HEADER HYDROLASE 29-AUG-23 8W6P TITLE CRYSTAL STRUCTURE OF DIMERIC MURINE SMPDL3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACID SPHINGOMYELINASE-LIKE PHOSPHODIESTERASE 3A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ASM-LIKE PHOSPHODIESTERASE 3A; COMPND 5 EC: 3.1.4.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SMPDL3A, ASML3A; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS INNATE IMMUNITY, LIPID METABOLISM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.ZHANG,P.LIU,S.FAN,Y.HOU REVDAT 1 20-DEC-23 8W6P 0 JRNL AUTH Y.HOU,Z.WANG,P.LIU,X.WEI,Z.ZHANG,S.FAN,L.ZHANG,F.HAN,Y.SONG, JRNL AUTH 2 L.CHU,C.ZHANG JRNL TITL SMPDL3A IS A CGAMP-DEGRADING ENZYME INDUCED BY LXR-MEDIATED JRNL TITL 2 LIPID METABOLISM TO RESTRICT CGAS-STING DNA SENSING. JRNL REF IMMUNITY V. 56 2492 2023 JRNL REFN ISSN 1074-7613 JRNL PMID 37890481 JRNL DOI 10.1016/J.IMMUNI.2023.10.001 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 89592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.230 REMARK 3 FREE R VALUE TEST SET COUNT : 2001 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 20.2700 - 4.5800 0.99 6506 148 0.1817 0.2038 REMARK 3 2 4.5800 - 3.6400 1.00 6408 148 0.1819 0.1943 REMARK 3 3 3.6400 - 3.1800 1.00 6384 140 0.1915 0.2419 REMARK 3 4 3.1800 - 2.8900 1.00 6404 150 0.2245 0.2407 REMARK 3 5 2.8900 - 2.6900 1.00 6363 146 0.2302 0.2230 REMARK 3 6 2.6900 - 2.5300 1.00 6361 144 0.2436 0.2591 REMARK 3 7 2.5300 - 2.4000 1.00 6335 144 0.2412 0.3002 REMARK 3 8 2.4000 - 2.3000 1.00 6361 146 0.2446 0.3157 REMARK 3 9 2.3000 - 2.2100 1.00 6344 146 0.2421 0.2625 REMARK 3 10 2.2100 - 2.1300 1.00 6375 144 0.2540 0.2743 REMARK 3 11 2.1300 - 2.0700 1.00 6331 142 0.2556 0.3023 REMARK 3 12 2.0700 - 2.0100 1.00 6306 147 0.2699 0.3507 REMARK 3 13 2.0100 - 1.9500 0.93 5977 139 0.2885 0.3311 REMARK 3 14 1.9500 - 1.9100 0.81 5136 117 0.3381 0.4069 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.00 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 : 0.010 7011 REMARK 3 ANGLE : 1.261 9577 REMARK 3 CHIRALITY : 0.061 1109 REMARK 3 PLANARITY : 0.008 1195 REMARK 3 DIHEDRAL : 7.844 1010 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8W6P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 05-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300039323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89995 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 20.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.76800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE [PH 5.5], 0.2M REMARK 280 AMMONIUM SULFATE AND 30% PEG 4000, VAPOR DIFFUSION, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 39.77850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.88925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.66775 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 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 ALA A 33 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 CE LYS A 383 O HOH A 605 1.37 REMARK 500 OH TYR B 82 O HOH B 601 1.84 REMARK 500 O HOH A 642 O HOH A 771 1.86 REMARK 500 O HIS B 39 O HOH B 602 1.86 REMARK 500 O HOH A 930 O HOH A 947 1.88 REMARK 500 O HOH B 854 O HOH B 909 1.89 REMARK 500 O HOH A 998 O HOH A 1001 1.89 REMARK 500 O HOH A 852 O HOH A 924 1.89 REMARK 500 O HOH A 964 O HOH A 994 1.89 REMARK 500 OD1 ASN B 308 O HOH B 603 1.89 REMARK 500 O HOH A 888 O HOH A 912 1.91 REMARK 500 O HOH B 812 O HOH B 896 1.93 REMARK 500 O2 PO4 B 506 O HOH B 604 1.94 REMARK 500 O HOH A 718 O HOH A 743 1.94 REMARK 500 O HOH A 936 O HOH A 953 1.96 REMARK 500 O SER A 413 O HOH A 602 1.96 REMARK 500 OE1 GLN B 391 O HOH B 605 1.97 REMARK 500 O HOH A 660 O HOH A 951 2.00 REMARK 500 O HOH A 906 O HOH A 908 2.01 REMARK 500 O HOH B 970 O HOH B 985 2.01 REMARK 500 NH2 ARG B 278 O HOH B 606 2.02 REMARK 500 O6 NAG B 503 O HOH B 607 2.02 REMARK 500 OE1 GLU A 231 O HOH A 603 2.03 REMARK 500 O HOH B 922 O HOH B 981 2.03 REMARK 500 OE1 GLN B 336 O HOH B 608 2.03 REMARK 500 O4 NAG D 1 O HOH A 999 2.04 REMARK 500 O HOH A 665 O HOH A 861 2.06 REMARK 500 O HOH B 795 O HOH B 880 2.06 REMARK 500 O HOH B 970 O HOH B 975 2.06 REMARK 500 OE1 GLU A 362 O HOH A 604 2.07 REMARK 500 O HOH B 851 O HOH B 933 2.08 REMARK 500 ND2 ASN B 232 O HOH B 609 2.09 REMARK 500 ND2 ASN B 364 O HOH B 610 2.10 REMARK 500 O HOH B 764 O HOH B 920 2.10 REMARK 500 O HOH B 965 O HOH B 972 2.11 REMARK 500 O HOH B 717 O HOH B 853 2.11 REMARK 500 OD2 ASP B 274 O HOH B 606 2.12 REMARK 500 NZ LYS A 383 O HOH A 605 2.12 REMARK 500 O3 NAG A 502 O HOH A 606 2.13 REMARK 500 OD2 ASP B 53 O HOH B 611 2.13 REMARK 500 O HOH B 873 O HOH B 880 2.13 REMARK 500 O HOH B 831 O HOH B 895 2.13 REMARK 500 O HOH B 884 O HOH B 961 2.14 REMARK 500 O HOH B 877 O HOH B 940 2.14 REMARK 500 O HOH A 742 O HOH A 910 2.15 REMARK 500 O VAL A 322 O HOH A 607 2.15 REMARK 500 O HOH A 979 O HOH A 984 2.15 REMARK 500 O HOH B 860 O HOH B 884 2.16 REMARK 500 O6 NAG B 505 O HOH B 612 2.16 REMARK 500 O HOH B 809 O HOH B 950 2.17 REMARK 500 REMARK 500 THIS ENTRY HAS 59 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 ND2 ASN A 303 C2' YA4 A 501 4554 1.79 REMARK 500 CG ASN A 303 O2' YA4 A 501 4554 1.97 REMARK 500 OD1 ASN A 303 O2' YA4 A 501 4554 2.19 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 LYS B 186 CD - CE - NZ ANGL. DEV. = -20.6 DEGREES REMARK 500 ASN B 308 N - CA - CB ANGL. DEV. = -11.4 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 ASP A 54 97.64 -62.25 REMARK 500 ASN A 69 63.93 -152.35 REMARK 500 THR A 105 37.27 -95.11 REMARK 500 ASP A 107 72.84 66.62 REMARK 500 ASP A 155 -15.12 79.83 REMARK 500 GLN A 156 49.37 -92.63 REMARK 500 HIS A 249 -75.50 -81.62 REMARK 500 HIS A 290 -43.71 73.20 REMARK 500 ASP A 341 -42.73 -138.74 REMARK 500 ASP A 379 -167.64 -167.13 REMARK 500 ASP A 412 105.22 -164.61 REMARK 500 ASP A 418 -169.81 -69.27 REMARK 500 HIS B 50 112.36 -171.94 REMARK 500 ASN B 69 65.51 -173.28 REMARK 500 THR B 105 44.94 -101.93 REMARK 500 ASP B 107 78.80 59.57 REMARK 500 ASP B 155 -14.90 74.43 REMARK 500 GLN B 156 46.58 -94.65 REMARK 500 ALA B 224 14.29 56.76 REMARK 500 HIS B 290 -41.38 72.85 REMARK 500 ASN B 305 108.53 -51.54 REMARK 500 ASN B 308 135.63 -172.17 REMARK 500 ASP B 341 -41.92 -137.24 REMARK 500 ASP B 379 -171.36 -170.37 REMARK 500 ASP B 418 -176.64 -69.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 998 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A1000 DISTANCE = 7.00 ANGSTROMS REMARK 525 HOH A1001 DISTANCE = 7.38 ANGSTROMS REMARK 525 HOH A1003 DISTANCE = 8.95 ANGSTROMS REMARK 525 HOH B 995 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH B 996 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH B 998 DISTANCE = 7.29 ANGSTROMS REMARK 525 HOH B 999 DISTANCE = 7.41 ANGSTROMS REMARK 525 HOH B1000 DISTANCE = 7.55 ANGSTROMS REMARK 525 HOH B1001 DISTANCE = 8.51 ANGSTROMS REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 YA4 A 501 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 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 42 OD1 REMARK 620 2 HIS A 44 NE2 107.8 REMARK 620 3 ASP A 107 OD2 90.5 87.8 REMARK 620 4 HIS A 292 NE2 86.3 101.6 170.6 REMARK 620 5 YA4 A 501 OP3 159.2 92.8 93.3 86.7 REMARK 620 6 HOH A 643 O 85.4 160.6 77.7 93.2 75.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 107 OD2 REMARK 620 2 ASN A 148 OD1 95.3 REMARK 620 3 HIS A 249 NE2 77.7 83.7 REMARK 620 4 HIS A 290 ND1 162.6 96.4 90.7 REMARK 620 5 YA4 A 501 OP1 97.2 89.2 170.8 95.9 REMARK 620 6 HOH A 643 O 86.4 173.1 103.1 83.5 84.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 507 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 42 OD1 REMARK 620 2 HIS B 44 NE2 104.7 REMARK 620 3 ASP B 107 OD2 79.2 85.2 REMARK 620 4 HIS B 292 NE2 96.6 102.2 172.3 REMARK 620 5 PO4 B 506 O2 157.9 95.0 92.9 88.7 REMARK 620 6 HOH B 604 O 138.6 61.8 61.5 123.9 45.5 REMARK 620 7 HOH B 639 O 84.0 159.9 78.6 94.6 74.3 99.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 508 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 107 OD2 REMARK 620 2 ASN B 148 OD1 94.0 REMARK 620 3 HIS B 249 NE2 79.5 77.6 REMARK 620 4 HIS B 290 ND1 164.2 95.5 90.2 REMARK 620 5 PO4 B 506 O1 95.9 87.7 164.1 97.1 REMARK 620 6 HOH B 639 O 86.6 179.3 103.0 84.0 91.8 REMARK 620 N 1 2 3 4 5 DBREF 8W6P A 33 445 UNP P70158 ASM3A_MOUSE 33 445 DBREF 8W6P B 33 445 UNP P70158 ASM3A_MOUSE 33 445 SEQRES 1 A 413 ALA VAL GLY GLN PHE TRP HIS VAL THR ASP LEU HIS LEU SEQRES 2 A 413 ASP PRO THR TYR HIS ILE THR ASP ASP ARG THR LYS VAL SEQRES 3 A 413 CYS ALA SER SER LYS GLY ALA ASN ALA SER ASN PRO GLY SEQRES 4 A 413 PRO PHE GLY ASP VAL LEU CYS ASP SER PRO TYR GLN LEU SEQRES 5 A 413 ILE LEU SER ALA PHE ASP PHE ILE LYS ASN SER GLY GLN SEQRES 6 A 413 GLU ALA SER PHE MET ILE TRP THR GLY ASP SER PRO PRO SEQRES 7 A 413 HIS VAL PRO VAL PRO GLU LEU SER THR GLY THR VAL ILE SEQRES 8 A 413 LYS VAL ILE THR ASN MET THR MET THR VAL GLN ASN LEU SEQRES 9 A 413 PHE PRO ASN LEU GLN VAL PHE PRO ALA LEU GLY ASN HIS SEQRES 10 A 413 ASP TYR TRP PRO GLN ASP GLN LEU PRO ILE VAL THR SER SEQRES 11 A 413 LYS VAL TYR SER ALA VAL ALA ASP LEU TRP LYS PRO TRP SEQRES 12 A 413 LEU GLY GLU GLU ALA ILE SER THR LEU LYS LYS GLY GLY SEQRES 13 A 413 PHE TYR SER GLN LYS VAL ALA SER ASN PRO GLY LEU ARG SEQRES 14 A 413 ILE ILE SER LEU ASN THR ASN LEU TYR TYR GLY PRO ASN SEQRES 15 A 413 ILE MET THR LEU ASN LYS THR ASP PRO ALA ASN GLN PHE SEQRES 16 A 413 GLU TRP LEU GLU ASN THR LEU ASN SER SER LEU TRP ASN SEQRES 17 A 413 LYS GLU LYS VAL TYR ILE ILE ALA HIS VAL PRO VAL GLY SEQRES 18 A 413 TYR LEU PRO TYR ALA THR ASP THR PRO ALA ILE ARG GLN SEQRES 19 A 413 TYR TYR ASN GLU LYS LEU LEU ASP ILE PHE ARG ARG TYR SEQRES 20 A 413 SER SER VAL ILE ALA GLY GLN PHE TYR GLY HIS THR HIS SEQRES 21 A 413 ARG ASP SER LEU MET VAL LEU SER ASP LYS ASN GLY ASN SEQRES 22 A 413 PRO LEU ASN SER VAL PHE VAL ALA PRO ALA VAL THR PRO SEQRES 23 A 413 VAL LYS GLY VAL LEU GLN LYS GLU THR ASN ASN PRO GLY SEQRES 24 A 413 VAL ARG LEU PHE GLN TYR LYS PRO GLY ASP TYR THR LEU SEQRES 25 A 413 LEU ASP MET VAL GLN TYR TYR LEU ASN LEU THR GLU ALA SEQRES 26 A 413 ASN LEU LYS GLY GLU SER ASN TRP THR LEU GLU TYR VAL SEQRES 27 A 413 LEU THR GLN ALA TYR SER VAL ALA ASP LEU GLN PRO LYS SEQRES 28 A 413 SER LEU TYR ALA LEU VAL GLN GLN PHE ALA THR LYS ASP SEQRES 29 A 413 SER LYS GLN PHE LEU LYS TYR TYR HIS TYR TYR PHE VAL SEQRES 30 A 413 SER TYR ASP SER SER ALA THR CYS ASP GLN HIS CYS LYS SEQRES 31 A 413 THR LEU GLN VAL CYS ALA ILE MET ASN LEU ASP SER MET SEQRES 32 A 413 SER TYR ASP ASP CYS LEU LYS GLN HIS LEU SEQRES 1 B 413 ALA VAL GLY GLN PHE TRP HIS VAL THR ASP LEU HIS LEU SEQRES 2 B 413 ASP PRO THR TYR HIS ILE THR ASP ASP ARG THR LYS VAL SEQRES 3 B 413 CYS ALA SER SER LYS GLY ALA ASN ALA SER ASN PRO GLY SEQRES 4 B 413 PRO PHE GLY ASP VAL LEU CYS ASP SER PRO TYR GLN LEU SEQRES 5 B 413 ILE LEU SER ALA PHE ASP PHE ILE LYS ASN SER GLY GLN SEQRES 6 B 413 GLU ALA SER PHE MET ILE TRP THR GLY ASP SER PRO PRO SEQRES 7 B 413 HIS VAL PRO VAL PRO GLU LEU SER THR GLY THR VAL ILE SEQRES 8 B 413 LYS VAL ILE THR ASN MET THR MET THR VAL GLN ASN LEU SEQRES 9 B 413 PHE PRO ASN LEU GLN VAL PHE PRO ALA LEU GLY ASN HIS SEQRES 10 B 413 ASP TYR TRP PRO GLN ASP GLN LEU PRO ILE VAL THR SER SEQRES 11 B 413 LYS VAL TYR SER ALA VAL ALA ASP LEU TRP LYS PRO TRP SEQRES 12 B 413 LEU GLY GLU GLU ALA ILE SER THR LEU LYS LYS GLY GLY SEQRES 13 B 413 PHE TYR SER GLN LYS VAL ALA SER ASN PRO GLY LEU ARG SEQRES 14 B 413 ILE ILE SER LEU ASN THR ASN LEU TYR TYR GLY PRO ASN SEQRES 15 B 413 ILE MET THR LEU ASN LYS THR ASP PRO ALA ASN GLN PHE SEQRES 16 B 413 GLU TRP LEU GLU ASN THR LEU ASN SER SER LEU TRP ASN SEQRES 17 B 413 LYS GLU LYS VAL TYR ILE ILE ALA HIS VAL PRO VAL GLY SEQRES 18 B 413 TYR LEU PRO TYR ALA THR ASP THR PRO ALA ILE ARG GLN SEQRES 19 B 413 TYR TYR ASN GLU LYS LEU LEU ASP ILE PHE ARG ARG TYR SEQRES 20 B 413 SER SER VAL ILE ALA GLY GLN PHE TYR GLY HIS THR HIS SEQRES 21 B 413 ARG ASP SER LEU MET VAL LEU SER ASP LYS ASN GLY ASN SEQRES 22 B 413 PRO LEU ASN SER VAL PHE VAL ALA PRO ALA VAL THR PRO SEQRES 23 B 413 VAL LYS GLY VAL LEU GLN LYS GLU THR ASN ASN PRO GLY SEQRES 24 B 413 VAL ARG LEU PHE GLN TYR LYS PRO GLY ASP TYR THR LEU SEQRES 25 B 413 LEU ASP MET VAL GLN TYR TYR LEU ASN LEU THR GLU ALA SEQRES 26 B 413 ASN LEU LYS GLY GLU SER ASN TRP THR LEU GLU TYR VAL SEQRES 27 B 413 LEU THR GLN ALA TYR SER VAL ALA ASP LEU GLN PRO LYS SEQRES 28 B 413 SER LEU TYR ALA LEU VAL GLN GLN PHE ALA THR LYS ASP SEQRES 29 B 413 SER LYS GLN PHE LEU LYS TYR TYR HIS TYR TYR PHE VAL SEQRES 30 B 413 SER TYR ASP SER SER ALA THR CYS ASP GLN HIS CYS LYS SEQRES 31 B 413 THR LEU GLN VAL CYS ALA ILE MET ASN LEU ASP SER MET SEQRES 32 B 413 SER TYR ASP ASP CYS LEU LYS GLN HIS LEU HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET FUC D 2 10 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 YA4 A 501 13 HET NAG A 502 14 HET NAG A 503 14 HET ZN A 504 1 HET ZN A 505 1 HET NAG B 501 14 HET FUC B 502 10 HET NAG B 503 14 HET NAG B 504 14 HET NAG B 505 14 HET PO4 B 506 5 HET ZN B 507 1 HET ZN B 508 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM YA4 [(2~{R},3~{S},4~{S})-3,4-BIS(OXIDANYL)OXOLAN-2- HETNAM 2 YA4 YL]METHOXY-SULFANYL-PHOSPHINIC ACID HETNAM ZN ZINC ION HETNAM PO4 PHOSPHATE 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 FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 3 NAG 13(C8 H15 N O6) FORMUL 4 FUC 2(C6 H12 O5) FORMUL 6 BMA C6 H12 O6 FORMUL 7 YA4 C5 H11 O6 P S FORMUL 10 ZN 4(ZN 2+) FORMUL 17 PO4 O4 P 3- FORMUL 20 HOH *804(H2 O) HELIX 1 AA1 CYS A 59 LYS A 63 5 5 HELIX 2 AA2 PRO A 81 ASN A 94 1 14 HELIX 3 AA3 PRO A 113 LEU A 117 5 5 HELIX 4 AA4 SER A 118 PHE A 137 1 20 HELIX 5 AA5 SER A 162 TRP A 172 1 11 HELIX 6 AA6 LYS A 173 LEU A 176 5 4 HELIX 7 AA7 GLY A 177 GLY A 188 1 12 HELIX 8 AA8 ASN A 206 TYR A 211 5 6 HELIX 9 AA9 ASP A 222 ALA A 224 5 3 HELIX 10 AB1 ASN A 225 ASN A 240 1 16 HELIX 11 AB2 ARG A 265 TYR A 279 1 15 HELIX 12 AB3 ASN A 353 GLY A 361 1 9 HELIX 13 AB4 LEU A 371 SER A 376 1 6 HELIX 14 AB5 GLN A 381 THR A 394 1 14 HELIX 15 AB6 SER A 397 PHE A 408 1 12 HELIX 16 AB7 ASP A 418 ASN A 431 1 14 HELIX 17 AB8 ASP A 433 LEU A 445 1 13 HELIX 18 AB9 ASP B 54 VAL B 58 5 5 HELIX 19 AC1 CYS B 59 LYS B 63 5 5 HELIX 20 AC2 PRO B 81 ASN B 94 1 14 HELIX 21 AC3 PRO B 113 LEU B 117 5 5 HELIX 22 AC4 SER B 118 PHE B 137 1 20 HELIX 23 AC5 SER B 162 LYS B 173 1 12 HELIX 24 AC6 PRO B 174 LEU B 176 5 3 HELIX 25 AC7 GLY B 177 GLY B 188 1 12 HELIX 26 AC8 ASN B 206 TYR B 211 5 6 HELIX 27 AC9 ASN B 214 LEU B 218 5 5 HELIX 28 AD1 ASP B 222 ALA B 224 5 3 HELIX 29 AD2 ASN B 225 ASN B 240 1 16 HELIX 30 AD3 ARG B 265 TYR B 279 1 15 HELIX 31 AD4 ASN B 353 GLY B 361 1 9 HELIX 32 AD5 LEU B 371 SER B 376 1 6 HELIX 33 AD6 GLN B 381 THR B 394 1 14 HELIX 34 AD7 SER B 397 PHE B 408 1 12 HELIX 35 AD8 ASP B 418 ASN B 431 1 14 HELIX 36 AD9 ASP B 433 LEU B 445 1 13 SHEET 1 AA1 6 GLN A 141 PRO A 144 0 SHEET 2 AA1 6 PHE A 101 TRP A 104 1 N MET A 102 O PHE A 143 SHEET 3 AA1 6 GLY A 35 VAL A 40 1 N TRP A 38 O ILE A 103 SHEET 4 AA1 6 GLY A 331 TYR A 337 -1 O PHE A 335 N PHE A 37 SHEET 5 AA1 6 LEU A 344 TYR A 351 -1 O VAL A 348 N LEU A 334 SHEET 6 AA1 6 THR A 366 VAL A 370 -1 O GLU A 368 N GLN A 349 SHEET 1 AA2 6 TYR A 190 LYS A 193 0 SHEET 2 AA2 6 LEU A 200 SER A 204 -1 O ILE A 202 N GLN A 192 SHEET 3 AA2 6 LYS A 243 ILE A 247 1 O ILE A 247 N ILE A 203 SHEET 4 AA2 6 ILE A 283 TYR A 288 1 O GLY A 285 N ILE A 246 SHEET 5 AA2 6 PRO A 306 VAL A 312 1 O PHE A 311 N TYR A 288 SHEET 6 AA2 6 SER A 295 SER A 300 -1 N LEU A 299 O LEU A 307 SHEET 1 AA3 6 GLN B 141 PRO B 144 0 SHEET 2 AA3 6 PHE B 101 TRP B 104 1 N TRP B 104 O PHE B 143 SHEET 3 AA3 6 GLY B 35 VAL B 40 1 N TRP B 38 O ILE B 103 SHEET 4 AA3 6 GLY B 331 TYR B 337 -1 O PHE B 335 N PHE B 37 SHEET 5 AA3 6 LEU B 344 TYR B 351 -1 O VAL B 348 N LEU B 334 SHEET 6 AA3 6 THR B 366 VAL B 370 -1 O GLU B 368 N GLN B 349 SHEET 1 AA4 6 TYR B 190 LYS B 193 0 SHEET 2 AA4 6 LEU B 200 SER B 204 -1 O ILE B 202 N GLN B 192 SHEET 3 AA4 6 LYS B 243 ILE B 247 1 O ILE B 247 N ILE B 203 SHEET 4 AA4 6 ILE B 283 TYR B 288 1 O PHE B 287 N ILE B 246 SHEET 5 AA4 6 PRO B 306 VAL B 312 1 O PHE B 311 N GLN B 286 SHEET 6 AA4 6 SER B 295 SER B 300 -1 N LEU B 299 O LEU B 307 SSBOND 1 CYS A 59 CYS A 78 1555 1555 2.05 SSBOND 2 CYS A 417 CYS A 421 1555 1555 2.03 SSBOND 3 CYS A 427 CYS A 440 1555 1555 2.01 SSBOND 4 CYS B 59 CYS B 78 1555 1555 2.05 SSBOND 5 CYS B 417 CYS B 421 1555 1555 2.04 SSBOND 6 CYS B 427 CYS B 440 1555 1555 2.03 LINK ND2 ASN A 66 C1 NAG A 502 1555 1555 1.44 LINK ND2 ASN A 128 C1 NAG A 503 1555 1555 1.44 LINK ND2 ASN A 235 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN A 303 O2' YA4 A 501 1555 4554 1.30 LINK ND2 ASN A 353 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN A 364 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN B 66 C1 NAG B 503 1555 1555 1.45 LINK ND2 ASN B 128 C1 NAG B 505 1555 1555 1.44 LINK ND2 ASN B 235 C1 NAG B 504 1555 1555 1.45 LINK ND2 ASN B 353 C1 NAG F 1 1555 1555 1.43 LINK C1 NAG B 501 O4 NAG B 505 1555 1555 1.46 LINK C1 FUC B 502 O6 NAG B 504 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O6 NAG D 1 C1 FUC D 2 1555 1555 1.43 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 1.45 LINK OD1 ASP A 42 ZN ZN A 505 1555 1555 2.10 LINK NE2 HIS A 44 ZN ZN A 505 1555 1555 2.22 LINK OD2 ASP A 107 ZN ZN A 504 1555 1555 2.40 LINK OD2 ASP A 107 ZN ZN A 505 1555 1555 2.39 LINK OD1 ASN A 148 ZN ZN A 504 1555 1555 2.16 LINK NE2 HIS A 249 ZN ZN A 504 1555 1555 2.27 LINK ND1 HIS A 290 ZN ZN A 504 1555 1555 2.34 LINK NE2 HIS A 292 ZN ZN A 505 1555 1555 2.26 LINK OP1 YA4 A 501 ZN ZN A 504 1555 1555 2.11 LINK OP3 YA4 A 501 ZN ZN A 505 1555 1555 2.46 LINK ZN ZN A 504 O HOH A 643 1555 1555 1.93 LINK ZN ZN A 505 O HOH A 643 1555 1555 2.36 LINK OD1 ASP B 42 ZN ZN B 507 1555 1555 2.10 LINK NE2 HIS B 44 ZN ZN B 507 1555 1555 2.31 LINK OD2 ASP B 107 ZN ZN B 507 1555 1555 2.33 LINK OD2 ASP B 107 ZN ZN B 508 1555 1555 2.48 LINK OD1 ASN B 148 ZN ZN B 508 1555 1555 2.35 LINK NE2 HIS B 249 ZN ZN B 508 1555 1555 2.27 LINK ND1 HIS B 290 ZN ZN B 508 1555 1555 2.28 LINK NE2 HIS B 292 ZN ZN B 507 1555 1555 2.29 LINK O2 PO4 B 506 ZN ZN B 507 1555 1555 2.45 LINK O1 PO4 B 506 ZN ZN B 508 1555 1555 2.16 LINK ZN ZN B 507 O HOH B 604 1555 1555 2.56 LINK ZN ZN B 507 O HOH B 639 1555 1555 2.46 LINK ZN ZN B 508 O HOH B 639 1555 1555 1.91 CISPEP 1 TRP A 152 PRO A 153 0 -4.24 CISPEP 2 TRP B 152 PRO B 153 0 -6.34 CRYST1 122.225 122.225 79.557 90.00 90.00 90.00 P 41 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 0.008182 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008182 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012570 0.00000