HEADER HYDROLASE 18-FEB-16 5I81 TITLE ASMASE WITH ZINC COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPHINGOMYELIN PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACID SPHINGOMYELINASE,ASMASE; COMPND 5 EC: 3.1.4.12; COMPND 6 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: SMPD1, ASM; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293S GNT1-; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PIRES2 KEYWDS ACID SPHINGOMYELINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.F.ZHOU,R.R.WEI REVDAT 4 24-MAR-21 5I81 1 SOURCE HETSYN LINK REVDAT 3 29-JUL-20 5I81 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 16-NOV-16 5I81 1 JRNL REVDAT 1 07-SEP-16 5I81 0 JRNL AUTH Y.F.ZHOU,M.C.METCALF,S.C.GARMAN,T.EDMUNDS,H.QIU,R.R.WEI JRNL TITL HUMAN ACID SPHINGOMYELINASE STRUCTURES PROVIDE INSIGHT TO JRNL TITL 2 MOLECULAR BASIS OF NIEMANN-PICK DISEASE. JRNL REF NAT COMMUN V. 7 13082 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27725636 JRNL DOI 10.1038/NCOMMS13082 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2229: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.940 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 88030 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 4369 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.8170 - 6.9826 1.00 2817 128 0.1735 0.1648 REMARK 3 2 6.9826 - 5.5458 1.00 2787 172 0.1785 0.1911 REMARK 3 3 5.5458 - 4.8458 1.00 2832 137 0.1455 0.1597 REMARK 3 4 4.8458 - 4.4032 1.00 2769 161 0.1332 0.1556 REMARK 3 5 4.4032 - 4.0879 1.00 2820 144 0.1447 0.1571 REMARK 3 6 4.0879 - 3.8470 1.00 2840 121 0.1565 0.1542 REMARK 3 7 3.8470 - 3.6544 1.00 2791 144 0.1761 0.1721 REMARK 3 8 3.6544 - 3.4954 1.00 2783 139 0.1838 0.2331 REMARK 3 9 3.4954 - 3.3609 1.00 2833 153 0.1994 0.2373 REMARK 3 10 3.3609 - 3.2450 1.00 2806 121 0.1950 0.2200 REMARK 3 11 3.2450 - 3.1436 1.00 2803 168 0.2191 0.2531 REMARK 3 12 3.1436 - 3.0537 1.00 2811 155 0.2132 0.2489 REMARK 3 13 3.0537 - 2.9733 1.00 2791 134 0.2205 0.2434 REMARK 3 14 2.9733 - 2.9008 1.00 2819 143 0.2198 0.2554 REMARK 3 15 2.9008 - 2.8349 1.00 2782 158 0.2174 0.2467 REMARK 3 16 2.8349 - 2.7746 1.00 2837 124 0.2042 0.2304 REMARK 3 17 2.7746 - 2.7191 1.00 2780 152 0.2110 0.2406 REMARK 3 18 2.7191 - 2.6678 1.00 2826 132 0.2069 0.2111 REMARK 3 19 2.6678 - 2.6201 1.00 2799 164 0.2036 0.2523 REMARK 3 20 2.6201 - 2.5757 1.00 2806 131 0.2015 0.2737 REMARK 3 21 2.5757 - 2.5342 1.00 2774 185 0.2071 0.2475 REMARK 3 22 2.5342 - 2.4952 1.00 2785 155 0.1990 0.2288 REMARK 3 23 2.4952 - 2.4585 1.00 2818 119 0.2169 0.2667 REMARK 3 24 2.4585 - 2.4239 1.00 2828 151 0.2085 0.2360 REMARK 3 25 2.4239 - 2.3911 1.00 2820 126 0.2227 0.2443 REMARK 3 26 2.3911 - 2.3601 1.00 2752 140 0.2336 0.2620 REMARK 3 27 2.3601 - 2.3306 1.00 2790 171 0.2428 0.2709 REMARK 3 28 2.3306 - 2.3025 0.99 2814 173 0.2460 0.2673 REMARK 3 29 2.3025 - 2.2757 0.96 2639 131 0.2516 0.2948 REMARK 3 30 2.2757 - 2.2501 0.90 2509 137 0.2834 0.3137 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 4585 REMARK 3 ANGLE : 1.171 6270 REMARK 3 CHIRALITY : 0.069 686 REMARK 3 PLANARITY : 0.008 782 REMARK 3 DIHEDRAL : 15.192 2649 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 87 THROUGH 147 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.4020 -49.0409 -43.9580 REMARK 3 T TENSOR REMARK 3 T11: 0.5662 T22: 0.9103 REMARK 3 T33: 0.5380 T12: -0.3006 REMARK 3 T13: -0.0460 T23: 0.0292 REMARK 3 L TENSOR REMARK 3 L11: 1.0797 L22: 3.6801 REMARK 3 L33: 1.2152 L12: 1.2942 REMARK 3 L13: 0.1996 L23: -0.6902 REMARK 3 S TENSOR REMARK 3 S11: -0.3621 S12: 0.5330 S13: 0.2030 REMARK 3 S21: -0.4027 S22: 0.4101 S23: 0.3683 REMARK 3 S31: -0.0088 S32: 0.0686 S33: -0.0383 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 148 THROUGH 181 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.0121 -62.0982 -27.7504 REMARK 3 T TENSOR REMARK 3 T11: 0.5600 T22: 0.6229 REMARK 3 T33: 0.5785 T12: -0.1907 REMARK 3 T13: -0.0712 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 3.2379 L22: 0.3057 REMARK 3 L33: 1.5568 L12: 0.8617 REMARK 3 L13: 2.0809 L23: 0.6920 REMARK 3 S TENSOR REMARK 3 S11: 0.3500 S12: 0.0782 S13: -0.8466 REMARK 3 S21: -0.0024 S22: 0.2146 S23: -0.1536 REMARK 3 S31: 0.4988 S32: -0.1568 S33: -0.5661 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 182 THROUGH 510 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.5386 -38.8394 -28.1774 REMARK 3 T TENSOR REMARK 3 T11: 0.3177 T22: 0.6473 REMARK 3 T33: 0.3847 T12: -0.1931 REMARK 3 T13: -0.0188 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 1.5856 L22: 1.0919 REMARK 3 L33: 1.3559 L12: 0.1837 REMARK 3 L13: 0.7167 L23: 0.1076 REMARK 3 S TENSOR REMARK 3 S11: -0.2416 S12: 0.7074 S13: 0.0865 REMARK 3 S21: -0.2703 S22: 0.2305 S23: 0.0159 REMARK 3 S31: -0.0646 S32: 0.3741 S33: 0.0152 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 511 THROUGH 611 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2575 -27.3396 -13.3480 REMARK 3 T TENSOR REMARK 3 T11: 0.3195 T22: 0.3755 REMARK 3 T33: 0.4031 T12: -0.0802 REMARK 3 T13: -0.1041 T23: 0.0370 REMARK 3 L TENSOR REMARK 3 L11: 1.7209 L22: 1.7502 REMARK 3 L33: 2.3363 L12: -0.5192 REMARK 3 L13: 0.8515 L23: -0.9868 REMARK 3 S TENSOR REMARK 3 S11: -0.3525 S12: 0.1693 S13: 0.4393 REMARK 3 S21: 0.0460 S22: 0.2188 S23: 0.1237 REMARK 3 S31: -0.3730 S32: 0.0122 S33: 0.1023 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5I81 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218054. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 5.0-5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28304, 1.07213 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88092 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 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 : 10.30 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.73200 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: SAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE, PHASER 2.5.7 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE PH 5.0-5.5, 12% GLYCEROL, PH 5.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 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 63.18833 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 126.37667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 63.18833 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 126.37667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.18833 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 126.37667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 63.18833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 126.37667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -341.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -66.31450 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -114.86008 REMARK 350 BIOMT3 2 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 47 REMARK 465 SER A 48 REMARK 465 ASP A 49 REMARK 465 SER A 50 REMARK 465 ARG A 51 REMARK 465 VAL A 52 REMARK 465 LEU A 53 REMARK 465 TRP A 54 REMARK 465 ALA A 55 REMARK 465 PRO A 56 REMARK 465 ALA A 57 REMARK 465 GLU A 58 REMARK 465 ALA A 59 REMARK 465 HIS A 60 REMARK 465 PRO A 61 REMARK 465 LEU A 62 REMARK 465 SER A 63 REMARK 465 PRO A 64 REMARK 465 GLN A 65 REMARK 465 GLY A 66 REMARK 465 HIS A 67 REMARK 465 PRO A 68 REMARK 465 ALA A 69 REMARK 465 ARG A 70 REMARK 465 LEU A 71 REMARK 465 HIS A 72 REMARK 465 ARG A 73 REMARK 465 ILE A 74 REMARK 465 VAL A 75 REMARK 465 PRO A 76 REMARK 465 ARG A 77 REMARK 465 LEU A 78 REMARK 465 ARG A 79 REMARK 465 ASP A 80 REMARK 465 VAL A 81 REMARK 465 PHE A 82 REMARK 465 GLY A 83 REMARK 465 PRO A 612 REMARK 465 ASP A 613 REMARK 465 GLY A 614 REMARK 465 SER A 615 REMARK 465 LEU A 616 REMARK 465 PRO A 617 REMARK 465 GLU A 618 REMARK 465 ALA A 619 REMARK 465 GLN A 620 REMARK 465 SER A 621 REMARK 465 LEU A 622 REMARK 465 TRP A 623 REMARK 465 PRO A 624 REMARK 465 ARG A 625 REMARK 465 PRO A 626 REMARK 465 LEU A 627 REMARK 465 PHE A 628 REMARK 465 CYS A 629 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O6 BMA C 3 C1 MAN D 1 1.62 REMARK 500 O7 NAG A 711 O HOH A 801 1.62 REMARK 500 O4 NAG B 2 C1 BMA A 705 1.63 REMARK 500 O4 NAG A 711 C1 NAG A 712 1.64 REMARK 500 O4 NAG A 713 C1 NAG A 714 1.64 REMARK 500 ND2 ASN A 175 C1 NAG A 702 1.65 REMARK 500 O1 SO4 A 717 O HOH A 802 1.85 REMARK 500 ND2 ASN A 335 O5 NAG B 1 2.12 REMARK 500 O HOH A 919 O HOH A 966 2.13 REMARK 500 NE2 GLN A 534 O HOH A 803 2.15 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 LEU A 307 CA - CB - CG ANGL. DEV. = -15.0 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 SER A 149 -85.33 -134.54 REMARK 500 ASP A 169 26.75 -140.78 REMARK 500 ASP A 220 52.28 -116.06 REMARK 500 CYS A 226 -158.68 -124.42 REMARK 500 ASP A 251 -164.54 -108.96 REMARK 500 THR A 276 43.34 -102.32 REMARK 500 ASP A 278 81.23 79.42 REMARK 500 ASN A 395 112.66 -170.02 REMARK 500 ASP A 398 69.10 15.24 REMARK 500 HIS A 425 -79.06 -94.92 REMARK 500 LEU A 432 153.19 -49.62 REMARK 500 HIS A 457 -41.46 75.02 REMARK 500 HIS A 459 -9.54 75.66 REMARK 500 SER A 473 -10.27 -142.20 REMARK 500 SER A 598 71.93 -104.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MAN D 1 REMARK 610 NAG A 702 REMARK 610 BMA A 705 REMARK 610 NAG A 712 REMARK 610 NAG A 714 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 716 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 206 OD1 REMARK 620 2 ASP A 278 OD2 79.3 REMARK 620 3 HIS A 459 NE2 100.9 177.8 REMARK 620 4 HOH A 891 O 101.3 75.1 102.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 715 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 278 OD2 REMARK 620 2 ASN A 318 OD1 98.5 REMARK 620 3 HIS A 425 NE2 89.5 84.9 REMARK 620 4 HIS A 457 ND1 166.4 95.0 93.3 REMARK 620 5 HOH A 891 O 80.8 132.6 142.2 88.9 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5I8R RELATED DB: PDB REMARK 900 RELATED ID: 5I85 RELATED DB: PDB DBREF 5I81 A 47 629 UNP P17405 ASM_HUMAN 47 629 SEQRES 1 A 583 LEU SER ASP SER ARG VAL LEU TRP ALA PRO ALA GLU ALA SEQRES 2 A 583 HIS PRO LEU SER PRO GLN GLY HIS PRO ALA ARG LEU HIS SEQRES 3 A 583 ARG ILE VAL PRO ARG LEU ARG ASP VAL PHE GLY TRP GLY SEQRES 4 A 583 ASN LEU THR CYS PRO ILE CYS LYS GLY LEU PHE THR ALA SEQRES 5 A 583 ILE ASN LEU GLY LEU LYS LYS GLU PRO ASN VAL ALA ARG SEQRES 6 A 583 VAL GLY SER VAL ALA ILE LYS LEU CYS ASN LEU LEU LYS SEQRES 7 A 583 ILE ALA PRO PRO ALA VAL CYS GLN SER ILE VAL HIS LEU SEQRES 8 A 583 PHE GLU ASP ASP MET VAL GLU VAL TRP ARG ARG SER VAL SEQRES 9 A 583 LEU SER PRO SER GLU ALA CYS GLY LEU LEU LEU GLY SER SEQRES 10 A 583 THR CYS GLY HIS TRP ASP ILE PHE SER SER TRP ASN ILE SEQRES 11 A 583 SER LEU PRO THR VAL PRO LYS PRO PRO PRO LYS PRO PRO SEQRES 12 A 583 SER PRO PRO ALA PRO GLY ALA PRO VAL SER ARG ILE LEU SEQRES 13 A 583 PHE LEU THR ASP LEU HIS TRP ASP HIS ASP TYR LEU GLU SEQRES 14 A 583 GLY THR ASP PRO ASP CYS ALA ASP PRO LEU CYS CYS ARG SEQRES 15 A 583 ARG GLY SER GLY LEU PRO PRO ALA SER ARG PRO GLY ALA SEQRES 16 A 583 GLY TYR TRP GLY GLU TYR SER LYS CYS ASP LEU PRO LEU SEQRES 17 A 583 ARG THR LEU GLU SER LEU LEU SER GLY LEU GLY PRO ALA SEQRES 18 A 583 GLY PRO PHE ASP MET VAL TYR TRP THR GLY ASP ILE PRO SEQRES 19 A 583 ALA HIS ASP VAL TRP HIS GLN THR ARG GLN ASP GLN LEU SEQRES 20 A 583 ARG ALA LEU THR THR VAL THR ALA LEU VAL ARG LYS PHE SEQRES 21 A 583 LEU GLY PRO VAL PRO VAL TYR PRO ALA VAL GLY ASN HIS SEQRES 22 A 583 GLU SER THR PRO VAL ASN SER PHE PRO PRO PRO PHE ILE SEQRES 23 A 583 GLU GLY ASN HIS SER SER ARG TRP LEU TYR GLU ALA MET SEQRES 24 A 583 ALA LYS ALA TRP GLU PRO TRP LEU PRO ALA GLU ALA LEU SEQRES 25 A 583 ARG THR LEU ARG ILE GLY GLY PHE TYR ALA LEU SER PRO SEQRES 26 A 583 TYR PRO GLY LEU ARG LEU ILE SER LEU ASN MET ASN PHE SEQRES 27 A 583 CYS SER ARG GLU ASN PHE TRP LEU LEU ILE ASN SER THR SEQRES 28 A 583 ASP PRO ALA GLY GLN LEU GLN TRP LEU VAL GLY GLU LEU SEQRES 29 A 583 GLN ALA ALA GLU ASP ARG GLY ASP LYS VAL HIS ILE ILE SEQRES 30 A 583 GLY HIS ILE PRO PRO GLY HIS CYS LEU LYS SER TRP SER SEQRES 31 A 583 TRP ASN TYR TYR ARG ILE VAL ALA ARG TYR GLU ASN THR SEQRES 32 A 583 LEU ALA ALA GLN PHE PHE GLY HIS THR HIS VAL ASP GLU SEQRES 33 A 583 PHE GLU VAL PHE TYR ASP GLU GLU THR LEU SER ARG PRO SEQRES 34 A 583 LEU ALA VAL ALA PHE LEU ALA PRO SER ALA THR THR TYR SEQRES 35 A 583 ILE GLY LEU ASN PRO GLY TYR ARG VAL TYR GLN ILE ASP SEQRES 36 A 583 GLY ASN TYR SER GLY SER SER HIS VAL VAL LEU ASP HIS SEQRES 37 A 583 GLU THR TYR ILE LEU ASN LEU THR GLN ALA ASN ILE PRO SEQRES 38 A 583 GLY ALA ILE PRO HIS TRP GLN LEU LEU TYR ARG ALA ARG SEQRES 39 A 583 GLU THR TYR GLY LEU PRO ASN THR LEU PRO THR ALA TRP SEQRES 40 A 583 HIS ASN LEU VAL TYR ARG MET ARG GLY ASP MET GLN LEU SEQRES 41 A 583 PHE GLN THR PHE TRP PHE LEU TYR HIS LYS GLY HIS PRO SEQRES 42 A 583 PRO SER GLU PRO CYS GLY THR PRO CYS ARG LEU ALA THR SEQRES 43 A 583 LEU CYS ALA GLN LEU SER ALA ARG ALA ASP SER PRO ALA SEQRES 44 A 583 LEU CYS ARG HIS LEU MET PRO ASP GLY SER LEU PRO GLU SEQRES 45 A 583 ALA GLN SER LEU TRP PRO ARG PRO LEU PHE CYS HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN D 1 11 HET BMA D 2 11 HET NAG A 701 14 HET NAG A 702 14 HET BMA A 705 11 HET NAG A 711 14 HET NAG A 712 14 HET NAG A 713 14 HET NAG A 714 14 HET ZN A 715 1 HET ZN A 716 1 HET SO4 A 717 5 HET SO4 A 718 5 HET SO4 A 719 5 HET SO4 A 720 5 HET SO4 A 721 5 HET SO4 A 722 5 HET SO4 A 723 5 HET SO4 A 724 5 HET SO4 A 725 5 HET SO4 A 726 5 HET SO4 A 727 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION 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 FORMUL 2 NAG 10(C8 H15 N O6) FORMUL 3 BMA 3(C6 H12 O6) FORMUL 4 MAN C6 H12 O6 FORMUL 12 ZN 2(ZN 2+) FORMUL 14 SO4 11(O4 S 2-) FORMUL 25 HOH *176(H2 O) HELIX 1 AA1 TRP A 84 ASN A 86 5 3 HELIX 2 AA2 LEU A 87 LYS A 104 1 18 HELIX 3 AA3 LYS A 105 LEU A 123 1 19 HELIX 4 AA4 PRO A 127 SER A 149 1 23 HELIX 5 AA5 SER A 152 GLY A 162 1 11 HELIX 6 AA6 PRO A 253 GLY A 263 1 11 HELIX 7 AA7 LEU A 264 GLY A 268 5 5 HELIX 8 AA8 THR A 288 GLY A 308 1 21 HELIX 9 AA9 SER A 338 TRP A 349 1 12 HELIX 10 AB1 PRO A 354 GLY A 365 1 12 HELIX 11 AB2 ASN A 381 SER A 386 5 6 HELIX 12 AB3 ASN A 389 ILE A 394 5 6 HELIX 13 AB4 ASP A 398 ALA A 400 5 3 HELIX 14 AB5 GLY A 401 GLY A 417 1 17 HELIX 15 AB6 PRO A 427 CYS A 431 5 5 HELIX 16 AB7 LEU A 432 TYR A 446 1 15 HELIX 17 AB8 ASN A 520 ASN A 525 1 6 HELIX 18 AB9 ALA A 539 GLY A 544 1 6 HELIX 19 AC1 LEU A 549 GLY A 562 1 14 HELIX 20 AC2 ASP A 563 HIS A 575 1 13 HELIX 21 AC3 GLY A 585 SER A 598 1 14 HELIX 22 AC4 SER A 603 ARG A 608 5 6 SHEET 1 AA1 6 VAL A 312 PRO A 314 0 SHEET 2 AA1 6 MET A 272 TRP A 275 1 N VAL A 273 O TYR A 313 SHEET 3 AA1 6 VAL A 198 LEU A 204 1 N LEU A 202 O TYR A 274 SHEET 4 AA1 6 GLY A 494 ASP A 501 -1 O ARG A 496 N PHE A 203 SHEET 5 AA1 6 VAL A 511 ILE A 518 -1 O LEU A 512 N GLN A 499 SHEET 6 AA1 6 GLN A 534 ARG A 538 -1 O LEU A 536 N THR A 516 SHEET 1 AA2 6 TYR A 367 TYR A 372 0 SHEET 2 AA2 6 LEU A 375 SER A 379 -1 O LEU A 377 N LEU A 369 SHEET 3 AA2 6 LYS A 419 ILE A 423 1 O LYS A 419 N ARG A 376 SHEET 4 AA2 6 LEU A 450 PHE A 455 1 O ALA A 451 N VAL A 420 SHEET 5 AA2 6 PRO A 475 LEU A 481 1 O PHE A 480 N PHE A 455 SHEET 6 AA2 6 GLU A 462 TYR A 467 -1 N PHE A 466 O LEU A 476 SSBOND 1 CYS A 89 CYS A 165 1555 1555 2.04 SSBOND 2 CYS A 92 CYS A 157 1555 1555 2.07 SSBOND 3 CYS A 120 CYS A 131 1555 1555 2.06 SSBOND 4 CYS A 221 CYS A 226 1555 1555 2.04 SSBOND 5 CYS A 227 CYS A 250 1555 1555 2.07 SSBOND 6 CYS A 385 CYS A 431 1555 1555 2.06 SSBOND 7 CYS A 584 CYS A 588 1555 1555 2.09 SSBOND 8 CYS A 594 CYS A 607 1555 1555 2.07 LINK ND2 ASN A 86 C1 NAG A 701 1555 1555 1.51 LINK ND2 ASN A 335 C1 NAG B 1 1555 1555 1.46 LINK ND2 ASN A 395 C1 NAG C 1 1555 1555 1.48 LINK ND2 ASN A 503 C1 NAG A 711 1555 1555 1.40 LINK ND2 ASN A 520 C1 NAG A 713 1555 1555 1.38 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.42 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.43 LINK O3 MAN D 1 C1 BMA D 2 1555 1555 1.39 LINK OD1 ASP A 206 ZN ZN A 716 1555 1555 2.20 LINK OD2 ASP A 278 ZN ZN A 715 1555 1555 2.40 LINK OD2 ASP A 278 ZN ZN A 716 1555 1555 2.23 LINK OD1 ASN A 318 ZN ZN A 715 1555 1555 2.16 LINK NE2 HIS A 425 ZN ZN A 715 1555 1555 2.10 LINK ND1 HIS A 457 ZN ZN A 715 1555 1555 2.22 LINK NE2 HIS A 459 ZN ZN A 716 1555 1555 2.05 LINK ZN ZN A 715 O HOH A 891 1555 1555 1.88 LINK ZN ZN A 716 O HOH A 891 1555 1555 2.36 CISPEP 1 GLY A 268 PRO A 269 0 5.07 CISPEP 2 THR A 322 PRO A 323 0 -12.36 CISPEP 3 TYR A 488 ILE A 489 0 -5.57 CRYST1 132.629 132.629 189.565 90.00 90.00 120.00 P 64 2 2 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 0.007540 0.004353 0.000000 0.00000 SCALE2 0.000000 0.008706 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005275 0.00000