN A 124 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 177 C1 NAG D 1 1555 1555 1.43 LINK ND2 ASN A 385 C1 NAG A 509 1555 1555 1.44 LINK ND2 ASN B 124 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN B 177 C1 NAG F 1 1555 1555 1.43 LINK ND2 ASN B 385 C1 NAG B 509 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.44 LINK O3 BMA D 3 C1 MAN D 4 1555 1555 1.45 LINK O6 BMA D 3 C1 MAN D 5 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 LINK O6 NAG E 1 C1 FUC E 3 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.43 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.43 LINK O3 BMA F 3 C1 MAN F 4 1555 1555 1.45 LINK O6 BMA F 3 C1 MAN F 5 1555 1555 1.45 CISPEP 1 PRO A 197 PRO A 198 0 2.14 CISPEP 2 PRO B 197 PRO B 198 0 2.13 CRYST1 153.309 114.304 68.574 90.00 96.43 90.00 C 1 2 1 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 0.006523 0.000000 0.000736 0.00000 SCALE2 0.000000 0.008749 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014675 0.00000