HEADER IMMUNE SYSTEM 25-JUL-11 3T46 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL COMPLEMENT INHIBITOR D (SCIN-D) AT TITLE 2 1.5 ANGSTROM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCIN-D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 29-114; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS; SOURCE 3 ORGANISM_TAXID: 158878; SOURCE 4 STRAIN: MU50; SOURCE 5 GENE: SAV0229, 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 13-SEP-23 3T46 1 REMARK SEQADV LINK REVDAT 2 18-JAN-12 3T46 1 JRNL REVDAT 1 23-NOV-11 3T46 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.530 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 10868 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1088 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 24.9970 - 2.9985 0.99 1485 165 0.2175 0.2221 REMARK 3 2 2.9985 - 2.3806 0.97 1293 144 0.2094 0.2205 REMARK 3 3 2.3806 - 2.0799 0.94 1211 135 0.2142 0.2297 REMARK 3 4 2.0799 - 1.8898 0.93 1215 135 0.2172 0.2624 REMARK 3 5 1.8898 - 1.7544 0.93 1185 131 0.2305 0.2862 REMARK 3 6 1.7544 - 1.6510 0.93 1165 130 0.2445 0.3473 REMARK 3 7 1.6510 - 1.5683 0.91 1135 126 0.2412 0.2775 REMARK 3 8 1.5683 - 1.5000 0.88 1091 122 0.2742 0.3047 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.53 REMARK 3 K_SOL : 0.49 REMARK 3 B_SOL : 40.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.90600 REMARK 3 B22 (A**2) : -0.90600 REMARK 3 B33 (A**2) : 2.73170 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 : 0.007 614 REMARK 3 ANGLE : 0.994 829 REMARK 3 CHIRALITY : 0.069 96 REMARK 3 PLANARITY : 0.004 108 REMARK 3 DIHEDRAL : 13.787 233 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 3T46 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_1000067014. 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 : 4.8 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 330 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11413 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3T48 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MG/ML PROTEIN, 0.1M BIS-TRIS, 15% REMARK 280 W/V PEG 3350, PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 175.06667 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 87.53333 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 131.30000 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 43.76667 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 218.83333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 175.06667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 87.53333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 43.76667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 131.30000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 218.83333 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL 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 BIOMT1 2 0.500000 -0.866025 0.000000 14.43000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 24.99349 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 43.76667 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A 101 LIES ON A SPECIAL POSITION. REMARK 375 NA NA A 102 LIES ON A SPECIAL POSITION. 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 -4 REMARK 465 SER A -3 REMARK 465 THR A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 SER A 1 REMARK 465 LYS A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 THR A 6 REMARK 465 SER A 7 REMARK 465 HIS A 8 REMARK 465 THR A 9 REMARK 465 TYR A 10 REMARK 465 GLN A 11 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T47 RELATED DB: PDB REMARK 900 RELATED ID: 3T48 RELATED DB: PDB REMARK 900 RELATED ID: 3T49 RELATED DB: PDB REMARK 900 RELATED ID: 3T4A RELATED DB: PDB DBREF 3T46 A 1 86 UNP Q99WZ4 Q99WZ4_STAAM 29 114 SEQADV 3T46 GLY A -4 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T46 SER A -3 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T46 THR A -2 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T46 GLY A -1 UNP Q99WZ4 EXPRESSION TAG SEQADV 3T46 SER A 0 UNP Q99WZ4 EXPRESSION TAG SEQRES 1 A 91 GLY SER THR GLY SER SER LYS SER GLU THR THR SER HIS SEQRES 2 A 91 THR TYR GLN HIS GLN ALA LEU VAL ASP GLN LEU HIS GLU SEQRES 3 A 91 LEU ILE ALA ASN THR ASP LEU ASN LYS LEU SER TYR LEU SEQRES 4 A 91 ASN LEU ASP ALA PHE GLN LYS ARG ASP ILE LEU ALA ALA SEQRES 5 A 91 HIS TYR ILE ALA LYS SER ALA ILE ARG THR LYS ASN LEU SEQRES 6 A 91 ASP GLN MET THR LYS ALA LYS GLN ARG LEU GLU SER ILE SEQRES 7 A 91 TYR ASN SER ILE SER ASN PRO LEU HIS SER GLN ASN ASN HET NA A 101 1 HET NA A 102 1 HET NA A 103 1 HET NA A 104 1 HETNAM NA SODIUM ION FORMUL 2 NA 4(NA 1+) FORMUL 6 HOH *68(H2 O) HELIX 1 1 HIS A 12 ASN A 25 1 14 HELIX 2 2 THR A 26 ASN A 35 5 10 HELIX 3 3 ASP A 37 THR A 57 1 21 HELIX 4 4 ASN A 59 ASN A 79 1 21 LINK OD2 ASP A 61 NA NA A 103 1555 1555 2.80 LINK O HOH A 93 NA NA A 101 1555 1555 3.05 SITE 1 AC1 2 LYS A 41 HOH A 93 SITE 1 AC2 1 ARG A 42 SITE 1 AC3 3 HIS A 12 LEU A 15 ASP A 61 SITE 1 AC4 5 ASN A 29 ARG A 56 GLN A 84 ASN A 85 SITE 2 AC4 5 HOH A 120 CRYST1 28.860 28.860 262.600 90.00 90.00 120.00 P 65 2 2 12 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 0.034650 0.020005 0.000000 0.00000 SCALE2 0.000000 0.040010 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003808 0.00000