HEADER LYASE 25-MAR-10 3MBB TITLE CRYSTAL STRUCTURE OF STSPL - APO FORM, AFTER TREATMENT WITH TITLE 2 SEMICARBAZIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SPHINGOSINE-1-PHOSPHATE LYASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.1.2.27; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYMBIOBACTERIUM THERMOPHILUM; SOURCE 3 ORGANISM_TAXID: 2734; SOURCE 4 GENE: STH1274; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PQE60 KEYWDS CARBOXY-LYASE ACTIVITY, PYRIDOXAL PHOSPHATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR F.BOURQUIN,M.G.GRUTTER,G.CAPITANI REVDAT 3 03-APR-24 3MBB 1 REMARK SEQADV LINK REVDAT 2 12-OCT-11 3MBB 1 LINK VERSN REVDAT 1 18-AUG-10 3MBB 0 JRNL AUTH F.BOURQUIN,H.RIEZMAN,G.CAPITANI,M.G.GRUTTER JRNL TITL STRUCTURE AND FUNCTION OF SPHINGOSINE-1-PHOSPHATE LYASE, A JRNL TITL 2 KEY ENZYME OF SPHINGOLIPID METABOLISM. JRNL REF STRUCTURE V. 18 1054 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20696404 JRNL DOI 10.1016/J.STR.2010.05.011 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.5_2 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 63122 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.390 REMARK 3 FREE R VALUE TEST SET COUNT : 875 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 29.4135 - 3.7249 1.00 10825 152 0.1711 0.1899 REMARK 3 2 3.7249 - 2.9575 1.00 10487 148 0.1776 0.2297 REMARK 3 3 2.9575 - 2.5839 1.00 10418 148 0.1827 0.2120 REMARK 3 4 2.5839 - 2.3477 1.00 10393 147 0.1817 0.2267 REMARK 3 5 2.3477 - 2.1795 1.00 10305 143 0.1867 0.2635 REMARK 3 6 2.1795 - 2.0510 0.95 9819 137 0.2113 0.2506 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 : 0.34 REMARK 3 B_SOL : 44.03 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.190 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) : -2.44740 REMARK 3 B22 (A**2) : 0.34550 REMARK 3 B33 (A**2) : 2.10190 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 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 : 0.007 7098 REMARK 3 ANGLE : 1.088 9711 REMARK 3 CHIRALITY : 0.073 1054 REMARK 3 PLANARITY : 0.012 1275 REMARK 3 DIHEDRAL : 16.590 2482 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 3MBB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058338. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 : LN2 COOLED FIXED EXIT SI(111) REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63157 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43100 REMARK 200 FOR SHELL : 4.500 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: NON-DEPOSITED BUT REFINED STRUCTURE OF DIMERIC REMARK 200 STSPL K311A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000 MME 17%, 0.15 M KSCN, 0.1 M REMARK 280 TRIS(HOAC) PH 8.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 28.82500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.39000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.39000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.82500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.49500 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: 14140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -138.0 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 0 REMARK 465 PRO A 1 REMARK 465 LEU A 2 REMARK 465 SER A 3 REMARK 465 ALA A 4 REMARK 465 PHE A 5 REMARK 465 SER A 6 REMARK 465 PRO A 7 REMARK 465 PRO A 8 REMARK 465 LEU A 9 REMARK 465 PRO A 10 REMARK 465 CYS A 11 REMARK 465 ASP A 12 REMARK 465 PRO A 13 REMARK 465 ALA A 14 REMARK 465 ARG A 15 REMARK 465 SER A 16 REMARK 465 HIS A 17 REMARK 465 PRO A 18 REMARK 465 THR A 19 REMARK 465 PRO A 20 REMARK 465 GLU A 21 REMARK 465 PHE A 22 REMARK 465 PRO A 23 REMARK 465 SER A 24 REMARK 465 SER A 25 REMARK 465 LEU A 26 REMARK 465 GLN A 27 REMARK 465 ASP A 28 REMARK 465 TYR A 29 REMARK 465 CYS A 30 REMARK 465 GLU A 31 REMARK 465 ILE A 32 REMARK 465 ARG A 33 REMARK 465 GLY A 34 REMARK 465 ILE A 35 REMARK 465 GLN A 36 REMARK 465 SER A 37 REMARK 465 GLN A 38 REMARK 465 PRO A 39 REMARK 465 PRO A 40 REMARK 465 ALA A 41 REMARK 465 ARG A 42 REMARK 465 ARG A 43 REMARK 465 ASP A 44 REMARK 465 PRO A 45 REMARK 465 THR A 46 REMARK 465 MET A 47 REMARK 465 ASP A 48 REMARK 465 TRP A 49 REMARK 465 LEU A 50 REMARK 465 ALA A 51 REMARK 465 SER A 52 REMARK 465 LEU A 53 REMARK 465 ARG A 54 REMARK 465 SER A 55 REMARK 465 GLN A 56 REMARK 465 ILE A 57 REMARK 465 HIS A 509 REMARK 465 HIS A 510 REMARK 465 HIS A 511 REMARK 465 HIS A 512 REMARK 465 HIS A 513 REMARK 465 MET B 0 REMARK 465 PRO B 1 REMARK 465 LEU B 2 REMARK 465 SER B 3 REMARK 465 ALA B 4 REMARK 465 PHE B 5 REMARK 465 SER B 6 REMARK 465 PRO B 7 REMARK 465 PRO B 8 REMARK 465 LEU B 9 REMARK 465 PRO B 10 REMARK 465 CYS B 11 REMARK 465 ASP B 12 REMARK 465 PRO B 13 REMARK 465 ALA B 14 REMARK 465 ARG B 15 REMARK 465 SER B 16 REMARK 465 HIS B 17 REMARK 465 PRO B 18 REMARK 465 THR B 19 REMARK 465 PRO B 20 REMARK 465 GLU B 21 REMARK 465 PHE B 22 REMARK 465 PRO B 23 REMARK 465 SER B 24 REMARK 465 SER B 25 REMARK 465 LEU B 26 REMARK 465 GLN B 27 REMARK 465 ASP B 28 REMARK 465 TYR B 29 REMARK 465 CYS B 30 REMARK 465 GLU B 31 REMARK 465 ILE B 32 REMARK 465 ARG B 33 REMARK 465 GLY B 34 REMARK 465 ILE B 35 REMARK 465 GLN B 36 REMARK 465 SER B 37 REMARK 465 GLN B 38 REMARK 465 PRO B 39 REMARK 465 PRO B 40 REMARK 465 ALA B 41 REMARK 465 ARG B 42 REMARK 465 ARG B 43 REMARK 465 ASP B 44 REMARK 465 PRO B 45 REMARK 465 THR B 46 REMARK 465 MET B 47 REMARK 465 ASP B 48 REMARK 465 TRP B 49 REMARK 465 LEU B 50 REMARK 465 ALA B 51 REMARK 465 SER B 52 REMARK 465 LEU B 53 REMARK 465 ARG B 54 REMARK 465 SER B 55 REMARK 465 GLN B 56 REMARK 465 HIS B 508 REMARK 465 HIS B 509 REMARK 465 HIS B 510 REMARK 465 HIS B 511 REMARK 465 HIS B 512 REMARK 465 HIS B 513 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 OH TY2 B 249 OD1 ASN B 432 2.12 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 ALA A 103 -60.11 75.94 REMARK 500 HIS A 106 -71.24 -110.85 REMARK 500 HIS A 129 75.17 -117.75 REMARK 500 ILE A 281 -55.35 -123.00 REMARK 500 ASP A 296 -152.26 -128.88 REMARK 500 LYS A 311 -106.35 -99.22 REMARK 500 SER A 397 -2.04 85.62 REMARK 500 TRP A 406 -14.30 -153.72 REMARK 500 ALA B 103 -59.62 75.85 REMARK 500 HIS B 106 -73.33 -108.56 REMARK 500 LEU B 151 35.25 -99.74 REMARK 500 ILE B 281 -50.56 -121.75 REMARK 500 ASP B 296 -152.27 -129.16 REMARK 500 LYS B 311 -108.15 -100.06 REMARK 500 TRP B 406 -12.94 -152.03 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 NA A 517 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 392 O REMARK 620 2 ARG A 393 O 75.2 REMARK 620 3 ILE A 395 O 72.9 106.5 REMARK 620 4 LEU A 398 O 102.6 158.5 92.9 REMARK 620 5 HOH A 547 O 99.6 82.8 165.5 76.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 515 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MAD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STSPL (SYMMETRIC FORM) REMARK 900 RELATED ID: 3MAU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STSPL IN COMPLEX WITH PHOSPHOETHANOLAMINE REMARK 900 RELATED ID: 3MAF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STSPL (ASYMMETRIC FORM) REMARK 900 RELATED ID: 3MC6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SCDPL1 DBREF 3MBB A 2 507 UNP Q67PY4 Q67PY4_SYMTH 2 507 DBREF 3MBB B 2 507 UNP Q67PY4 Q67PY4_SYMTH 2 507 SEQADV 3MBB MET A 0 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB PRO A 1 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS A 508 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS A 509 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS A 510 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS A 511 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS A 512 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS A 513 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB MET B 0 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB PRO B 1 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS B 508 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS B 509 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS B 510 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS B 511 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS B 512 UNP Q67PY4 EXPRESSION TAG SEQADV 3MBB HIS B 513 UNP Q67PY4 EXPRESSION TAG SEQRES 1 A 514 MET PRO LEU SER ALA PHE SER PRO PRO LEU PRO CYS ASP SEQRES 2 A 514 PRO ALA ARG SER HIS PRO THR PRO GLU PHE PRO SER SER SEQRES 3 A 514 LEU GLN ASP TYR CYS GLU ILE ARG GLY ILE GLN SER GLN SEQRES 4 A 514 PRO PRO ALA ARG ARG ASP PRO THR MET ASP TRP LEU ALA SEQRES 5 A 514 SER LEU ARG SER GLN ILE LYS PRO TYR ARG ASP ARG PHE SEQRES 6 A 514 PRO SER HIS ALA ARG LEU PRO ARG ALA GLY LEU PRO ARG SEQRES 7 A 514 ALA GLU ILE LEU ALA GLU ILE ALA ALA MET GLY ALA ALA SEQRES 8 A 514 GLU SER PRO ALA TRP ARG ASP GLY TYR ALA SER GLY ALA SEQRES 9 A 514 VAL TYR HIS GLY ASP GLU HIS HIS ILE ALA PHE LEU ASN SEQRES 10 A 514 GLU VAL TYR ALA LEU GLN SER GLN SER ASN PRO LEU HIS SEQRES 11 A 514 PRO ASP LEU TRP PRO SER THR ALA LYS PHE GLU ALA GLU SEQRES 12 A 514 VAL VAL ALA MET THR ALA HIS MET LEU GLY GLY ASP ALA SEQRES 13 A 514 ALA GLY GLY THR VAL CYS GLY THR VAL THR SER GLY GLY SEQRES 14 A 514 THR GLU SER LEU LEU LEU ALA MET LYS THR TYR ARG ASP SEQRES 15 A 514 TRP ALA ARG ALA THR LYS GLY ILE THR ALA PRO GLU ALA SEQRES 16 A 514 VAL VAL PRO VAL SER ALA HIS ALA ALA PHE ASP LYS ALA SEQRES 17 A 514 ALA GLN TYR PHE GLY ILE LYS LEU VAL ARG THR PRO LEU SEQRES 18 A 514 ASP ALA ASP TYR ARG ALA ASP VAL ALA ALA MET ARG GLU SEQRES 19 A 514 ALA ILE THR PRO ASN THR VAL VAL VAL ALA GLY SER ALA SEQRES 20 A 514 PRO GLY TY2 PRO HIS GLY VAL VAL ASP PRO ILE PRO GLU SEQRES 21 A 514 ILE ALA ALA LEU ALA ALA GLU HIS GLY ILE GLY CYS HIS SEQRES 22 A 514 VAL ASP ALA CYS LEU GLY GLY PHE ILE LEU PRO TRP ALA SEQRES 23 A 514 GLU ARG LEU GLY TYR PRO VAL PRO PRO PHE ASP PHE ARG SEQRES 24 A 514 LEU GLU GLY VAL THR SER VAL SER ALA ASP THR HIS LYS SEQRES 25 A 514 TYR GLY TYR GLY ALA LYS GLY THR SER VAL ILE LEU TYR SEQRES 26 A 514 ARG ARG PRO ASP LEU LEU HIS TYR GLN TYR PHE ILE ALA SEQRES 27 A 514 ALA ASP TRP PRO GLY GLY LEU TYR PHE SER PRO THR PHE SEQRES 28 A 514 ALA GLY SER ARG PRO GLY ALA LEU SER ALA THR ALA TRP SEQRES 29 A 514 ALA ALA MET LEU SER LEU GLY GLU GLU GLY TYR LEU ASP SEQRES 30 A 514 ALA THR ARG ARG ILE LEU GLN ALA ALA ASP ARG LEU LYS SEQRES 31 A 514 ALA GLY VAL ARG ALA ILE PRO SER LEU LYS ILE LEU GLY SEQRES 32 A 514 ASP PRO LEU TRP VAL ILE ALA VAL ALA SER ASP GLU LEU SEQRES 33 A 514 ASN ILE TYR GLN VAL MET GLU GLU MET ALA GLY ARG GLY SEQRES 34 A 514 TRP ARG LEU ASN GLY LEU HIS ARG PRO PRO ALA PHE HIS SEQRES 35 A 514 VAL ALA LEU THR LEU ARG HIS THR GLU PRO GLY VAL VAL SEQRES 36 A 514 ASP ARG PHE LEU ALA ASP LEU GLN ASP ALA VAL ALA GLN SEQRES 37 A 514 VAL ARG ALA HIS PRO GLU LYS ALA THR GLY MET ALA PRO SEQRES 38 A 514 VAL TYR GLY MET ALA ALA ALA ALA PRO PRO GLU LEU VAL SEQRES 39 A 514 ARG GLN VAL LEU THR GLY PHE ILE ASP LEU LEU TYR GLU SEQRES 40 A 514 VAL HIS HIS HIS HIS HIS HIS SEQRES 1 B 514 MET PRO LEU SER ALA PHE SER PRO PRO LEU PRO CYS ASP SEQRES 2 B 514 PRO ALA ARG SER HIS PRO THR PRO GLU PHE PRO SER SER SEQRES 3 B 514 LEU GLN ASP TYR CYS GLU ILE ARG GLY ILE GLN SER GLN SEQRES 4 B 514 PRO PRO ALA ARG ARG ASP PRO THR MET ASP TRP LEU ALA SEQRES 5 B 514 SER LEU ARG SER GLN ILE LYS PRO TYR ARG ASP ARG PHE SEQRES 6 B 514 PRO SER HIS ALA ARG LEU PRO ARG ALA GLY LEU PRO ARG SEQRES 7 B 514 ALA GLU ILE LEU ALA GLU ILE ALA ALA MET GLY ALA ALA SEQRES 8 B 514 GLU SER PRO ALA TRP ARG ASP GLY TYR ALA SER GLY ALA SEQRES 9 B 514 VAL TYR HIS GLY ASP GLU HIS HIS ILE ALA PHE LEU ASN SEQRES 10 B 514 GLU VAL TYR ALA LEU GLN SER GLN SER ASN PRO LEU HIS SEQRES 11 B 514 PRO ASP LEU TRP PRO SER THR ALA LYS PHE GLU ALA GLU SEQRES 12 B 514 VAL VAL ALA MET THR ALA HIS MET LEU GLY GLY ASP ALA SEQRES 13 B 514 ALA GLY GLY THR VAL CYS GLY THR VAL THR SER GLY GLY SEQRES 14 B 514 THR GLU SER LEU LEU LEU ALA MET LYS THR TYR ARG ASP SEQRES 15 B 514 TRP ALA ARG ALA THR LYS GLY ILE THR ALA PRO GLU ALA SEQRES 16 B 514 VAL VAL PRO VAL SER ALA HIS ALA ALA PHE ASP LYS ALA SEQRES 17 B 514 ALA GLN TYR PHE GLY ILE LYS LEU VAL ARG THR PRO LEU SEQRES 18 B 514 ASP ALA ASP TYR ARG ALA ASP VAL ALA ALA MET ARG GLU SEQRES 19 B 514 ALA ILE THR PRO ASN THR VAL VAL VAL ALA GLY SER ALA SEQRES 20 B 514 PRO GLY TY2 PRO HIS GLY VAL VAL ASP PRO ILE PRO GLU SEQRES 21 B 514 ILE ALA ALA LEU ALA ALA GLU HIS GLY ILE GLY CYS HIS SEQRES 22 B 514 VAL ASP ALA CYS LEU GLY GLY PHE ILE LEU PRO TRP ALA SEQRES 23 B 514 GLU ARG LEU GLY TYR PRO VAL PRO PRO PHE ASP PHE ARG SEQRES 24 B 514 LEU GLU GLY VAL THR SER VAL SER ALA ASP THR HIS LYS SEQRES 25 B 514 TYR GLY TYR GLY ALA LYS GLY THR SER VAL ILE LEU TYR SEQRES 26 B 514 ARG ARG PRO ASP LEU LEU HIS TYR GLN TYR PHE ILE ALA SEQRES 27 B 514 ALA ASP TRP PRO GLY GLY LEU TYR PHE SER PRO THR PHE SEQRES 28 B 514 ALA GLY SER ARG PRO GLY ALA LEU SER ALA THR ALA TRP SEQRES 29 B 514 ALA ALA MET LEU SER LEU GLY GLU GLU GLY TYR LEU ASP SEQRES 30 B 514 ALA THR ARG ARG ILE LEU GLN ALA ALA ASP ARG LEU LYS SEQRES 31 B 514 ALA GLY VAL ARG ALA ILE PRO SER LEU LYS ILE LEU GLY SEQRES 32 B 514 ASP PRO LEU TRP VAL ILE ALA VAL ALA SER ASP GLU LEU SEQRES 33 B 514 ASN ILE TYR GLN VAL MET GLU GLU MET ALA GLY ARG GLY SEQRES 34 B 514 TRP ARG LEU ASN GLY LEU HIS ARG PRO PRO ALA PHE HIS SEQRES 35 B 514 VAL ALA LEU THR LEU ARG HIS THR GLU PRO GLY VAL VAL SEQRES 36 B 514 ASP ARG PHE LEU ALA ASP LEU GLN ASP ALA VAL ALA GLN SEQRES 37 B 514 VAL ARG ALA HIS PRO GLU LYS ALA THR GLY MET ALA PRO SEQRES 38 B 514 VAL TYR GLY MET ALA ALA ALA ALA PRO PRO GLU LEU VAL SEQRES 39 B 514 ARG GLN VAL LEU THR GLY PHE ILE ASP LEU LEU TYR GLU SEQRES 40 B 514 VAL HIS HIS HIS HIS HIS HIS MODRES 3MBB TY2 A 249 TYR 3-AMINO-L-TYROSINE MODRES 3MBB TY2 B 249 TYR 3-AMINO-L-TYROSINE HET TY2 A 249 26 HET TY2 B 249 26 HET PO4 A 514 5 HET PO4 A 515 5 HET EDO A 516 4 HET NA A 517 1 HET PO4 B 514 5 HET PO4 B 515 5 HETNAM TY2 3-AMINO-L-TYROSINE HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 1 TY2 2(C9 H12 N2 O3) FORMUL 3 PO4 4(O4 P 3-) FORMUL 5 EDO C2 H6 O2 FORMUL 6 NA NA 1+ FORMUL 9 HOH *577(H2 O) HELIX 1 1 PRO A 76 ASP A 97 1 22 HELIX 2 2 ASP A 108 SER A 123 1 16 HELIX 3 3 TRP A 133 LEU A 151 1 19 HELIX 4 4 GLY A 152 GLY A 157 5 6 HELIX 5 5 GLY A 167 GLY A 188 1 22 HELIX 6 6 ALA A 202 GLY A 212 1 11 HELIX 7 7 ASP A 227 ILE A 235 1 9 HELIX 8 8 PRO A 256 HIS A 267 1 12 HELIX 9 9 ILE A 281 LEU A 288 1 8 HELIX 10 10 ARG A 326 HIS A 331 1 6 HELIX 11 11 PRO A 355 ILE A 395 1 41 HELIX 12 12 ASN A 416 ARG A 427 1 12 HELIX 13 13 THR A 445 GLU A 450 5 6 HELIX 14 14 GLY A 452 HIS A 471 1 20 HELIX 15 15 MET A 478 ALA A 488 1 11 HELIX 16 16 PRO A 489 TYR A 505 1 17 HELIX 17 17 PRO B 76 ASP B 97 1 22 HELIX 18 18 ASP B 108 GLN B 122 1 15 HELIX 19 19 TRP B 133 LEU B 151 1 19 HELIX 20 20 GLY B 152 GLY B 157 5 6 HELIX 21 21 GLY B 167 GLY B 188 1 22 HELIX 22 22 ALA B 202 GLY B 212 1 11 HELIX 23 23 ASP B 227 ILE B 235 1 9 HELIX 24 24 PRO B 256 HIS B 267 1 12 HELIX 25 25 ILE B 281 LEU B 288 1 8 HELIX 26 26 ARG B 326 HIS B 331 1 6 HELIX 27 27 PRO B 355 ALA B 394 1 40 HELIX 28 28 ASN B 416 GLY B 426 1 11 HELIX 29 29 THR B 445 GLU B 450 5 6 HELIX 30 30 GLY B 452 HIS B 471 1 20 HELIX 31 31 MET B 478 ALA B 488 1 11 HELIX 32 32 PRO B 489 TYR B 505 1 17 SHEET 1 A 7 CYS A 161 THR A 165 0 SHEET 2 A 7 SER A 320 TYR A 324 -1 O TYR A 324 N CYS A 161 SHEET 3 A 7 SER A 304 ALA A 307 -1 N VAL A 305 O LEU A 323 SHEET 4 A 7 GLY A 270 ALA A 275 1 N VAL A 273 O SER A 304 SHEET 5 A 7 THR A 239 SER A 245 1 N GLY A 244 O ASP A 274 SHEET 6 A 7 GLU A 193 PRO A 197 1 N GLU A 193 O VAL A 240 SHEET 7 A 7 LYS A 214 THR A 218 1 O VAL A 216 N ALA A 194 SHEET 1 B 2 PHE A 335 ALA A 337 0 SHEET 2 B 2 TYR A 345 SER A 347 -1 O TYR A 345 N ALA A 337 SHEET 1 C 4 LYS A 399 ILE A 400 0 SHEET 2 C 4 VAL A 407 ALA A 411 -1 O ALA A 411 N LYS A 399 SHEET 3 C 4 ALA A 439 ALA A 443 -1 O PHE A 440 N VAL A 410 SHEET 4 C 4 ASN A 432 LEU A 434 -1 N LEU A 434 O ALA A 439 SHEET 1 D 7 CYS B 161 THR B 165 0 SHEET 2 D 7 SER B 320 TYR B 324 -1 O TYR B 324 N CYS B 161 SHEET 3 D 7 SER B 304 ALA B 307 -1 N VAL B 305 O LEU B 323 SHEET 4 D 7 GLY B 270 ALA B 275 1 N VAL B 273 O SER B 304 SHEET 5 D 7 THR B 239 SER B 245 1 N GLY B 244 O ASP B 274 SHEET 6 D 7 GLU B 193 PRO B 197 1 N GLU B 193 O VAL B 240 SHEET 7 D 7 LYS B 214 THR B 218 1 O VAL B 216 N ALA B 194 SHEET 1 E 2 PHE B 335 ALA B 337 0 SHEET 2 E 2 TYR B 345 SER B 347 -1 O SER B 347 N PHE B 335 SHEET 1 F 4 LYS B 399 ILE B 400 0 SHEET 2 F 4 VAL B 407 ALA B 411 -1 O ALA B 411 N LYS B 399 SHEET 3 F 4 ALA B 439 ALA B 443 -1 O PHE B 440 N VAL B 410 SHEET 4 F 4 ASN B 432 LEU B 434 -1 N LEU B 434 O ALA B 439 LINK C GLY A 248 N ATY2 A 249 1555 1555 1.33 LINK C GLY A 248 N BTY2 A 249 1555 1555 1.33 LINK C ATY2 A 249 N PRO A 250 1555 1555 1.34 LINK C BTY2 A 249 N PRO A 250 1555 1555 1.34 LINK C GLY B 248 N ATY2 B 249 1555 1555 1.32 LINK C GLY B 248 N BTY2 B 249 1555 1555 1.33 LINK C ATY2 B 249 N PRO B 250 1555 1555 1.34 LINK C BTY2 B 249 N PRO B 250 1555 1555 1.34 LINK O VAL A 392 NA NA A 517 1555 1555 3.16 LINK O ARG A 393 NA NA A 517 1555 1555 2.88 LINK O ILE A 395 NA NA A 517 1555 1555 2.73 LINK O LEU A 398 NA NA A 517 1555 1555 2.81 LINK NA NA A 517 O HOH A 547 1555 1555 3.04 CISPEP 1 ALA A 246 PRO A 247 0 -3.16 CISPEP 2 ARG A 436 PRO A 437 0 5.37 CISPEP 3 ALA B 246 PRO B 247 0 -4.57 CISPEP 4 ARG B 436 PRO B 437 0 3.91 SITE 1 AC1 10 GLY A 102 ALA A 103 TYR A 105 LYS A 311 SITE 2 AC1 10 HOH A 540 HOH A 572 HOH A 618 HOH A 650 SITE 3 AC1 10 ASN B 126 HIS B 129 SITE 1 AC2 11 GLY A 168 THR A 169 TY2 A 249 ASP A 308 SITE 2 AC2 11 HIS A 310 LYS A 311 HOH A 540 HOH A 668 SITE 3 AC2 11 SER B 353 HOH B 518 HOH B 637 SITE 1 AC3 7 ALA A 120 LEU A 121 GLN A 122 SER A 123 SITE 2 AC3 7 GLN A 124 HOH A 523 ILE B 112 SITE 1 AC4 6 VAL A 392 ARG A 393 ILE A 395 LEU A 398 SITE 2 AC4 6 HOH A 547 HOH B 543 SITE 1 AC5 11 ASN A 126 HIS A 129 GLY B 102 ALA B 103 SITE 2 AC5 11 TYR B 105 LYS B 311 HOH B 569 HOH B 570 SITE 3 AC5 11 HOH B 613 HOH B 642 HOH B 800 SITE 1 AC6 11 SER A 353 HOH A 605 GLY B 168 THR B 169 SITE 2 AC6 11 TY2 B 249 ASP B 308 HIS B 310 LYS B 311 SITE 3 AC6 11 HOH B 525 HOH B 526 HOH B 800 CRYST1 57.650 126.990 136.780 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 0.017346 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007875 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007311 0.00000