HEADER LIPID BINDING PROTEIN 20-DEC-14 4UEX TITLE STRUCTURE OF HUMAN SAPOSIN A AT LYSOSOMAL PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROSAPOSIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 60-142; COMPND 5 SYNONYM: PROACTIVATOR POLYPEPTIDE, PROTEIN A, CEREBROSIDE SULFATE AC COMPND 6 TIVATOR, CSACT, DISPERSIN, SPHINGOLIPID ACTIVATOR PROTEIN 1, SAP-1 , COMPND 7 SULFATIDE/GM1 ACTIVATOR, A1 ACTIVATOR, CO-BETA-GLUCOSIDASE, GLUC COMPND 8 OSYLCERAMIDASE ACTIVATOR, SPHINGOLIPID ACTIVATOR PROTEIN 2, SAP-2, COMPND 9 COMPONENT C, PROTEIN C, SAPOSIN A; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ORIGAMI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS LIPID BINDING PROTEIN, SAPOSIN A, SAPOSIN, SAP, LIPID TRANSFER KEYWDS 2 PROTEIN, SPHINGOLIPID ACTIVATOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.H.HILL,R.J.READ,J.E.DEANE REVDAT 3 20-DEC-23 4UEX 1 REMARK REVDAT 2 29-MAY-19 4UEX 1 REMARK REVDAT 1 15-JUL-15 4UEX 0 JRNL AUTH C.H.HILL,R.J.READ,J.E.DEANE JRNL TITL STRUCTURE OF HUMAN SAPOSIN A AT LYSOSOMAL PH. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 895 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 26144235 JRNL DOI 10.1107/S2053230X15008584 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 12737 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 612 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 34.1261 - 2.8569 0.99 3085 159 0.1818 0.1951 REMARK 3 2 2.8569 - 2.2678 0.99 3019 163 0.1762 0.2119 REMARK 3 3 2.2678 - 1.9811 0.99 3021 153 0.1798 0.2242 REMARK 3 4 1.9811 - 1.8000 0.98 3000 137 0.2367 0.2843 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.004 1338 REMARK 3 ANGLE : 0.807 1821 REMARK 3 CHIRALITY : 0.032 214 REMARK 3 PLANARITY : 0.004 237 REMARK 3 DIHEDRAL : 13.314 517 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -1.9235 8.0717 -16.6722 REMARK 3 T TENSOR REMARK 3 T11: 0.1613 T22: 0.1670 REMARK 3 T33: 0.1598 T12: 0.0197 REMARK 3 T13: -0.0094 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.4616 L22: 0.7236 REMARK 3 L33: 1.4646 L12: 0.0339 REMARK 3 L13: -0.0576 L23: 0.4594 REMARK 3 S TENSOR REMARK 3 S11: -0.0646 S12: -0.1018 S13: 0.0892 REMARK 3 S21: -0.1209 S22: -0.0269 S23: 0.0240 REMARK 3 S31: -0.0653 S32: 0.0319 S33: -0.0063 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -7.6727 12.0912 0.7954 REMARK 3 T TENSOR REMARK 3 T11: 0.1752 T22: 0.1772 REMARK 3 T33: 0.2053 T12: -0.0156 REMARK 3 T13: 0.0066 T23: -0.0230 REMARK 3 L TENSOR REMARK 3 L11: 0.3416 L22: 0.5718 REMARK 3 L33: 0.6910 L12: 0.0557 REMARK 3 L13: 0.2456 L23: 0.3818 REMARK 3 S TENSOR REMARK 3 S11: -0.0409 S12: -0.0047 S13: 0.0648 REMARK 3 S21: 0.0003 S22: -0.0270 S23: 0.1424 REMARK 3 S31: 0.0098 S32: -0.0326 S33: -0.0008 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 4UEX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1290062637. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : KIRKPATRICK BAEZ BIMORPH MIRROR REMARK 200 PAIR FOR HORIZONTAL AND VERTICAL REMARK 200 FOCUSSING REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12753 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 34.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: PDB ENTRY 2DOB REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SITTING-DROP VAPOUR DIFFUSION: 400 NL REMARK 280 DROP (200 NL PROTEIN AT 19.6 MG/ML IN 150 MM NACL, 50 MM TRIS PH REMARK 280 7.4 MIXED WITH 200 NL RESERVOIR SOLUTION) WAS EQUILIBRATED REMARK 280 AGAINST A 80 UL RESERVOIR OF 0.2 M LITHIUM SULPHATE, 0.1 M REMARK 280 SODIUM ACETATE PH 4.8 AND 25% W/V POLYETHYLENE GLYCOL 4000, REMARK 280 VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.34500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A -1 REMARK 465 SER A 81 REMARK 465 LEU A 82 REMARK 465 GLN A 83 REMARK 465 MET B -1 REMARK 465 SER B 81 REMARK 465 LEU B 82 REMARK 465 GLN B 83 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 GLU A 80 CG CD OE1 OE2 REMARK 470 GLU B 80 CG CD OE1 OE2 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 GLU A 65 27.39 81.71 REMARK 500 GLU A 65 23.96 81.71 REMARK 500 GLU B 65 34.04 74.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 UNIPROT REFERENCE IS TO THE POLYPROTEIN PRECURSOR PSAP ( REMARK 999 PROSAPOSIN). THE SEQUENCE OF THE SAPOSIN A PROTEIN IS 60- REMARK 999 142 IN THIS RECORD. AN ADDITIONAL MG IS PRESENT AT THE N- REMARK 999 TERMINUS OF THE EXPRESSION CONSTRUCT AS A RESULT OF THE REMARK 999 CLONING STRATEGY. THE C-TERMINAL SLQ ARE NOT MODELLED AS REMARK 999 THEY ARE DISORDERED. DBREF 4UEX A 1 83 UNP P07602 SAP_HUMAN 60 142 DBREF 4UEX B 1 83 UNP P07602 SAP_HUMAN 60 142 SEQADV 4UEX MET A -1 UNP P07602 EXPRESSION TAG SEQADV 4UEX GLY A 0 UNP P07602 EXPRESSION TAG SEQADV 4UEX MET B -1 UNP P07602 EXPRESSION TAG SEQADV 4UEX GLY B 0 UNP P07602 EXPRESSION TAG SEQRES 1 A 85 MET GLY SER LEU PRO CYS ASP ILE CYS LYS ASP VAL VAL SEQRES 2 A 85 THR ALA ALA GLY ASP MET LEU LYS ASP ASN ALA THR GLU SEQRES 3 A 85 GLU GLU ILE LEU VAL TYR LEU GLU LYS THR CYS ASP TRP SEQRES 4 A 85 LEU PRO LYS PRO ASN MET SER ALA SER CYS LYS GLU ILE SEQRES 5 A 85 VAL ASP SER TYR LEU PRO VAL ILE LEU ASP ILE ILE LYS SEQRES 6 A 85 GLY GLU MET SER ARG PRO GLY GLU VAL CYS SER ALA LEU SEQRES 7 A 85 ASN LEU CYS GLU SER LEU GLN SEQRES 1 B 85 MET GLY SER LEU PRO CYS ASP ILE CYS LYS ASP VAL VAL SEQRES 2 B 85 THR ALA ALA GLY ASP MET LEU LYS ASP ASN ALA THR GLU SEQRES 3 B 85 GLU GLU ILE LEU VAL TYR LEU GLU LYS THR CYS ASP TRP SEQRES 4 B 85 LEU PRO LYS PRO ASN MET SER ALA SER CYS LYS GLU ILE SEQRES 5 B 85 VAL ASP SER TYR LEU PRO VAL ILE LEU ASP ILE ILE LYS SEQRES 6 B 85 GLY GLU MET SER ARG PRO GLY GLU VAL CYS SER ALA LEU SEQRES 7 B 85 ASN LEU CYS GLU SER LEU GLN FORMUL 3 HOH *26(H2 O) HELIX 1 1 SER A 1 ASP A 20 1 20 HELIX 2 2 THR A 23 LEU A 38 1 16 HELIX 3 3 LYS A 40 GLY A 64 1 25 HELIX 4 4 ARG A 68 LEU A 76 1 9 HELIX 5 5 SER B 1 ASP B 20 1 20 HELIX 6 6 THR B 23 LEU B 38 1 16 HELIX 7 7 LYS B 40 GLY B 64 1 25 HELIX 8 8 ARG B 68 LEU B 76 1 9 SSBOND 1 CYS A 4 CYS A 79 1555 1555 2.03 SSBOND 2 CYS A 7 CYS A 73 1555 1555 2.04 SSBOND 3 CYS A 35 CYS A 47 1555 1555 2.04 SSBOND 4 CYS B 4 CYS B 79 1555 1555 2.04 SSBOND 5 CYS B 7 CYS B 73 1555 1555 2.04 SSBOND 6 CYS B 35 CYS B 47 1555 1555 2.03 CRYST1 34.170 58.690 35.160 90.00 93.10 90.00 P 1 21 1 4 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 0.029265 0.000000 0.001585 0.00000 SCALE2 0.000000 0.017039 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028483 0.00000