HEADER LIPID BINDING PROTEIN 06-MAR-24 9AXG TITLE HUMAN SAPOSIN B IN THE PRESENCE OF GLOBOTRIAOSYLCERAMIDE-NBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAPOSIN-B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CEREBROSIDE SULFATE ACTIVATOR,CSACT,DISPERSIN,SPHINGOLIPID COMPND 5 ACTIVATOR PROTEIN 1,SAP-1,SULFATIDE/GM1 ACTIVATOR; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: N-TERMINAL GAS LINKER FROM PURIFICATION. FRAGMENT COMPND 8 CORRESPONDS TO RESIDUES 195-273 OF CANONICAL ISOFORM P07602-1. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PSAP, GLBA, SAP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SHUFFLE EXPRESS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS SAPOSIN, SAPOSIN B, SAPB, FABRY DISEASE, LYSOSOMAL, ACTIVATOR KEYWDS 2 PROTEIN, GLOBOTRIAOSYLCERAMIDE, GB3, NITROBENZOXADIAZOLE, NBD, LIPID KEYWDS 3 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.K.SAWYER,S.C.GARMAN REVDAT 3 24-APR-24 9AXG 1 JRNL REVDAT 2 17-APR-24 9AXG 1 JRNL REVDAT 1 13-MAR-24 9AXG 0 JRNL AUTH T.K.SAWYER,E.ARAL,J.V.STAROS,C.E.BOBST,S.C.GARMAN JRNL TITL HUMAN SAPOSIN B LIGAND BINDING AND PRESENTATION TO JRNL TITL 2 ALPHA-GALACTOSIDASE A. JRNL REF BIORXIV 2024 JRNL REFN ISSN 2692-8205 JRNL PMID 38617236 JRNL DOI 10.1101/2024.04.04.584535 REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 6241 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920 REMARK 3 FREE R VALUE TEST SET COUNT : 619 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 34.8300 - 4.2600 0.99 1426 153 0.2259 0.2382 REMARK 3 2 4.2500 - 3.3800 1.00 1387 178 0.2444 0.3467 REMARK 3 3 3.3800 - 2.9500 1.00 1405 150 0.3009 0.3322 REMARK 3 4 2.9500 - 2.6800 1.00 1404 138 0.2833 0.3400 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.373 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.334 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 82.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 93.94 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 : 0.008 1175 REMARK 3 ANGLE : 0.962 1587 REMARK 3 CHIRALITY : 0.050 187 REMARK 3 PLANARITY : 0.007 212 REMARK 3 DIHEDRAL : 7.697 165 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -12.6700 -13.4676 -6.0861 REMARK 3 T TENSOR REMARK 3 T11: 0.4446 T22: 0.4181 REMARK 3 T33: 0.6167 T12: -0.0730 REMARK 3 T13: 0.0408 T23: 0.0239 REMARK 3 L TENSOR REMARK 3 L11: 3.7064 L22: 3.8712 REMARK 3 L33: 7.3823 L12: -0.1581 REMARK 3 L13: -0.9991 L23: 0.8677 REMARK 3 S TENSOR REMARK 3 S11: -0.0478 S12: -0.0652 S13: 0.2094 REMARK 3 S21: 0.0559 S22: 0.0020 S23: -0.1469 REMARK 3 S31: -0.2861 S32: -0.0621 S33: 0.0375 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 9AXG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1000282231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6246 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 REMARK 200 RESOLUTION RANGE LOW (A) : 34.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.04320 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.0700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.510 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 500 NL OF PROTEIN-LIPID COMPLEX (0.82 REMARK 280 MM SAPB PLUS 0.87 MM GB3-NBD) WAS MIXED WITH 250 NL OF RESERVOIR REMARK 280 SOLUTION (3.1-3.3 M MALONATE PH 5) AND EQUILIBRATED AGAINST 70 REMARK 280 UL RESERVOIRS AT 20 C., PH 5.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 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 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 29.06033 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 58.12067 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 29.06033 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 58.12067 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: 1740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 GLU A 79 REMARK 465 GLU B 79 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 5 CG CD OE1 NE2 REMARK 470 GLN A 26 CG CD OE1 NE2 REMARK 470 ARG A 38 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 LEU A 73 CG CD1 CD2 REMARK 470 ASP A 78 CG OD1 OD2 REMARK 470 GLU B 30 CG CD OE1 OE2 REMARK 470 GLU B 35 CG CD OE1 OE2 REMARK 470 LEU B 39 CG CD1 CD2 REMARK 470 ILE B 46 CG1 CG2 CD1 REMARK 470 TYR B 50 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR B 54 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE B 57 CG1 CG2 CD1 REMARK 470 MET B 61 CG SD CE REMARK 470 LEU B 73 CG CD1 CD2 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 HIS B 64 34.27 -90.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9AVS RELATED DB: PDB REMARK 900 CONTAINS THE SAME SAPOSIN B PROTEIN COMPLEXED WITH ALPHA- REMARK 900 GALACTOSIDASE A DBREF 9AXG A 1 79 UNP P07602 SAP_HUMAN 195 273 DBREF 9AXG B 1 79 UNP P07602 SAP_HUMAN 195 273 SEQADV 9AXG GLY A -2 UNP P07602 EXPRESSION TAG SEQADV 9AXG ALA A -1 UNP P07602 EXPRESSION TAG SEQADV 9AXG SER A 0 UNP P07602 EXPRESSION TAG SEQADV 9AXG GLY B -2 UNP P07602 EXPRESSION TAG SEQADV 9AXG ALA B -1 UNP P07602 EXPRESSION TAG SEQADV 9AXG SER B 0 UNP P07602 EXPRESSION TAG SEQRES 1 A 82 GLY ALA SER GLY ASP VAL CYS GLN ASP CYS ILE GLN MET SEQRES 2 A 82 VAL THR ASP ILE GLN THR ALA VAL ARG THR ASN SER THR SEQRES 3 A 82 PHE VAL GLN ALA LEU VAL GLU HIS VAL LYS GLU GLU CYS SEQRES 4 A 82 ASP ARG LEU GLY PRO GLY MET ALA ASP ILE CYS LYS ASN SEQRES 5 A 82 TYR ILE SER GLN TYR SER GLU ILE ALA ILE GLN MET MET SEQRES 6 A 82 MET HIS MET GLN PRO LYS GLU ILE CYS ALA LEU VAL GLY SEQRES 7 A 82 PHE CYS ASP GLU SEQRES 1 B 82 GLY ALA SER GLY ASP VAL CYS GLN ASP CYS ILE GLN MET SEQRES 2 B 82 VAL THR ASP ILE GLN THR ALA VAL ARG THR ASN SER THR SEQRES 3 B 82 PHE VAL GLN ALA LEU VAL GLU HIS VAL LYS GLU GLU CYS SEQRES 4 B 82 ASP ARG LEU GLY PRO GLY MET ALA ASP ILE CYS LYS ASN SEQRES 5 B 82 TYR ILE SER GLN TYR SER GLU ILE ALA ILE GLN MET MET SEQRES 6 B 82 MET HIS MET GLN PRO LYS GLU ILE CYS ALA LEU VAL GLY SEQRES 7 B 82 PHE CYS ASP GLU HET MLI B 101 7 HETNAM MLI MALONATE ION FORMUL 3 MLI C3 H2 O4 2- FORMUL 4 HOH *3(H2 O) HELIX 1 AA1 GLY A 1 ASN A 21 1 21 HELIX 2 AA2 THR A 23 GLU A 35 1 13 HELIX 3 AA3 CYS A 36 LEU A 39 5 4 HELIX 4 AA4 GLY A 42 HIS A 64 1 23 HELIX 5 AA5 GLN A 66 GLY A 75 1 10 HELIX 6 AA6 ALA B -1 ASN B 21 1 23 HELIX 7 AA7 THR B 23 CYS B 36 1 14 HELIX 8 AA8 ASP B 37 LEU B 39 5 3 HELIX 9 AA9 GLY B 40 HIS B 64 1 25 HELIX 10 AB1 GLN B 66 VAL B 74 1 9 SSBOND 1 CYS A 4 CYS A 77 1555 1555 2.03 SSBOND 2 CYS A 7 CYS A 71 1555 1555 2.04 SSBOND 3 CYS A 36 CYS A 47 1555 1555 2.04 SSBOND 4 CYS B 4 CYS B 77 1555 1555 2.03 SSBOND 5 CYS B 7 CYS B 71 1555 1555 2.04 SSBOND 6 CYS B 36 CYS B 47 1555 1555 2.04 CRYST1 66.908 66.908 87.181 90.00 90.00 120.00 P 64 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 0.014946 0.008629 0.000000 0.00000 SCALE2 0.000000 0.017258 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011470 0.00000