HEADER COMPLEMENT 19-MAY-98 1C3D TITLE X-RAY CRYSTAL STRUCTURE OF C3D: A C3 FRAGMENT AND LIGAND FOR TITLE 2 COMPLEMENT RECEPTOR 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C3D; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: BL21; SOURCE 6 CELLULAR_LOCATION: SERUM; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PET 15B; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: BL21 KEYWDS COMPLEMENT, C3, C3D, ALPHA-ALPHA BARREL EXPDTA X-RAY DIFFRACTION AUTHOR B.NAGAR,R.G.JONES,R.J.DIEFENBACH,D.E.ISENMAN,J.M.RINI REVDAT 6 16-OCT-24 1C3D 1 REMARK SEQADV REVDAT 5 14-MAR-18 1C3D 1 SEQADV REVDAT 4 13-JUL-11 1C3D 1 VERSN REVDAT 3 24-FEB-09 1C3D 1 VERSN REVDAT 2 18-NOV-98 1C3D 3 SOURCE COMPND REMARK HETATM REVDAT 2 2 3 CONECT REVDAT 1 07-OCT-98 1C3D 0 JRNL AUTH B.NAGAR,R.G.JONES,R.J.DIEFENBACH,D.E.ISENMAN,J.M.RINI JRNL TITL X-RAY CRYSTAL STRUCTURE OF C3D: A C3 FRAGMENT AND LIGAND FOR JRNL TITL 2 COMPLEMENT RECEPTOR 2. JRNL REF SCIENCE V. 280 1277 1998 JRNL REFN ISSN 0036-8075 JRNL PMID 9596584 JRNL DOI 10.1126/SCIENCE.280.5367.1277 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 131592.300 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 78.4 REMARK 3 NUMBER OF REFLECTIONS : 24149 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 SET) : 0.188 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1668 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 38.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1829 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 129 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2317 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.85000 REMARK 3 B22 (A**2) : -4.71000 REMARK 3 B33 (A**2) : 3.86000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.240 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.940 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.900 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 22.900; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 18.620; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX_3.1.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX_3.1.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1C3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172168. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-97 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.993 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : CRYSTALS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29818 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 24.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 42.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIWAVELENGTH ANOMALOUS REMARK 200 DIFFRACTION REMARK 200 SOFTWARE USED: PHASES, X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 12% PEG REMARK 280 20K, 100 MM MES BUFFER, PH 6.5, 10 MM DTT 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 30.41000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.58000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.18900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.58000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.41000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.18900 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: 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 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 ASN A 143 -2.37 -59.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 298 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 299 DBREF 1C3D A 3 294 UNP P01024 CO3_HUMAN 996 1287 SEQADV 1C3D ALA A 17 UNP P01024 CYS 1010 ENGINEERED MUTATION SEQRES 1 A 294 MET LEU ASP ALA GLU ARG LEU LYS HIS LEU ILE VAL THR SEQRES 2 A 294 PRO SER GLY ALA GLY GLU GLN ASN MET ILE GLY MET THR SEQRES 3 A 294 PRO THR VAL ILE ALA VAL HIS TYR LEU ASP GLU THR GLU SEQRES 4 A 294 GLN TRP GLU LYS PHE GLY LEU GLU LYS ARG GLN GLY ALA SEQRES 5 A 294 LEU GLU LEU ILE LYS LYS GLY TYR THR GLN GLN LEU ALA SEQRES 6 A 294 PHE ARG GLN PRO SER SER ALA PHE ALA ALA PHE VAL LYS SEQRES 7 A 294 ARG ALA PRO SER THR TRP LEU THR ALA TYR VAL VAL LYS SEQRES 8 A 294 VAL PHE SER LEU ALA VAL ASN LEU ILE ALA ILE ASP SER SEQRES 9 A 294 GLN VAL LEU CYS GLY ALA VAL LYS TRP LEU ILE LEU GLU SEQRES 10 A 294 LYS GLN LYS PRO ASP GLY VAL PHE GLN GLU ASP ALA PRO SEQRES 11 A 294 VAL ILE HIS GLN GLU MET ILE GLY GLY LEU ARG ASN ASN SEQRES 12 A 294 ASN GLU LYS ASP MET ALA LEU THR ALA PHE VAL LEU ILE SEQRES 13 A 294 SER LEU GLN GLU ALA LYS ASP ILE CYS GLU GLU GLN VAL SEQRES 14 A 294 ASN SER LEU PRO GLY SER ILE THR LYS ALA GLY ASP PHE SEQRES 15 A 294 LEU GLU ALA ASN TYR MET ASN LEU GLN ARG SER TYR THR SEQRES 16 A 294 VAL ALA ILE ALA GLY TYR ALA LEU ALA GLN MET GLY ARG SEQRES 17 A 294 LEU LYS GLY PRO LEU LEU ASN LYS PHE LEU THR THR ALA SEQRES 18 A 294 LYS ASP LYS ASN ARG TRP GLU ASP PRO GLY LYS GLN LEU SEQRES 19 A 294 TYR ASN VAL GLU ALA THR SER TYR ALA LEU LEU ALA LEU SEQRES 20 A 294 LEU GLN LEU LYS ASP PHE ASP PHE VAL PRO PRO VAL VAL SEQRES 21 A 294 ARG TRP LEU ASN GLU GLN ARG TYR TYR GLY GLY GLY TYR SEQRES 22 A 294 GLY SER THR GLN ALA THR PHE MET VAL PHE GLN ALA LEU SEQRES 23 A 294 ALA GLN TYR GLN LYS ASP ALA PRO HET GOL A 295 6 HET GOL A 296 6 HET GOL A 297 6 HET GOL A 298 6 HET GOL A 299 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 5(C3 H8 O3) FORMUL 7 HOH *102(H2 O) HELIX 1 1 ALA A 4 LEU A 10 5 7 HELIX 2 2 GLN A 20 GLU A 37 1 18 HELIX 3 3 LEU A 46 PHE A 66 5 21 HELIX 4 4 THR A 83 LEU A 95 1 13 HELIX 5 5 SER A 104 LYS A 118 1 15 HELIX 6 6 GLN A 134 ARG A 141 5 8 HELIX 7 7 LYS A 146 GLU A 160 1 15 HELIX 8 8 LYS A 162 CYS A 165 1 4 HELIX 9 9 LEU A 172 ASN A 189 1 18 HELIX 10 10 SER A 193 MET A 206 1 14 HELIX 11 11 GLY A 211 THR A 220 1 10 HELIX 12 12 LYS A 222 LYS A 224 5 3 HELIX 13 13 GLN A 233 GLN A 249 1 17 HELIX 14 14 PHE A 253 GLN A 266 1 14 HELIX 15 15 THR A 276 ASP A 292 1 17 SSBOND 1 CYS A 108 CYS A 165 1555 1555 2.04 SITE 1 AC1 6 THR A 13 PRO A 14 SER A 15 GLN A 20 SITE 2 AC1 6 GLY A 24 HOH A 360 SITE 1 AC2 7 TRP A 84 GLU A 127 PRO A 130 VAL A 131 SITE 2 AC2 7 GLN A 134 ILE A 137 HOH A 400 SITE 1 AC3 4 GLN A 191 LYS A 216 THR A 220 HOH A 372 SITE 1 AC4 7 ILE A 23 PRO A 27 GLY A 271 GLY A 272 SITE 2 AC4 7 HOH A 310 HOH A 328 HOH A 348 SITE 1 AC5 7 VAL A 97 ASN A 98 LEU A 99 ILE A 100 SITE 2 AC5 7 ARG A 226 TRP A 262 HOH A 390 CRYST1 60.820 64.378 87.160 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 0.016442 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015533 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011473 0.00000