HEADER LIPID BINDING PROTEIN 13-JUL-21 7P4T TITLE TETRAMERIC STRUCTURE OF MURINE SAPA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAPOSIN-A; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PSAP, SGP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SAPOSIN, DISULFIDE, LIPID TRANSFER, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SHAMIN,J.E.DEANE REVDAT 3 07-FEB-24 7P4T 1 REMARK REVDAT 2 17-MAY-23 7P4T 1 JRNL REVDAT 1 25-MAY-22 7P4T 0 JRNL AUTH M.SHAMIN,S.J.SPRATLEY,S.C.GRAHAM,J.E.DEANE JRNL TITL A TETRAMERIC ASSEMBLY OF SAPOSIN A: INCREASING STRUCTURAL JRNL TITL 2 DIVERSITY IN LIPID TRANSFER PROTEINS. JRNL REF CONTACT V. 4 10523 2021 JRNL REFN ISSN 2515-2564 JRNL PMID 37143956 JRNL DOI 10.1177/25152564211052382 REMARK 2 REMARK 2 RESOLUTION. 3.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 3.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 79.1 REMARK 3 NUMBER OF REFLECTIONS : 5571 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.272 REMARK 3 FREE R VALUE : 0.304 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 113.0 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 : 0.003 2464 REMARK 3 ANGLE : 0.774 3344 REMARK 3 CHIRALITY : 0.046 408 REMARK 3 PLANARITY : 0.005 424 REMARK 3 DIHEDRAL : 13.687 1564 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 7P4T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292117012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : NULL REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5576 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.170 REMARK 200 RESOLUTION RANGE LOW (A) : 52.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.17800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 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: 4DDJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23.25% (W/V) PEG 3350, 0.1 M BIS-TRIS REMARK 280 PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 209.57267 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 104.78633 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 157.17950 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 52.39317 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 261.96583 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: TETRAMERIC 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 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 SER A 81 REMARK 465 LEU A 82 REMARK 465 GLN A 83 REMARK 465 SER B 81 REMARK 465 LEU B 82 REMARK 465 GLN B 83 REMARK 465 SER C 81 REMARK 465 LEU C 82 REMARK 465 GLN C 83 REMARK 465 SER D 81 REMARK 465 LEU D 82 REMARK 465 GLN D 83 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 ASN A 68 88.45 -170.69 REMARK 500 ASN B 68 74.96 56.33 REMARK 500 ASN B 77 29.61 46.78 REMARK 500 PRO C 3 -4.69 -57.55 REMARK 500 MET C 66 -2.17 65.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 7P4T A 1 83 UNP Q61207 SAP_MOUSE 60 142 DBREF 7P4T B 1 83 UNP Q61207 SAP_MOUSE 60 142 DBREF 7P4T C 1 83 UNP Q61207 SAP_MOUSE 60 142 DBREF 7P4T D 1 83 UNP Q61207 SAP_MOUSE 60 142 SEQRES 1 A 83 SER LEU PRO CYS ASP ILE CYS LYS THR VAL VAL THR GLU SEQRES 2 A 83 ALA GLY ASN LEU LEU LYS ASP ASN ALA THR GLN GLU GLU SEQRES 3 A 83 ILE LEU HIS TYR LEU GLU LYS THR CYS GLU TRP ILE HIS SEQRES 4 A 83 ASP SER SER LEU SER ALA SER CYS LYS GLU VAL VAL ASP SEQRES 5 A 83 SER TYR LEU PRO VAL ILE LEU ASP MET ILE LYS GLY GLU SEQRES 6 A 83 MET SER ASN PRO GLY GLU VAL CYS SER ALA LEU ASN LEU SEQRES 7 A 83 CYS GLN SER LEU GLN SEQRES 1 B 83 SER LEU PRO CYS ASP ILE CYS LYS THR VAL VAL THR GLU SEQRES 2 B 83 ALA GLY ASN LEU LEU LYS ASP ASN ALA THR GLN GLU GLU SEQRES 3 B 83 ILE LEU HIS TYR LEU GLU LYS THR CYS GLU TRP ILE HIS SEQRES 4 B 83 ASP SER SER LEU SER ALA SER CYS LYS GLU VAL VAL ASP SEQRES 5 B 83 SER TYR LEU PRO VAL ILE LEU ASP MET ILE LYS GLY GLU SEQRES 6 B 83 MET SER ASN PRO GLY GLU VAL CYS SER ALA LEU ASN LEU SEQRES 7 B 83 CYS GLN SER LEU GLN SEQRES 1 C 83 SER LEU PRO CYS ASP ILE CYS LYS THR VAL VAL THR GLU SEQRES 2 C 83 ALA GLY ASN LEU LEU LYS ASP ASN ALA THR GLN GLU GLU SEQRES 3 C 83 ILE LEU HIS TYR LEU GLU LYS THR CYS GLU TRP ILE HIS SEQRES 4 C 83 ASP SER SER LEU SER ALA SER CYS LYS GLU VAL VAL ASP SEQRES 5 C 83 SER TYR LEU PRO VAL ILE LEU ASP MET ILE LYS GLY GLU SEQRES 6 C 83 MET SER ASN PRO GLY GLU VAL CYS SER ALA LEU ASN LEU SEQRES 7 C 83 CYS GLN SER LEU GLN SEQRES 1 D 83 SER LEU PRO CYS ASP ILE CYS LYS THR VAL VAL THR GLU SEQRES 2 D 83 ALA GLY ASN LEU LEU LYS ASP ASN ALA THR GLN GLU GLU SEQRES 3 D 83 ILE LEU HIS TYR LEU GLU LYS THR CYS GLU TRP ILE HIS SEQRES 4 D 83 ASP SER SER LEU SER ALA SER CYS LYS GLU VAL VAL ASP SEQRES 5 D 83 SER TYR LEU PRO VAL ILE LEU ASP MET ILE LYS GLY GLU SEQRES 6 D 83 MET SER ASN PRO GLY GLU VAL CYS SER ALA LEU ASN LEU SEQRES 7 D 83 CYS GLN SER LEU GLN HELIX 1 AA1 SER A 1 ASP A 20 1 20 HELIX 2 AA2 ASP A 20 GLU A 36 1 17 HELIX 3 AA3 ASP A 40 GLU A 65 1 26 HELIX 4 AA4 ASN A 68 ALA A 75 1 8 HELIX 5 AA5 LEU B 2 ASP B 20 1 19 HELIX 6 AA6 ASP B 20 GLU B 36 1 17 HELIX 7 AA7 ASP B 40 SER B 67 1 28 HELIX 8 AA8 PRO B 69 ALA B 75 1 7 HELIX 9 AA9 LEU C 2 ASP C 20 1 19 HELIX 10 AB1 ASP C 20 GLU C 36 1 17 HELIX 11 AB2 ASP C 40 GLU C 65 1 26 HELIX 12 AB3 ASN C 68 VAL C 72 5 5 HELIX 13 AB4 LEU D 2 ASP D 20 1 19 HELIX 14 AB5 ASP D 20 CYS D 35 1 16 HELIX 15 AB6 GLU D 36 ILE D 38 5 3 HELIX 16 AB7 ASP D 40 SER D 67 1 28 HELIX 17 AB8 ASN D 68 SER D 74 1 7 SSBOND 1 CYS A 4 CYS A 79 1555 1555 2.03 SSBOND 2 CYS A 7 CYS A 73 1555 1555 2.02 SSBOND 3 CYS A 35 CYS A 47 1555 1555 2.04 SSBOND 4 CYS B 4 CYS B 79 1555 1555 2.03 SSBOND 5 CYS B 7 CYS B 73 1555 1555 2.03 SSBOND 6 CYS B 35 CYS B 47 1555 1555 2.03 SSBOND 7 CYS C 4 CYS C 79 1555 1555 2.04 SSBOND 8 CYS C 7 CYS C 73 1555 1555 2.03 SSBOND 9 CYS C 35 CYS C 47 1555 1555 2.02 SSBOND 10 CYS D 4 CYS D 79 1555 1555 2.03 SSBOND 11 CYS D 7 CYS D 73 1555 1555 2.03 SSBOND 12 CYS D 35 CYS D 47 1555 1555 2.03 CRYST1 48.489 48.489 314.359 90.00 90.00 120.00 P 65 24 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 0.020623 0.011907 0.000000 0.00000 SCALE2 0.000000 0.023814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003181 0.00000