HEADER LIPID BINDING PROTEIN 20-DEC-07 3BQP TITLE CRYSTAL STRUCTURE OF HUMAN SAPOSIN D (ORTHORHOMBIC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROACTIVATOR POLYPEPTIDE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SAPOSIN D, RESIDUES 405-484; COMPND 5 SYNONYM: CERAMIDE ACTIVATOR PROTEIN; 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: PSAP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) ROSETTA-GAMI 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-16 KEYWDS SAPOSIN, SPHINGOLIPID ACTIVATOR PROTEIN, LIPID BINDING KEYWDS 2 PROTEIN, ACID CERAMIDASE,FARBER DISEASE, LIPID METABOLISM, KEYWDS 3 LYSOSOME, SPHINGOLIPID METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR G.G.PRIVE,K.POPOVIC REVDAT 3 24-FEB-09 3BQP 1 VERSN REVDAT 2 20-MAY-08 3BQP 1 JRNL REVDAT 1 05-FEB-08 3BQP 0 JRNL AUTH K.POPOVIC,G.G.PRIVE JRNL TITL STRUCTURES OF THE HUMAN CERAMIDE ACTIVATOR PROTEIN JRNL TITL 2 SAPOSIN D. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 589 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18453694 JRNL DOI 10.1107/S0907444908003120 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.177 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.176 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2010 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 38323 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.173 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.171 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1822 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 34980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1271 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 198 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1417.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 11 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 13278 REMARK 3 NUMBER OF RESTRAINTS : 16744 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.062 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.067 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.019 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.055 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.090 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE REMARK 3 R (NO CUTOFF) REMARK 4 REMARK 4 3BQP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-07. REMARK 100 THE RCSB ID CODE IS RCSB045848. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38323 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.21800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8K, MAGNESIUM CHLORIDE, REMARK 280 TRIS.HCL BUFFER, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.22500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.28500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.72500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.28500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.22500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.72500 REMARK 290 SMTRY3 4 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 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 LYS A 21 CG CD CE NZ REMARK 470 ASN A 22 CG OD1 ND2 REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 GLU B 20 CB CG CD OE1 OE2 REMARK 470 LYS B 21 CB CG CD CE NZ REMARK 470 ASN B 22 CB CG OD1 ND2 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 B 11 CB - CG - CD1 ANGL. DEV. = -15.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 MG A 81 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 642 O REMARK 620 2 HOH A 630 O 85.0 REMARK 620 3 HOH A 673 O 85.5 90.5 REMARK 620 4 HOH A 654 O 167.7 90.3 106.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 82 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 674 O REMARK 620 2 HOH A 675 O 87.7 REMARK 620 3 HOH A 585 O 91.0 87.7 REMARK 620 4 HOH B 633 O 91.2 175.7 88.2 REMARK 620 5 HOH B 632 O 95.1 94.4 173.6 89.9 REMARK 620 6 HOH A 606 O 175.1 89.6 84.8 91.2 89.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 83 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 676 O REMARK 620 2 HOH A 677 O 87.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 81 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 82 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 83 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BQQ RELATED DB: PDB DBREF 3BQP A 1 80 UNP P07602 SAP_HUMAN 405 484 DBREF 3BQP B 1 80 UNP P07602 SAP_HUMAN 405 484 SEQRES 1 A 80 ASP GLY GLY PHE CYS GLU VAL CYS LYS LYS LEU VAL GLY SEQRES 2 A 80 TYR LEU ASP ARG ASN LEU GLU LYS ASN SER THR LYS GLN SEQRES 3 A 80 GLU ILE LEU ALA ALA LEU GLU LYS GLY CYS SER PHE LEU SEQRES 4 A 80 PRO ASP PRO TYR GLN LYS GLN CYS ASP GLN PHE VAL ALA SEQRES 5 A 80 GLU TYR GLU PRO VAL LEU ILE GLU ILE LEU VAL GLU VAL SEQRES 6 A 80 MET ASP PRO SER PHE VAL CYS LEU LYS ILE GLY ALA CYS SEQRES 7 A 80 PRO SER SEQRES 1 B 80 ASP GLY GLY PHE CYS GLU VAL CYS LYS LYS LEU VAL GLY SEQRES 2 B 80 TYR LEU ASP ARG ASN LEU GLU LYS ASN SER THR LYS GLN SEQRES 3 B 80 GLU ILE LEU ALA ALA LEU GLU LYS GLY CYS SER PHE LEU SEQRES 4 B 80 PRO ASP PRO TYR GLN LYS GLN CYS ASP GLN PHE VAL ALA SEQRES 5 B 80 GLU TYR GLU PRO VAL LEU ILE GLU ILE LEU VAL GLU VAL SEQRES 6 B 80 MET ASP PRO SER PHE VAL CYS LEU LYS ILE GLY ALA CYS SEQRES 7 B 80 PRO SER HET MG A 81 1 HET MG A 82 1 HET MG A 83 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 3(MG 2+) FORMUL 6 HOH *198(H2 O) HELIX 1 1 PHE A 4 LEU A 19 1 16 HELIX 2 2 THR A 24 CYS A 36 1 13 HELIX 3 3 SER A 37 LEU A 39 5 3 HELIX 4 4 PRO A 40 PRO A 42 5 3 HELIX 5 5 TYR A 43 VAL A 63 1 21 HELIX 6 6 ASP A 67 ILE A 75 1 9 HELIX 7 7 PHE B 4 LEU B 19 1 16 HELIX 8 8 THR B 24 CYS B 36 1 13 HELIX 9 9 SER B 37 LEU B 39 5 3 HELIX 10 10 PRO B 40 PRO B 42 5 3 HELIX 11 11 TYR B 43 VAL B 63 1 21 HELIX 12 12 ASP B 67 ILE B 75 1 9 SSBOND 1 CYS A 5 CYS A 78 1555 1555 2.08 SSBOND 2 CYS A 8 CYS A 72 1555 1555 2.01 SSBOND 3 CYS A 36 CYS A 47 1555 1555 2.08 SSBOND 4 CYS B 5 CYS B 78 1555 1555 2.11 SSBOND 5 CYS B 8 CYS B 72 1555 1555 2.04 SSBOND 6 CYS B 36 CYS B 47 1555 1555 2.08 LINK MG MG A 81 O HOH A 642 1555 1555 1.83 LINK MG MG A 81 O HOH A 630 1555 1555 1.98 LINK MG MG A 81 O HOH A 673 1555 1555 1.97 LINK MG MG A 81 O HOH A 654 1555 1555 1.97 LINK MG MG A 82 O HOH A 674 1555 1555 1.98 LINK MG MG A 82 O HOH A 675 1555 1555 2.04 LINK MG MG A 82 O HOH A 585 1555 1555 2.13 LINK MG MG A 82 O HOH B 633 1555 1555 2.09 LINK MG MG A 82 O HOH B 632 1555 1555 2.07 LINK MG MG A 82 O HOH A 606 1555 1555 2.10 LINK MG MG A 83 O HOH A 676 1555 1555 1.92 LINK MG MG A 83 O HOH A 677 1555 1555 1.93 SITE 1 AC1 6 HOH A 628 HOH A 630 HOH A 631 HOH A 642 SITE 2 AC1 6 HOH A 654 HOH A 673 SITE 1 AC2 6 HOH A 585 HOH A 606 HOH A 674 HOH A 675 SITE 2 AC2 6 HOH B 632 HOH B 633 SITE 1 AC3 5 HOH A 676 HOH A 677 HOH B 560 HOH B 627 SITE 2 AC3 5 HOH B 629 CRYST1 40.450 61.450 64.570 90.00 90.00 90.00 P 21 21 21 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 0.024722 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016273 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015487 0.00000