HEADER IMMUNE SYSTEM 25-JUL-11 3T48 TITLE CRYSTAL STRUCTURE OF TRUNCATED FORM OF STAPHYLOCOCCAL COMPLEMENT TITLE 2 INHIBITOR D (SCIN-D) AT 1.5 ANGSTROM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCIN-D; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SCIN-D, RESIDUES 37-111; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 158878; SOURCE 4 STRAIN: MU50; SOURCE 5 GENE: SAV_0229; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7HMT KEYWDS SECRETED, VIRULENCE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.L.GARCIA,B.V.GEISBRECHT,B.J.SUMMERS REVDAT 3 08-NOV-17 3T48 1 REMARK REVDAT 2 18-JAN-12 3T48 1 JRNL REVDAT 1 23-NOV-11 3T48 0 JRNL AUTH B.L.GARCIA,B.J.SUMMERS,Z.LIN,K.X.RAMYAR,D.RICKLIN, JRNL AUTH 2 D.V.KAMATH,Z.Q.FU,J.D.LAMBRIS,B.V.GEISBRECHT JRNL TITL DIVERSITY IN THE C3B CONVERTASE CONTACT RESIDUES AND JRNL TITL 2 TERTIARY STRUCTURES OF THE STAPHYLOCOCCAL COMPLEMENT JRNL TITL 3 INHIBITOR (SCIN) PROTEIN FAMILY. JRNL REF J.BIOL.CHEM. V. 287 628 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22086928 JRNL DOI 10.1074/JBC.M111.298984 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.130 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 21583 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.270 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 27.6105 - 3.6129 1.00 1460 150 0.1737 0.1968 REMARK 3 2 3.6129 - 2.8686 1.00 1450 148 0.1628 0.1921 REMARK 3 3 2.8686 - 2.5063 1.00 1457 149 0.1525 0.2101 REMARK 3 4 2.5063 - 2.2772 0.99 1431 146 0.1381 0.1732 REMARK 3 5 2.2772 - 2.1141 0.99 1440 146 0.1370 0.1724 REMARK 3 6 2.1141 - 1.9895 0.98 1409 145 0.1336 0.1805 REMARK 3 7 1.9895 - 1.8899 0.97 1402 142 0.1363 0.1847 REMARK 3 8 1.8899 - 1.8076 0.98 1393 143 0.1434 0.2051 REMARK 3 9 1.8076 - 1.7380 0.97 1400 142 0.1472 0.2000 REMARK 3 10 1.7380 - 1.6781 0.95 1409 144 0.1425 0.1855 REMARK 3 11 1.6781 - 1.6256 0.97 1351 139 0.1426 0.2094 REMARK 3 12 1.6256 - 1.5792 0.93 1372 140 0.1433 0.1911 REMARK 3 13 1.5792 - 1.5376 0.95 1321 134 0.1609 0.2342 REMARK 3 14 1.5376 - 1.5001 0.86 1288 132 0.1653 0.2227 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 1.01 REMARK 3 K_SOL : 0.47 REMARK 3 B_SOL : 40.04 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.49180 REMARK 3 B22 (A**2) : 0.49380 REMARK 3 B33 (A**2) : -1.98560 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.49410 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 : 0.011 1175 REMARK 3 ANGLE : 1.144 1587 REMARK 3 CHIRALITY : 0.066 185 REMARK 3 PLANARITY : 0.004 203 REMARK 3 DIHEDRAL : 14.813 447 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 3T48 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97243 REMARK 200 MONOCHROMATOR : SI(220) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21840 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.30800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE 2.14 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MG/ML PROTEIN, 0.1M BIS-TRIS, 30% REMARK 280 PEG 8000, 20 MM SODIUM THIOCYANATE, PH 5.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 47.13850 REMARK 290 SMTRY3 2 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 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 GLY A 3 REMARK 465 SER A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 SER A 7 REMARK 465 HIS A 8 REMARK 465 THR A 9 REMARK 465 TYR A 10 REMARK 465 HIS A 82 REMARK 465 SER A 83 REMARK 465 GLY B 3 REMARK 465 SER B 4 REMARK 465 THR B 5 REMARK 465 GLY B 6 REMARK 465 SER B 7 REMARK 465 HIS B 8 REMARK 465 ASN B 79 REMARK 465 PRO B 80 REMARK 465 LEU B 81 REMARK 465 HIS B 82 REMARK 465 SER B 83 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T46 RELATED DB: PDB REMARK 900 RELATED ID: 3T47 RELATED DB: PDB REMARK 900 RELATED ID: 3T49 RELATED DB: PDB REMARK 900 RELATED ID: 3T4A RELATED DB: PDB DBREF 3T48 A 8 83 UNP Q99WZ4 Q99WZ4_STAAM 36 111 DBREF 3T48 B 8 83 UNP Q99WZ4 Q99WZ4_STAAM 36 111 SEQADV 3T48 GLY A 3 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T48 SER A 4 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T48 THR A 5 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T48 GLY A 6 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T48 SER A 7 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T48 GLY B 3 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T48 SER B 4 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T48 THR B 5 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T48 GLY B 6 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T48 SER B 7 UNP Q99WZ4 EXPRESSION TAG SEQRES 1 A 81 GLY SER THR GLY SER HIS THR TYR GLN HIS GLN ALA LEU SEQRES 2 A 81 VAL ASP GLN LEU HIS GLU LEU ILE ALA ASN THR ASP LEU SEQRES 3 A 81 ASN LYS LEU SER TYR LEU ASN LEU ASP ALA PHE GLN LYS SEQRES 4 A 81 ARG ASP ILE LEU ALA ALA HIS TYR ILE ALA LYS SER ALA SEQRES 5 A 81 ILE ARG THR LYS ASN LEU ASP GLN MSE THR LYS ALA LYS SEQRES 6 A 81 GLN ARG LEU GLU SER ILE TYR ASN SER ILE SER ASN PRO SEQRES 7 A 81 LEU HIS SER SEQRES 1 B 81 GLY SER THR GLY SER HIS THR TYR GLN HIS GLN ALA LEU SEQRES 2 B 81 VAL ASP GLN LEU HIS GLU LEU ILE ALA ASN THR ASP LEU SEQRES 3 B 81 ASN LYS LEU SER TYR LEU ASN LEU ASP ALA PHE GLN LYS SEQRES 4 B 81 ARG ASP ILE LEU ALA ALA HIS TYR ILE ALA LYS SER ALA SEQRES 5 B 81 ILE ARG THR LYS ASN LEU ASP GLN MSE THR LYS ALA LYS SEQRES 6 B 81 GLN ARG LEU GLU SER ILE TYR ASN SER ILE SER ASN PRO SEQRES 7 B 81 LEU HIS SER MODRES 3T48 MSE A 63 MET SELENOMETHIONINE MODRES 3T48 MSE B 63 MET SELENOMETHIONINE HET MSE A 63 16 HET MSE B 63 17 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 HOH *135(H2 O) HELIX 1 1 GLN A 11 THR A 26 1 16 HELIX 2 2 ASP A 27 ASN A 35 5 9 HELIX 3 3 ASP A 37 THR A 57 1 21 HELIX 4 4 ASN A 59 ASN A 79 1 21 HELIX 5 5 THR B 9 ASN B 25 1 17 HELIX 6 6 ASP B 27 SER B 32 1 6 HELIX 7 7 TYR B 33 ASN B 35 5 3 HELIX 8 8 ASP B 37 LYS B 58 1 22 HELIX 9 9 ASN B 59 ILE B 77 1 19 LINK C GLN A 62 N MSE A 63 1555 1555 1.33 LINK C MSE A 63 N THR A 64 1555 1555 1.33 LINK C GLN B 62 N MSE B 63 1555 1555 1.32 LINK C MSE B 63 N THR B 64 1555 1555 1.33 CRYST1 26.095 94.277 29.097 90.00 97.14 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 0.038322 0.000000 0.004801 0.00000 SCALE2 0.000000 0.010607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034636 0.00000