HEADER IMMUNE SYSTEM 10-JUL-09 3I9G TITLE CRYSTAL STRUCTURE OF THE LT1009 (SONEPCIZUMAB) ANTIBODY FAB TITLE 2 FRAGMENT IN COMPLEX WITH SPHINGOSINE-1-PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SONEPCIZUMAB ANTIBODY FAB FRAGMENT, HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: FAB FRAGMENT; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SONEPCIZUMAB ANTIBODY FAB FRAGMENT, LIGHT CHAIN; COMPND 8 CHAIN: L; COMPND 9 FRAGMENT: FAB FRAGMENT; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 GENE: IGG1K; SOURCE 5 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: CHO CELLS; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 13 EXPRESSION_SYSTEM_CELL_LINE: CHO CELLS KEYWDS ANTIBODY, FAB, SPHINGOSINE-1-PHOSPHATE, CALCIUM, KEYWDS 2 IMMUNOGLOBIN, IGG, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.HUXFORD REVDAT 2 24-NOV-09 3I9G 1 JRNL REVDAT 1 29-SEP-09 3I9G 0 JRNL AUTH J.M.WOJCIAK,N.ZHU,K.T.SCHUERENBERG,K.MORENO, JRNL AUTH 2 W.S.SHESTOWSKY,M.HIRAIWA,R.SABBADINI,T.HUXFORD JRNL TITL THE CRYSTAL STRUCTURE OF SPHINGOSINE-1-PHOSPHATE IN JRNL TITL 2 COMPLEX WITH A FAB FRAGMENT REVEALS METAL BRIDGING JRNL TITL 3 OF AN ANTIBODY AND ITS ANTIGEN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 17717 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19815502 JRNL DOI 10.1073/PNAS.0906153106 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.O'BRIEN,S.T.JONES,D.G.WILLIAMS,H.B.CUNNINGHAM, REMARK 1 AUTH 2 K.MORENO,B.VISENTIN,A.GENTILE,J.VEKICH, REMARK 1 AUTH 3 W.SHESTOWSKY,M.HIRAIWA,R.MATTEO,A.CAVALLI, REMARK 1 AUTH 4 D.GROTJAHN,M.GRANT,G.HANSEN,M.A.CAMPBELL, REMARK 1 AUTH 5 R.SABBADINI REMARK 1 TITL PRODUCTION AND CHARACTERIZATION OF MONOCLONAL REMARK 1 TITL 2 ANTI-SPHINGOSINE-1-PHOSPHATE ANTIBODIES REMARK 1 REF J.LIPID RES. 2009 REMARK 1 REFN ISSN 0022-2275 REMARK 1 PMID 19509417 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 50430 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) : 0.190 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2548 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2601 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3361 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54000 REMARK 3 B22 (A**2) : -1.26000 REMARK 3 B33 (A**2) : 0.72000 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): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.810 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3471 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4715 ; 1.542 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 433 ; 8.849 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;35.921 ;24.752 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 567 ;15.264 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;21.612 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 527 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2595 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1442 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2341 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 287 ; 0.137 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 12 ; 0.223 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 27 ; 0.110 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.153 ; 0.200 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): 2235 ; 0.913 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3527 ; 1.506 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1431 ; 2.102 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1188 ; 3.370 ; 4.500 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 : 1.40 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 REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 3I9G COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-09. REMARK 100 THE RCSB ID CODE IS RCSB054131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50494 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.40900 REMARK 200 FOR SHELL : 2.180 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 (%): 64.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MICROLITER OF 12 MG/ML S1P:FAB REMARK 280 COMPLEX WAS MIXED WITH 1 MICROLITER AND SEALED OVER 1 ML OF REMARK 280 RESERVOIR SOLUTION CONTAINING 22% (W/V) POLYETHYLENE GLYCOL REMARK 280 3350, 100 MM MGSO4, 100 MM SODIUM CITRATE (PH 6.0) AND 10% (V/ REMARK 280 V) ETHYLENE GLYCOL., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K 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 33.02600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.35950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.44450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.35950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.02600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.44450 REMARK 290 SMTRY3 4 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: 4620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L 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 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 H 551 O HOH L 771 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 GLY H 106 N - CA - C ANGL. DEV. = -26.3 DEGREES 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 SER H 127 -158.27 -153.27 REMARK 500 SER H 132 -77.40 -58.97 REMARK 500 ASP H 144 61.14 64.24 REMARK 500 LEU H 175 114.65 15.65 REMARK 500 SER H 187 9.39 -66.16 REMARK 500 ASP L 30 -123.23 48.65 REMARK 500 GLU L 50 133.73 -38.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN H 105 GLY H 106 93.29 REMARK 500 SER H 173 GLY H 174 -55.22 REMARK 500 GLY H 174 LEU H 175 55.37 REMARK 500 SER H 188 LEU H 189 -53.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU H 175 19.2 L L OUTSIDE RANGE 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 CA L 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP L 30 OD1 REMARK 620 2 ASP L 31 OD1 83.4 REMARK 620 3 ASP L 32 OD1 92.4 88.4 REMARK 620 4 S1P L 401 O25 83.9 166.2 86.5 REMARK 620 5 HOH L 501 O 170.3 87.3 84.5 105.0 REMARK 620 6 HOH L 504 O 87.0 89.4 177.8 95.5 95.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA L 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP L 30 OD2 REMARK 620 2 ASP L 32 OD2 97.9 REMARK 620 3 ASP L 92 OD2 89.6 93.0 REMARK 620 4 S1P L 401 O25 96.8 85.6 173.6 REMARK 620 5 HOH L 502 O 168.5 93.2 87.1 86.7 REMARK 620 6 HOH L 503 O 82.9 170.0 97.0 84.5 86.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA L 301 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA L 302 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG L 303 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG L 305 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG L 307 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE S1P L 401 DBREF 3I9G H 1 214 PDB 3I9G 3I9G 1 214 DBREF 3I9G L 1 213 PDB 3I9G 3I9G 1 213 SEQRES 1 H 222 GLU VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 H 222 PRO GLY GLU SER LEU LYS ILE SER CYS GLN SER PHE GLY SEQRES 3 H 222 TYR ILE PHE ILE ASP HIS THR ILE HIS TRP MET ARG GLN SEQRES 4 H 222 MET PRO GLY GLN GLY LEU GLU TRP MET GLY ALA ILE SER SEQRES 5 H 222 PRO ARG HIS ASP ILE THR LYS TYR ASN GLU MET PHE ARG SEQRES 6 H 222 GLY GLN VAL THR ILE SER ALA ASP LYS SER SER SER THR SEQRES 7 H 222 ALA TYR LEU GLN TRP SER SER LEU LYS ALA SER ASP THR SEQRES 8 H 222 ALA MET TYR PHE CYS ALA ARG GLY GLY PHE TYR GLY SER SEQRES 9 H 222 THR ILE TRP PHE ASP PHE TRP GLY GLN GLY THR MET VAL SEQRES 10 H 222 THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE SEQRES 11 H 222 PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR SEQRES 12 H 222 ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU SEQRES 13 H 222 PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER SEQRES 14 H 222 GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY SEQRES 15 H 222 LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SEQRES 16 H 222 SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS SEQRES 17 H 222 LYS PRO SER ASN THR LYS VAL ASP LYS ARG VAL GLU PRO SEQRES 18 H 222 LYS SEQRES 1 L 213 GLU THR THR VAL THR GLN SER PRO SER PHE LEU SER ALA SEQRES 2 L 213 SER VAL GLY ASP ARG VAL THR ILE THR CYS ILE THR THR SEQRES 3 L 213 THR ASP ILE ASP ASP ASP MET ASN TRP PHE GLN GLN GLU SEQRES 4 L 213 PRO GLY LYS ALA PRO LYS LEU LEU ILE SER GLU GLY ASN SEQRES 5 L 213 ILE LEU ARG PRO GLY VAL PRO SER ARG PHE SER SER SER SEQRES 6 L 213 GLY TYR GLY THR ASP PHE THR LEU THR ILE SER LYS LEU SEQRES 7 L 213 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS LEU GLN SER SEQRES 8 L 213 ASP ASN LEU PRO PHE THR PHE GLY GLN GLY THR LYS LEU SEQRES 9 L 213 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 213 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 213 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 213 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 213 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 213 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 213 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 213 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 213 PHE ASN ARG GLY GLU HET CA L 301 1 HET CA L 302 1 HET MG L 303 1 HET MG L 304 1 HET MG L 305 1 HET MG L 306 1 HET MG L 307 1 HET S1P L 401 25 HETNAM CA CALCIUM ION HETNAM MG MAGNESIUM ION HETNAM S1P (2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1-YL HETNAM 2 S1P DIHYDROGEN PHOSPHATE HETSYN S1P SPHINGOSINE 1-PHOSPHATE FORMUL 3 CA 2(CA 2+) FORMUL 5 MG 5(MG 2+) FORMUL 10 S1P C18 H38 N O5 P FORMUL 11 HOH *283(H2 O) HELIX 1 1 ILE H 28 HIS H 32 5 5 HELIX 2 2 LYS H 83 THR H 87 5 5 HELIX 3 3 SER H 156 ALA H 158 5 3 HELIX 4 4 SER H 187 LEU H 189 5 3 HELIX 5 5 LYS H 201 ASN H 204 5 4 HELIX 6 6 GLN L 79 PHE L 83 5 5 HELIX 7 7 SER L 121 LYS L 126 1 6 HELIX 8 8 LYS L 183 LYS L 188 1 6 SHEET 1 A 4 GLN H 3 GLN H 6 0 SHEET 2 A 4 LEU H 18 PHE H 25 -1 O GLN H 23 N VAL H 5 SHEET 3 A 4 THR H 77 TRP H 82 -1 O ALA H 78 N CYS H 22 SHEET 4 A 4 THR H 68 ASP H 72 -1 N ASP H 72 O THR H 77 SHEET 1 B 6 GLU H 10 LYS H 12 0 SHEET 2 B 6 THR H 107 VAL H 111 1 O MET H 108 N GLU H 10 SHEET 3 B 6 ALA H 88 GLY H 95 -1 N TYR H 90 O THR H 107 SHEET 4 B 6 THR H 33 GLN H 39 -1 N MET H 37 O PHE H 91 SHEET 5 B 6 GLU H 46 SER H 52 -1 O MET H 48 N TRP H 36 SHEET 6 B 6 ILE H 56 TYR H 59 -1 O LYS H 58 N ALA H 50 SHEET 1 C 4 SER H 120 LEU H 124 0 SHEET 2 C 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 C 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 C 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 D 4 SER H 120 LEU H 124 0 SHEET 2 D 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 D 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 D 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 E 3 THR H 151 TRP H 154 0 SHEET 2 E 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 E 3 THR H 205 ARG H 210 -1 O THR H 205 N HIS H 200 SHEET 1 F 4 VAL L 4 SER L 7 0 SHEET 2 F 4 VAL L 19 THR L 25 -1 O ILE L 24 N THR L 5 SHEET 3 F 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 F 4 PHE L 62 GLY L 66 -1 N SER L 63 O THR L 74 SHEET 1 G 6 PHE L 10 ALA L 13 0 SHEET 2 G 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 G 6 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 G 6 MET L 33 GLN L 38 -1 N GLN L 38 O THR L 85 SHEET 5 G 6 LYS L 45 SER L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 G 6 ILE L 53 LEU L 54 -1 O ILE L 53 N SER L 49 SHEET 1 H 4 PHE L 10 ALA L 13 0 SHEET 2 H 4 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 H 4 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 H 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 I 4 SER L 114 PHE L 118 0 SHEET 2 I 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 I 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 I 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 J 4 ALA L 153 LEU L 154 0 SHEET 2 J 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 J 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 J 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.10 SSBOND 2 CYS H 140 CYS H 196 1555 1555 2.07 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.06 SSBOND 4 CYS L 134 CYS L 194 1555 1555 2.06 LINK OD1 ASP L 30 CA CA L 301 1555 1555 2.11 LINK OD2 ASP L 30 CA CA L 302 1555 1555 2.19 LINK OD1 ASP L 31 CA CA L 301 1555 1555 2.21 LINK OD1 ASP L 32 CA CA L 301 1555 1555 2.19 LINK OD2 ASP L 32 CA CA L 302 1555 1555 2.12 LINK OD2 ASP L 92 CA CA L 302 1555 1555 2.16 LINK CA CA L 301 O25 S1P L 401 1555 1555 2.31 LINK CA CA L 302 O25 S1P L 401 1555 1555 2.25 LINK CA CA L 301 O HOH L 501 1555 1555 2.15 LINK CA CA L 301 O HOH L 504 1555 1555 2.34 LINK CA CA L 302 O HOH L 502 1555 1555 2.20 LINK CA CA L 302 O HOH L 503 1555 1555 2.29 LINK MG MG L 303 O HOH L 658 1555 1555 2.12 CISPEP 1 PHE H 146 PRO H 147 0 -3.15 CISPEP 2 GLU H 148 PRO H 149 0 -5.57 CISPEP 3 LEU H 189 GLY H 190 0 -1.16 CISPEP 4 SER L 7 PRO L 8 0 -3.15 CISPEP 5 LEU L 94 PRO L 95 0 -1.43 CISPEP 6 TYR L 140 PRO L 141 0 5.88 SITE 1 AC1 6 ASP L 30 ASP L 31 ASP L 32 S1P L 401 SITE 2 AC1 6 HOH L 501 HOH L 504 SITE 1 AC2 6 ASP L 30 ASP L 32 ASP L 92 S1P L 401 SITE 2 AC2 6 HOH L 502 HOH L 503 SITE 1 AC3 4 SER L 12 ASP L 92 LYS L 107 HOH L 658 SITE 1 AC4 2 TYR H 59 ARG H 64 SITE 1 AC5 1 ASP H 208 SITE 1 AC6 16 THR H 33 GLY H 99 SER H 100 ASP L 30 SITE 2 AC6 16 ASP L 32 GLU L 50 SER L 91 ASP L 92 SITE 3 AC6 16 LEU L 94 CA L 301 CA L 302 HOH L 502 SITE 4 AC6 16 HOH L 503 HOH L 504 HOH L 505 HOH L 506 CRYST1 66.052 70.889 138.719 90.00 90.00 90.00 P 21 21 21 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 0.015140 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007209 0.00000