HEADER LYASE 02-SEP-22 8AYF TITLE CRYSTAL STRUCTURE OF HUMAN SPHINGOSINE-1-PHOSPHATE LYASE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPHINGOSINE-1-PHOSPHATE LYASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: S1PL,SP-LYASE 1,SPL 1,HSPL,SPHINGOSINE-1-PHOSPHATE ALDOLASE; COMPND 5 EC: 4.1.2.27; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: EXPRESSED AS A DELETION MUTANT OF THE FIRST 81 COMPND 8 RESIDUES - DELTA81 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SGPL1, KIAA1252; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-B KEYWDS S1P, LIPID, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR G.GIARDINA,F.CATALANO,G.PAMPALONE,B.CELLINI REVDAT 3 03-JAN-24 8AYF 1 JRNL REVDAT 2 15-NOV-23 8AYF 1 REMARK REVDAT 1 13-SEP-23 8AYF 0 JRNL AUTH B.CELLINI,G.PAMPALONE,E.CAMAIONI,M.PARIANO,F.CATALANO, JRNL AUTH 2 T.ZELANTE,M.DINDO,L.MACCHIONI,A.DI VEROLI,R.GALARINI, JRNL AUTH 3 F.PAOLETTI,M.DAVIDESCU,C.STINCARDINI,G.VASCELLI,M.M.BELLET, JRNL AUTH 4 J.SABA,S.GIOVAGNOLI,G.GIARDINA,L.ROMANI,C.COSTANTINI JRNL TITL DUAL SPECIES SPHINGOSINE-1-PHOSPHATE LYASE INHIBITORS TO JRNL TITL 2 COMBINE ANTIFUNGAL AND ANTI-INFLAMMATORY ACTIVITIES IN JRNL TITL 3 CYSTIC FIBROSIS: A FEASIBILITY STUDY. JRNL REF SCI REP V. 13 22692 2023 JRNL REFN ESSN 2045-2322 JRNL PMID 38123809 JRNL DOI 10.1038/S41598-023-50121-4 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 57.3 REMARK 3 NUMBER OF REFLECTIONS : 45105 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2499 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 149 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 2.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE SET COUNT : 5 REMARK 3 BIN FREE R VALUE : 0.4210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6858 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 319 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.288 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.121 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.289 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7079 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 6472 ; 0.011 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9599 ; 1.408 ; 1.642 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15042 ; 0.518 ; 1.556 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 896 ; 6.440 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 36 ; 5.549 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1125 ;16.486 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1064 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8047 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1439 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 8AYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI111 WITH LN2 REMARK 200 CLOSED LOOP COOLING REMARK 200 OPTICS : CILINDRICAL MIRROR WITH 50 NM PT REMARK 200 -COATING RADIUS (CALCULATED) = REMARK 200 14 KM DISTANCE FROM SOURCE = REMARK 200 21200 MM INCIDENCE ANGLE = 3 REMARK 200 MRAD ACTIVE LENGTH = 1200 MM 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47604 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 57.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4Q6R REMARK 200 REMARK 200 REMARK: PLATELETS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: HSPL 108UM IN TRIS REMARK 280 -HCL 20 MM PH 8.0 NACL 150 MM DTT 1MM GLYCEROL 5% PRECIPITANT: REMARK 280 (HIT G4 OF MOLECULAR DIMENSION SCREEN MORPHEUS) 0.02M SODIUM REMARK 280 FORMATE; 0.02M AMMONIUM ACETATE; 0.02M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE; 0.02M POTASSIUM SODIUM TARTRATE TETRAHYDRATE; 0.02M REMARK 280 SODIUM OXAMATE; IMIDAZOLE 0.05M; MES MONOHYDRATE (ACID) 0.05M; REMARK 280 12.5% V/V MPD; 12.5% PEG 1000; 12.5% W/V PEG 3350 MIXING VOLUMES: REMARK 280 0.3 + 0.3 UL, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K 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 63.70500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 14490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -102.0 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 MET A 81 REMARK 465 PRO A 82 REMARK 465 ILE A 83 REMARK 465 ILE A 84 REMARK 465 GLY A 85 REMARK 465 ARG A 86 REMARK 465 LYS A 87 REMARK 465 ILE A 88 REMARK 465 GLN A 89 REMARK 465 ASP A 90 REMARK 465 LYS A 91 REMARK 465 LEU A 92 REMARK 465 ASN A 93 REMARK 465 LYS A 94 REMARK 465 THR A 95 REMARK 465 LYS A 96 REMARK 465 ASP A 97 REMARK 465 ASP A 98 REMARK 465 ILE A 99 REMARK 465 SER A 100 REMARK 465 LYS A 101 REMARK 465 ASN A 102 REMARK 465 MET A 103 REMARK 465 SER A 104 REMARK 465 PHE A 105 REMARK 465 LEU A 106 REMARK 465 LYS A 107 REMARK 465 VAL A 108 REMARK 465 ASP A 109 REMARK 465 LYS A 110 REMARK 465 THR A 554 REMARK 465 VAL A 555 REMARK 465 THR A 556 REMARK 465 GLN A 557 REMARK 465 GLY A 558 REMARK 465 SER A 559 REMARK 465 GLN A 560 REMARK 465 MET A 561 REMARK 465 ASN A 562 REMARK 465 GLY A 563 REMARK 465 SER A 564 REMARK 465 PRO A 565 REMARK 465 LYS A 566 REMARK 465 PRO A 567 REMARK 465 HIS A 568 REMARK 465 HIS A 569 REMARK 465 HIS A 570 REMARK 465 HIS A 571 REMARK 465 HIS A 572 REMARK 465 HIS A 573 REMARK 465 HIS A 574 REMARK 465 MET B 81 REMARK 465 PRO B 82 REMARK 465 ILE B 83 REMARK 465 ILE B 84 REMARK 465 GLY B 85 REMARK 465 ARG B 86 REMARK 465 LYS B 87 REMARK 465 ILE B 88 REMARK 465 GLN B 89 REMARK 465 ASP B 90 REMARK 465 LYS B 91 REMARK 465 LEU B 92 REMARK 465 ASN B 93 REMARK 465 LYS B 94 REMARK 465 THR B 95 REMARK 465 LYS B 96 REMARK 465 ASP B 97 REMARK 465 ASP B 98 REMARK 465 ILE B 99 REMARK 465 SER B 100 REMARK 465 LYS B 101 REMARK 465 ASN B 102 REMARK 465 MET B 103 REMARK 465 SER B 104 REMARK 465 PHE B 105 REMARK 465 THR B 554 REMARK 465 VAL B 555 REMARK 465 THR B 556 REMARK 465 GLN B 557 REMARK 465 GLY B 558 REMARK 465 SER B 559 REMARK 465 GLN B 560 REMARK 465 MET B 561 REMARK 465 ASN B 562 REMARK 465 GLY B 563 REMARK 465 SER B 564 REMARK 465 PRO B 565 REMARK 465 LYS B 566 REMARK 465 PRO B 567 REMARK 465 HIS B 568 REMARK 465 HIS B 569 REMARK 465 HIS B 570 REMARK 465 HIS B 571 REMARK 465 HIS B 572 REMARK 465 HIS B 573 REMARK 465 HIS B 574 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 131 CD CE NZ REMARK 470 LYS A 155 CD CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 ARG A 270 NE CZ NH1 NH2 REMARK 470 LYS A 307 CE NZ REMARK 470 LYS A 369 CE NZ REMARK 470 LYS A 438 CD CE NZ REMARK 470 LYS A 518 CD CE NZ REMARK 470 LEU B 106 CG CD1 CD2 REMARK 470 LYS B 107 CG CD CE NZ REMARK 470 ASP B 109 CG OD1 OD2 REMARK 470 LYS B 110 CG CD CE NZ REMARK 470 LYS B 131 CG CD CE NZ REMARK 470 LYS B 155 CE NZ REMARK 470 LYS B 162 CD CE NZ REMARK 470 LYS B 231 CG CD CE NZ REMARK 470 LYS B 263 CG CD CE NZ REMARK 470 LYS B 303 CD CE NZ REMARK 470 LYS B 425 CD CE NZ REMARK 470 LYS B 438 CG CD CE NZ REMARK 470 ARG B 495 NE CZ NH1 NH2 REMARK 470 LYS B 516 CG CD CE NZ REMARK 470 LYS B 518 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MET A 537 CG SD CE 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 O HOH B 728 O HOH B 827 1.96 REMARK 500 CG LYS A 131 O HOH A 817 2.13 REMARK 500 O ASP B 137 O HOH B 701 2.15 REMARK 500 CH3 ACT A 601 O HOH A 841 2.15 REMARK 500 O ALA A 241 NH2 ARG A 258 2.16 REMARK 500 O HOH A 837 O HOH B 860 2.18 REMARK 500 O HOH B 718 O HOH B 848 2.19 REMARK 500 SG CYS A 317 O HOH A 704 2.19 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 THR A 148 -56.46 76.43 REMARK 500 SER A 151 -65.15 -124.68 REMARK 500 PHE A 337 -11.62 -143.81 REMARK 500 ASP A 338 -166.25 -104.94 REMARK 500 LLP A 353 -101.68 -102.39 REMARK 500 ASN A 436 40.11 -106.36 REMARK 500 LEU A 448 -138.79 -121.43 REMARK 500 ASP B 109 62.93 -115.13 REMARK 500 LYS B 110 141.42 176.00 REMARK 500 ASP B 137 59.80 -106.27 REMARK 500 THR B 148 -61.48 78.05 REMARK 500 SER B 151 -59.46 -130.18 REMARK 500 HIS B 174 71.37 -118.89 REMARK 500 PHE B 337 -5.22 -145.03 REMARK 500 ASP B 338 -165.72 -107.83 REMARK 500 LLP B 353 -104.21 -94.64 REMARK 500 LEU B 448 -135.42 -119.08 REMARK 500 REMARK 500 REMARK: NULL DBREF 8AYF A 81 568 UNP O95470 SGPL1_HUMAN 81 568 DBREF 8AYF B 81 568 UNP O95470 SGPL1_HUMAN 81 568 SEQADV 8AYF HIS A 569 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS A 570 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS A 571 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS A 572 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS A 573 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS A 574 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS B 569 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS B 570 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS B 571 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS B 572 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS B 573 UNP O95470 EXPRESSION TAG SEQADV 8AYF HIS B 574 UNP O95470 EXPRESSION TAG SEQRES 1 A 494 MET PRO ILE ILE GLY ARG LYS ILE GLN ASP LYS LEU ASN SEQRES 2 A 494 LYS THR LYS ASP ASP ILE SER LYS ASN MET SER PHE LEU SEQRES 3 A 494 LYS VAL ASP LYS GLU TYR VAL LYS ALA LEU PRO SER GLN SEQRES 4 A 494 GLY LEU SER SER SER ALA VAL LEU GLU LYS LEU LYS GLU SEQRES 5 A 494 TYR SER SER MET ASP ALA PHE TRP GLN GLU GLY ARG ALA SEQRES 6 A 494 SER GLY THR VAL TYR SER GLY GLU GLU LYS LEU THR GLU SEQRES 7 A 494 LEU LEU VAL LYS ALA TYR GLY ASP PHE ALA TRP SER ASN SEQRES 8 A 494 PRO LEU HIS PRO ASP ILE PHE PRO GLY LEU ARG LYS ILE SEQRES 9 A 494 GLU ALA GLU ILE VAL ARG ILE ALA CYS SER LEU PHE ASN SEQRES 10 A 494 GLY GLY PRO ASP SER CYS GLY CYS VAL THR SER GLY GLY SEQRES 11 A 494 THR GLU SER ILE LEU MET ALA CYS LYS ALA TYR ARG ASP SEQRES 12 A 494 LEU ALA PHE GLU LYS GLY ILE LYS THR PRO GLU ILE VAL SEQRES 13 A 494 ALA PRO GLN SER ALA HIS ALA ALA PHE ASN LYS ALA ALA SEQRES 14 A 494 SER TYR PHE GLY MET LYS ILE VAL ARG VAL PRO LEU THR SEQRES 15 A 494 LYS MET MET GLU VAL ASP VAL ARG ALA MET ARG ARG ALA SEQRES 16 A 494 ILE SER ARG ASN THR ALA MET LEU VAL CYS SER THR PRO SEQRES 17 A 494 GLN PHE PRO HIS GLY VAL ILE ASP PRO VAL PRO GLU VAL SEQRES 18 A 494 ALA LYS LEU ALA VAL LYS TYR LYS ILE PRO LEU HIS VAL SEQRES 19 A 494 ASP ALA CYS LEU GLY GLY PHE LEU ILE VAL PHE MET GLU SEQRES 20 A 494 LYS ALA GLY TYR PRO LEU GLU HIS PRO PHE ASP PHE ARG SEQRES 21 A 494 VAL LYS GLY VAL THR SER ILE SER ALA ASP THR HIS LLP SEQRES 22 A 494 TYR GLY TYR ALA PRO LYS GLY SER SER LEU VAL LEU TYR SEQRES 23 A 494 SER ASP LYS LYS TYR ARG ASN TYR GLN PHE PHE VAL ASP SEQRES 24 A 494 THR ASP TRP GLN GLY GLY ILE TYR ALA SER PRO THR ILE SEQRES 25 A 494 ALA GLY SER ARG PRO GLY GLY ILE SER ALA ALA CYS TRP SEQRES 26 A 494 ALA ALA LEU MET HIS PHE GLY GLU ASN GLY TYR VAL GLU SEQRES 27 A 494 ALA THR LYS GLN ILE ILE LYS THR ALA ARG PHE LEU LYS SEQRES 28 A 494 SER GLU LEU GLU ASN ILE LYS GLY ILE PHE VAL PHE GLY SEQRES 29 A 494 ASN PRO GLN LEU SER VAL ILE ALA LEU GLY SER ARG ASP SEQRES 30 A 494 PHE ASP ILE TYR ARG LEU SER ASN LEU MET THR ALA LYS SEQRES 31 A 494 GLY TRP ASN LEU ASN GLN LEU GLN PHE PRO PRO SER ILE SEQRES 32 A 494 HIS PHE CYS ILE THR LEU LEU HIS ALA ARG LYS ARG VAL SEQRES 33 A 494 ALA ILE GLN PHE LEU LYS ASP ILE ARG GLU SER VAL THR SEQRES 34 A 494 GLN ILE MET LYS ASN PRO LYS ALA LYS THR THR GLY MET SEQRES 35 A 494 GLY ALA ILE TYR GLY MET ALA GLN THR THR VAL ASP ARG SEQRES 36 A 494 ASN MET VAL ALA GLU LEU SER SER VAL PHE LEU ASP SER SEQRES 37 A 494 LEU TYR SER THR ASP THR VAL THR GLN GLY SER GLN MET SEQRES 38 A 494 ASN GLY SER PRO LYS PRO HIS HIS HIS HIS HIS HIS HIS SEQRES 1 B 494 MET PRO ILE ILE GLY ARG LYS ILE GLN ASP LYS LEU ASN SEQRES 2 B 494 LYS THR LYS ASP ASP ILE SER LYS ASN MET SER PHE LEU SEQRES 3 B 494 LYS VAL ASP LYS GLU TYR VAL LYS ALA LEU PRO SER GLN SEQRES 4 B 494 GLY LEU SER SER SER ALA VAL LEU GLU LYS LEU LYS GLU SEQRES 5 B 494 TYR SER SER MET ASP ALA PHE TRP GLN GLU GLY ARG ALA SEQRES 6 B 494 SER GLY THR VAL TYR SER GLY GLU GLU LYS LEU THR GLU SEQRES 7 B 494 LEU LEU VAL LYS ALA TYR GLY ASP PHE ALA TRP SER ASN SEQRES 8 B 494 PRO LEU HIS PRO ASP ILE PHE PRO GLY LEU ARG LYS ILE SEQRES 9 B 494 GLU ALA GLU ILE VAL ARG ILE ALA CYS SER LEU PHE ASN SEQRES 10 B 494 GLY GLY PRO ASP SER CYS GLY CYS VAL THR SER GLY GLY SEQRES 11 B 494 THR GLU SER ILE LEU MET ALA CYS LYS ALA TYR ARG ASP SEQRES 12 B 494 LEU ALA PHE GLU LYS GLY ILE LYS THR PRO GLU ILE VAL SEQRES 13 B 494 ALA PRO GLN SER ALA HIS ALA ALA PHE ASN LYS ALA ALA SEQRES 14 B 494 SER TYR PHE GLY MET LYS ILE VAL ARG VAL PRO LEU THR SEQRES 15 B 494 LYS MET MET GLU VAL ASP VAL ARG ALA MET ARG ARG ALA SEQRES 16 B 494 ILE SER ARG ASN THR ALA MET LEU VAL CYS SER THR PRO SEQRES 17 B 494 GLN PHE PRO HIS GLY VAL ILE ASP PRO VAL PRO GLU VAL SEQRES 18 B 494 ALA LYS LEU ALA VAL LYS TYR LYS ILE PRO LEU HIS VAL SEQRES 19 B 494 ASP ALA CYS LEU GLY GLY PHE LEU ILE VAL PHE MET GLU SEQRES 20 B 494 LYS ALA GLY TYR PRO LEU GLU HIS PRO PHE ASP PHE ARG SEQRES 21 B 494 VAL LYS GLY VAL THR SER ILE SER ALA ASP THR HIS LLP SEQRES 22 B 494 TYR GLY TYR ALA PRO LYS GLY SER SER LEU VAL LEU TYR SEQRES 23 B 494 SER ASP LYS LYS TYR ARG ASN TYR GLN PHE PHE VAL ASP SEQRES 24 B 494 THR ASP TRP GLN GLY GLY ILE TYR ALA SER PRO THR ILE SEQRES 25 B 494 ALA GLY SER ARG PRO GLY GLY ILE SER ALA ALA CYS TRP SEQRES 26 B 494 ALA ALA LEU MET HIS PHE GLY GLU ASN GLY TYR VAL GLU SEQRES 27 B 494 ALA THR LYS GLN ILE ILE LYS THR ALA ARG PHE LEU LYS SEQRES 28 B 494 SER GLU LEU GLU ASN ILE LYS GLY ILE PHE VAL PHE GLY SEQRES 29 B 494 ASN PRO GLN LEU SER VAL ILE ALA LEU GLY SER ARG ASP SEQRES 30 B 494 PHE ASP ILE TYR ARG LEU SER ASN LEU MET THR ALA LYS SEQRES 31 B 494 GLY TRP ASN LEU ASN GLN LEU GLN PHE PRO PRO SER ILE SEQRES 32 B 494 HIS PHE CYS ILE THR LEU LEU HIS ALA ARG LYS ARG VAL SEQRES 33 B 494 ALA ILE GLN PHE LEU LYS ASP ILE ARG GLU SER VAL THR SEQRES 34 B 494 GLN ILE MET LYS ASN PRO LYS ALA LYS THR THR GLY MET SEQRES 35 B 494 GLY ALA ILE TYR GLY MET ALA GLN THR THR VAL ASP ARG SEQRES 36 B 494 ASN MET VAL ALA GLU LEU SER SER VAL PHE LEU ASP SER SEQRES 37 B 494 LEU TYR SER THR ASP THR VAL THR GLN GLY SER GLN MET SEQRES 38 B 494 ASN GLY SER PRO LYS PRO HIS HIS HIS HIS HIS HIS HIS MODRES 8AYF LLP A 353 LYS MODIFIED RESIDUE MODRES 8AYF LLP B 353 LYS MODIFIED RESIDUE HET LLP A 353 24 HET LLP B 353 24 HET ACT A 601 8 HET GOL A 602 6 HET ACT B 601 8 HET GOL B 602 6 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *319(H2 O) HELIX 1 AA1 SER A 122 GLU A 132 1 11 HELIX 2 AA2 TYR A 133 SER A 135 5 3 HELIX 3 AA3 ASP A 137 GLU A 142 1 6 HELIX 4 AA4 GLU A 153 PHE A 167 1 15 HELIX 5 AA5 PHE A 178 PHE A 196 1 19 HELIX 6 AA6 GLY A 209 LYS A 228 1 20 HELIX 7 AA7 ALA A 243 GLY A 253 1 11 HELIX 8 AA8 ASP A 268 ALA A 275 1 8 HELIX 9 AA9 PRO A 297 LYS A 309 1 13 HELIX 10 AB1 GLY A 319 VAL A 324 1 6 HELIX 11 AB2 PHE A 325 GLY A 330 1 6 HELIX 12 AB3 ASP A 368 ASN A 373 1 6 HELIX 13 AB4 PRO A 397 GLU A 435 1 39 HELIX 14 AB5 ASP A 459 LYS A 470 1 12 HELIX 15 AB6 THR A 488 ARG A 495 1 8 HELIX 16 AB7 VAL A 496 LYS A 513 1 18 HELIX 17 AB8 GLY A 521 THR A 532 1 12 HELIX 18 AB9 ASP A 534 TYR A 550 1 17 HELIX 19 AC1 SER B 122 SER B 135 1 14 HELIX 20 AC2 GLU B 153 PHE B 167 1 15 HELIX 21 AC3 PHE B 178 PHE B 196 1 19 HELIX 22 AC4 GLY B 209 LYS B 228 1 20 HELIX 23 AC5 ALA B 243 GLY B 253 1 11 HELIX 24 AC6 ASP B 268 ILE B 276 1 9 HELIX 25 AC7 PRO B 297 TYR B 308 1 12 HELIX 26 AC8 GLY B 319 VAL B 324 1 6 HELIX 27 AC9 ASP B 368 ASN B 373 1 6 HELIX 28 AD1 TYR B 374 PHE B 376 5 3 HELIX 29 AD2 PRO B 397 GLU B 435 1 39 HELIX 30 AD3 ILE B 460 LYS B 470 1 11 HELIX 31 AD4 THR B 488 ARG B 495 1 8 HELIX 32 AD5 VAL B 496 ASN B 514 1 19 HELIX 33 AD6 THR B 520 THR B 532 1 13 HELIX 34 AD7 ASP B 534 TYR B 550 1 17 SHEET 1 AA1 7 CYS A 203 THR A 207 0 SHEET 2 AA1 7 SER A 362 TYR A 366 -1 O TYR A 366 N CYS A 203 SHEET 3 AA1 7 VAL A 344 ALA A 349 -1 N ILE A 347 O LEU A 365 SHEET 4 AA1 7 LEU A 312 ASP A 315 1 N VAL A 314 O SER A 346 SHEET 5 AA1 7 THR A 280 SER A 286 1 N CYS A 285 O ASP A 315 SHEET 6 AA1 7 GLU A 234 PRO A 238 1 N GLU A 234 O ALA A 281 SHEET 7 AA1 7 LYS A 255 VAL A 259 1 O VAL A 257 N ILE A 235 SHEET 1 AA2 2 PHE A 377 ASP A 379 0 SHEET 2 AA2 2 TYR A 387 SER A 389 -1 O TYR A 387 N ASP A 379 SHEET 1 AA3 4 PHE A 441 VAL A 442 0 SHEET 2 AA3 4 VAL A 450 GLY A 454 -1 O GLY A 454 N PHE A 441 SHEET 3 AA3 4 ILE A 483 CYS A 486 -1 O ILE A 483 N LEU A 453 SHEET 4 AA3 4 ASN A 475 GLN A 476 -1 N ASN A 475 O HIS A 484 SHEET 1 AA4 7 CYS B 203 THR B 207 0 SHEET 2 AA4 7 SER B 362 TYR B 366 -1 O SER B 362 N THR B 207 SHEET 3 AA4 7 SER B 346 ALA B 349 -1 N ILE B 347 O LEU B 365 SHEET 4 AA4 7 LEU B 312 ALA B 316 1 N VAL B 314 O SER B 346 SHEET 5 AA4 7 THR B 280 SER B 286 1 N CYS B 285 O ASP B 315 SHEET 6 AA4 7 GLU B 234 PRO B 238 1 N GLU B 234 O ALA B 281 SHEET 7 AA4 7 LYS B 255 VAL B 259 1 O VAL B 257 N ILE B 235 SHEET 1 AA5 2 PHE B 377 ASP B 379 0 SHEET 2 AA5 2 TYR B 387 SER B 389 -1 O TYR B 387 N ASP B 379 SHEET 1 AA6 4 PHE B 441 VAL B 442 0 SHEET 2 AA6 4 VAL B 450 GLY B 454 -1 O GLY B 454 N PHE B 441 SHEET 3 AA6 4 SER B 482 CYS B 486 -1 O ILE B 483 N LEU B 453 SHEET 4 AA6 4 ASN B 475 LEU B 477 -1 N LEU B 477 O SER B 482 LINK C HIS A 352 N LLP A 353 1555 1555 1.34 LINK C LLP A 353 N TYR A 354 1555 1555 1.33 LINK C HIS B 352 N LLP B 353 1555 1555 1.35 LINK C LLP B 353 N TYR B 354 1555 1555 1.34 CISPEP 1 THR A 287 PRO A 288 0 -1.29 CISPEP 2 PHE A 479 PRO A 480 0 7.34 CISPEP 3 THR B 287 PRO B 288 0 0.61 CISPEP 4 PHE B 479 PRO B 480 0 7.08 CRYST1 59.160 127.410 66.950 90.00 104.85 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 0.016903 0.000000 0.004483 0.00000 SCALE2 0.000000 0.007849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015453 0.00000