HEADER HYDROLASE/HYDROLASE INHIBITOR 09-FEB-12 4DO5 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 FRAGMENT: UNP RESIDUES 18-411; COMPND 5 SYNONYM: ALPHA-GALACTOSIDASE B; COMPND 6 EC: 3.2.1.49; COMPND 7 ENGINEERED: YES; COMPND 8 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: NAGA; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HI-FIVE; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PIB/V5-HIS-TOPO TA KEYWDS PHARMACOLOGICAL CHAPERONE, BETA/ALPHA)8 BARREL, GLYCOSIDASE, KEYWDS 2 CARBOHYDRATE-BINDING PROTEIN, GLYCOPROTEIN, LYSOSOME, HYDROLASE, KEYWDS 3 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.E.CLARK,S.C.GARMAN REVDAT 6 06-NOV-24 4DO5 1 REMARK REVDAT 5 13-SEP-23 4DO5 1 HETSYN REVDAT 4 29-JUL-20 4DO5 1 CAVEAT COMPND REMARK SEQADV REVDAT 4 2 1 HETNAM LINK SITE ATOM REVDAT 3 15-NOV-17 4DO5 1 REMARK REVDAT 2 21-NOV-12 4DO5 1 JRNL REVDAT 1 10-OCT-12 4DO5 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. 1.51 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 178628 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 9021 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) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8577 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE SET COUNT : 454 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6279 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 338 REMARK 3 SOLVENT ATOMS : 1022 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.18000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.839 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 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): 6921 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4672 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9435 ; 1.361 ; 2.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11326 ; 0.886 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 813 ; 6.291 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 310 ;35.257 ;24.065 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1078 ;12.461 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;18.342 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1027 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7527 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1369 ; 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): 4007 ; 2.627 ;12.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1610 ; 1.047 ;12.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6478 ; 3.859 ;16.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2914 ; 5.924 ;20.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2957 ; 8.533 ;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): 56.9588 -1.2228 10.1632 REMARK 3 T TENSOR REMARK 3 T11: 0.0605 T22: 0.0457 REMARK 3 T33: 0.0210 T12: -0.0077 REMARK 3 T13: -0.0068 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 1.0832 L22: 0.3359 REMARK 3 L33: 0.4028 L12: 0.0782 REMARK 3 L13: -0.1640 L23: -0.1296 REMARK 3 S TENSOR REMARK 3 S11: 0.0296 S12: 0.0227 S13: 0.1145 REMARK 3 S21: 0.0281 S22: 0.0232 S23: 0.0138 REMARK 3 S31: -0.0253 S32: 0.0359 S33: -0.0528 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): 26.2569 3.2564 10.9694 REMARK 3 T TENSOR REMARK 3 T11: 0.0402 T22: 0.0682 REMARK 3 T33: 0.1268 T12: 0.0283 REMARK 3 T13: 0.0201 T23: 0.0624 REMARK 3 L TENSOR REMARK 3 L11: 1.4161 L22: 1.5984 REMARK 3 L33: 0.8093 L12: -0.0773 REMARK 3 L13: -0.3054 L23: -0.2714 REMARK 3 S TENSOR REMARK 3 S11: 0.0550 S12: 0.0474 S13: 0.1630 REMARK 3 S21: 0.0961 S22: 0.1005 S23: 0.3325 REMARK 3 S31: -0.1109 S32: -0.1662 S33: -0.1555 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): 21.9069 -31.5738 21.9240 REMARK 3 T TENSOR REMARK 3 T11: 0.0791 T22: 0.0887 REMARK 3 T33: 0.1304 T12: -0.0064 REMARK 3 T13: 0.0004 T23: 0.0728 REMARK 3 L TENSOR REMARK 3 L11: 1.1464 L22: 1.6086 REMARK 3 L33: 0.8008 L12: 0.3842 REMARK 3 L13: -0.5275 L23: -0.5363 REMARK 3 S TENSOR REMARK 3 S11: -0.0537 S12: 0.0817 S13: 0.0077 REMARK 3 S21: 0.1212 S22: 0.1948 S23: 0.3951 REMARK 3 S31: 0.0079 S32: -0.1400 S33: -0.1410 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): 51.6099 -37.1646 16.4726 REMARK 3 T TENSOR REMARK 3 T11: 0.0702 T22: 0.0646 REMARK 3 T33: 0.1811 T12: 0.0312 REMARK 3 T13: 0.0018 T23: 0.0200 REMARK 3 L TENSOR REMARK 3 L11: 2.1708 L22: 1.7057 REMARK 3 L33: 1.0984 L12: 0.3362 REMARK 3 L13: -0.6808 L23: -0.2340 REMARK 3 S TENSOR REMARK 3 S11: -0.1420 S12: -0.0647 S13: -0.4222 REMARK 3 S21: -0.0130 S22: -0.0206 S23: -0.4399 REMARK 3 S31: 0.1560 S32: 0.2030 S33: 0.1627 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 4DO5 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_1000070572. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-08 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 : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 178912 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.64400 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 (%): 62.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 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 77.17600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.25650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.17600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.25650 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: 9380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 35.0 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 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 692 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1148 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 ASN A 405 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 -135.38 52.04 REMARK 500 CYS A 38 42.32 -108.57 REMARK 500 ASP A 78 -147.82 -113.73 REMARK 500 CYS A 80 19.29 81.93 REMARK 500 LYS A 149 35.06 70.84 REMARK 500 LYS A 149 33.92 70.84 REMARK 500 ASP A 252 -177.55 95.82 REMARK 500 ASN A 258 -140.10 -99.42 REMARK 500 LEU A 280 77.96 -105.77 REMARK 500 SER A 283 87.71 -156.20 REMARK 500 ASP A 346 -70.86 -114.43 REMARK 500 ARG B 37 -133.16 51.20 REMARK 500 ASP B 45 59.13 -141.42 REMARK 500 ASP B 78 -150.61 -114.61 REMARK 500 LYS B 149 34.80 72.80 REMARK 500 ASP B 252 -177.94 93.60 REMARK 500 ASN B 258 -140.59 -101.43 REMARK 500 LEU B 280 77.62 -109.04 REMARK 500 SER B 283 89.18 -158.27 REMARK 500 ASP B 346 -70.51 -118.15 REMARK 500 SER B 363 -18.37 85.04 REMARK 500 REMARK 500 REMARK: NULL 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: 4DO6 RELATED DB: PDB REMARK 900 GLUCOSE SOAK DBREF 4DO5 A 18 411 UNP P17050 NAGAB_HUMAN 18 411 DBREF 4DO5 B 18 411 UNP P17050 NAGAB_HUMAN 18 411 SEQADV 4DO5 GLN A 201 UNP P17050 ASN 201 ENGINEERED MUTATION SEQADV 4DO5 HIS A 412 UNP P17050 EXPRESSION TAG SEQADV 4DO5 HIS A 413 UNP P17050 EXPRESSION TAG SEQADV 4DO5 HIS A 414 UNP P17050 EXPRESSION TAG SEQADV 4DO5 HIS A 415 UNP P17050 EXPRESSION TAG SEQADV 4DO5 HIS A 416 UNP P17050 EXPRESSION TAG SEQADV 4DO5 HIS A 417 UNP P17050 EXPRESSION TAG SEQADV 4DO5 GLN B 201 UNP P17050 ASN 201 ENGINEERED MUTATION SEQADV 4DO5 HIS B 412 UNP P17050 EXPRESSION TAG SEQADV 4DO5 HIS B 413 UNP P17050 EXPRESSION TAG SEQADV 4DO5 HIS B 414 UNP P17050 EXPRESSION TAG SEQADV 4DO5 HIS B 415 UNP P17050 EXPRESSION TAG SEQADV 4DO5 HIS B 416 UNP P17050 EXPRESSION TAG SEQADV 4DO5 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 4DO5 ASN B 177 ASN GLYCOSYLATION SITE MODRES 4DO5 ASN B 124 ASN GLYCOSYLATION SITE MODRES 4DO5 ASN A 124 ASN GLYCOSYLATION SITE MODRES 4DO5 ASN A 177 ASN GLYCOSYLATION SITE MODRES 4DO5 ASN A 385 ASN GLYCOSYLATION SITE MODRES 4DO5 ASN B 385 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 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 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 508 14 HET DGJ A 509 11 HET CIT A 510 13 HET GOL A 511 6 HET GOL A 512 6 HET GOL A 513 6 HET GOL A 514 6 HET GOL A 515 6 HET GOL A 516 6 HET GOL A 517 6 HET GOL A 518 6 HET NAG B 508 14 HET DGJ B 509 11 HET CIT B 510 13 HET GOL B 511 6 HET GOL B 512 6 HET GOL B 513 6 HET GOL B 514 6 HET GOL B 515 6 HET GOL B 516 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM DGJ (2R,3S,4R,5S)-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL HETNAM CIT CITRIC ACID 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 DGJ 1-DEOXYGALACTONOJIRIMYCIN HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAG 10(C8 H15 N O6) FORMUL 4 BMA 2(C6 H12 O6) FORMUL 4 MAN 4(C6 H12 O6) FORMUL 8 DGJ 2(C6 H13 N O4) FORMUL 9 CIT 2(C6 H8 O7) FORMUL 10 GOL 14(C3 H8 O3) FORMUL 27 HOH *1022(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 LYS A 149 1 13 HELIX 7 7 THR A 161 THR A 179 1 19 HELIX 8 8 TRP A 189 GLY A 194 5 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 ALA A 243 1 9 HELIX 12 12 SER A 262 LEU A 276 1 15 HELIX 13 13 SER A 290 GLN A 298 1 9 HELIX 14 14 ASN A 299 GLN A 307 1 9 HELIX 15 15 GLY A 356 ASN A 359 5 4 HELIX 16 16 ALA B 32 ARG B 37 1 6 HELIX 17 17 SER B 51 ASP B 65 1 15 HELIX 18 18 GLY B 66 GLY B 71 1 6 HELIX 19 19 GLY B 101 LEU B 112 1 12 HELIX 20 20 THR B 134 ASP B 136 5 3 HELIX 21 21 LYS B 137 LYS B 149 1 13 HELIX 22 22 THR B 161 GLY B 180 1 20 HELIX 23 23 TRP B 189 GLY B 194 5 6 HELIX 24 24 GLN B 201 CYS B 209 1 9 HELIX 25 25 SER B 221 HIS B 235 1 15 HELIX 26 26 HIS B 235 GLN B 240 1 6 HELIX 27 27 PRO B 241 ALA B 243 5 3 HELIX 28 28 SER B 262 LEU B 276 1 15 HELIX 29 29 SER B 290 GLN B 298 1 9 HELIX 30 30 ASN B 299 GLN B 307 1 9 HELIX 31 31 SER B 332 LYS B 334 5 3 HELIX 32 32 LEU B 355 ASN B 359 5 5 HELIX 33 33 LYS B 404 SER B 409 1 6 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 HIS A 318 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 GLU A 367 O TYR A 401 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 354 0 SHEET 2 D 2 ASN A 385 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 GLY B 117 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 GLU B 367 O TYR B 401 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 2.05 SSBOND 2 CYS A 42 CYS A 49 1555 1555 2.04 SSBOND 3 CYS A 127 CYS A 158 1555 1555 2.12 SSBOND 4 CYS A 187 CYS A 209 1555 1555 2.05 SSBOND 5 CYS B 38 CYS B 80 1555 1555 2.04 SSBOND 6 CYS B 42 CYS B 49 1555 1555 2.06 SSBOND 7 CYS B 127 CYS B 158 1555 1555 2.06 SSBOND 8 CYS B 187 CYS B 209 1555 1555 2.01 LINK ND2 ASN A 124 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 177 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN A 385 C1 NAG A 508 1555 1555 1.45 LINK ND2 ASN B 124 C1 NAG E 1 1555 1555 1.43 LINK ND2 ASN B 177 C1 NAG F 1 1555 1555 1.43 LINK ND2 ASN B 385 C1 NAG B 508 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.43 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.43 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 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 3.08 CISPEP 2 PRO B 197 PRO B 198 0 3.87 CRYST1 154.352 114.513 68.553 90.00 95.64 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 0.006479 0.000000 0.000639 0.00000 SCALE2 0.000000 0.008733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014658 0.00000