HEADER IMMUNE SYSTEM 11-APR-02 1IW2 TITLE X-RAY STRUCTURE OF HUMAN COMPLEMENT PROTEIN C8GAMMA AT PH=7.O COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT PROTEIN C8GAMMA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COMPLEMENT COMPONENT C8 GAMMA CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HIGH FIVE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PBLUE BAC KEYWDS LIPOCALIN, BETA BARREL, CALYX, MAC, COMPLEMENT, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR E.ORTLUND,C.L.PARKER,S.F.SCHRECK,S.GINELL,W.MINOR,J.M.SODETZ, AUTHOR 2 L.LEBIODA REVDAT 7 13-NOV-24 1IW2 1 REMARK REVDAT 6 27-DEC-23 1IW2 1 REMARK REVDAT 5 13-APR-22 1IW2 1 AUTHOR JRNL REVDAT 4 10-NOV-21 1IW2 1 SEQADV REVDAT 3 24-FEB-09 1IW2 1 VERSN REVDAT 2 07-JAN-03 1IW2 1 REMARK REVDAT 1 12-JUN-02 1IW2 0 JRNL AUTH E.ORTLUND,C.L.PARKER,S.F.SCHRECK,S.GINELL,W.MINOR, JRNL AUTH 2 J.M.SODETZ,L.LEBIODA JRNL TITL CRYSTAL STRUCTURE OF HUMAN COMPLEMENT PROTEIN C8GAMMA AT 1.2 JRNL TITL 2 A RESOLUTION REVEALS A LIPOCALIN FOLD AND A DISTINCT LIGAND JRNL TITL 3 BINDING SITE. JRNL REF BIOCHEMISTRY V. 41 7030 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12033936 JRNL DOI 10.1021/BI025696I REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 509116.070 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 14162 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) : 0.233 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1453 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2002 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 243 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.63000 REMARK 3 B22 (A**2) : -3.58000 REMARK 3 B33 (A**2) : 1.95000 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.620 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 43.24 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IW2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-02. REMARK 100 THE DEPOSITION ID IS D_1000005326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-99 REMARK 200 TEMPERATURE (KELVIN) : 94 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14388 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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 (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.13800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM CITRATE, PH 4.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 21.07000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.60700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.45200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.60700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.07000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.45200 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 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 GLN A 1 REMARK 465 LYS A 2 REMARK 465 PRO A 3 REMARK 465 GLN A 4 REMARK 465 ARG A 5 REMARK 465 PRO A 6 REMARK 465 ARG A 7 REMARK 465 ARG A 8 REMARK 465 PRO A 9 REMARK 465 ARG A 41 REMARK 465 PHE A 42 REMARK 465 LEU A 43 REMARK 465 GLN A 44 REMARK 465 GLU A 45 REMARK 465 GLN A 46 REMARK 465 GLY A 47 REMARK 465 HIS A 48 REMARK 465 ARG A 181 REMARK 465 ARG A 182 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 GLN A 95 128.63 -34.17 REMARK 500 ALA A 96 101.13 -56.60 REMARK 500 ARG A 97 -2.26 -54.72 REMARK 500 ARG A 100 129.78 113.54 REMARK 500 TYR A 112 -27.63 68.20 REMARK 500 SER A 114 -36.86 -144.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LF7 RELATED DB: PDB REMARK 900 1LF7 CONTAINS HIGH RESOLUTION X-RAY STRUCTURE OF HUMAN COMPLEMENT REMARK 900 PROTEIN C8GAMMA DBREF 1IW2 A 1 182 UNP P07360 CO8G_HUMAN 21 202 SEQADV 1IW2 GLY A 40 UNP P07360 CYS 60 ENGINEERED MUTATION SEQRES 1 A 182 GLN LYS PRO GLN ARG PRO ARG ARG PRO ALA SER PRO ILE SEQRES 2 A 182 SER THR ILE GLN PRO LYS ALA ASN PHE ASP ALA GLN GLN SEQRES 3 A 182 PHE ALA GLY THR TRP LEU LEU VAL ALA VAL GLY SER ALA SEQRES 4 A 182 GLY ARG PHE LEU GLN GLU GLN GLY HIS ARG ALA GLU ALA SEQRES 5 A 182 THR THR LEU HIS VAL ALA PRO GLN GLY THR ALA MET ALA SEQRES 6 A 182 VAL SER THR PHE ARG LYS LEU ASP GLY ILE CYS TRP GLN SEQRES 7 A 182 VAL ARG GLN LEU TYR GLY ASP THR GLY VAL LEU GLY ARG SEQRES 8 A 182 PHE LEU LEU GLN ALA ARG GLY ALA ARG GLY ALA VAL HIS SEQRES 9 A 182 VAL VAL VAL ALA GLU THR ASP TYR GLN SER PHE ALA VAL SEQRES 10 A 182 LEU TYR LEU GLU ARG ALA GLY GLN LEU SER VAL LYS LEU SEQRES 11 A 182 TYR ALA ARG SER LEU PRO VAL SER ASP SER VAL LEU SER SEQRES 12 A 182 GLY PHE GLU GLN ARG VAL GLN GLU ALA HIS LEU THR GLU SEQRES 13 A 182 ASP GLN ILE PHE TYR PHE PRO LYS TYR GLY PHE CYS GLU SEQRES 14 A 182 ALA ALA ASP GLN PHE HIS VAL LEU ASP GLU VAL ARG ARG FORMUL 2 HOH *108(H2 O) HELIX 1 1 SER A 11 ILE A 16 5 6 HELIX 2 2 ASP A 23 ALA A 28 1 6 HELIX 3 3 SER A 138 ALA A 152 1 15 HELIX 4 4 THR A 155 ASP A 157 5 3 HELIX 5 5 ASP A 172 PHE A 174 5 3 SHEET 1 A14 VAL A 176 ASP A 178 0 SHEET 2 A14 ILE A 75 ASP A 85 1 O GLN A 78 N LEU A 177 SHEET 3 A14 ALA A 63 LEU A 72 -1 O MET A 64 N TYR A 83 SHEET 4 A14 THR A 53 GLN A 60 -1 O THR A 54 N PHE A 69 SHEET 5 A14 GLY A 29 GLY A 37 -1 N GLY A 29 O VAL A 57 SHEET 6 A14 GLN A 125 ALA A 132 -1 O VAL A 128 N GLY A 37 SHEET 7 A14 PHE A 115 ARG A 122 -1 O ALA A 116 N TYR A 131 SHEET 8 A14 VAL A 103 THR A 110 -1 O HIS A 104 N GLU A 121 SHEET 9 A14 ARG A 91 LEU A 94 -1 N PHE A 92 O VAL A 105 SHEET 10 A14 ILE A 75 ASP A 85 -1 N GLY A 84 O LEU A 93 SHEET 11 A14 ALA A 63 LEU A 72 -1 O MET A 64 N TYR A 83 SHEET 12 A14 THR A 53 GLN A 60 -1 O THR A 54 N PHE A 69 SHEET 13 A14 GLY A 29 GLY A 37 -1 N GLY A 29 O VAL A 57 SHEET 14 A14 ILE A 159 TYR A 161 -1 N PHE A 160 O VAL A 36 SSBOND 1 CYS A 76 CYS A 168 1555 1555 2.04 CISPEP 1 LEU A 135 PRO A 136 0 0.40 CRYST1 42.140 58.904 71.214 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 0.023730 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014042 0.00000