HEADER TRANSPORT PROTEIN,LIGAND BINDING PROTEIN13-FEB-07 2OVD TITLE CRYSTAL STRUCTURE OF HUMAN COMPLEMENT PROTEIN C8GAMMA WITH LAURATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT COMPONENT 8, GAMMA POLYPEPTIDE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COMPLEMENT PROTEIN C8GAMMA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: C8G; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI B(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-17B KEYWDS LIPOCALIN; BETA BARREL, TRANSPORT PROTEIN, LIGAND BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.CHISWELL,L.L.LOVELACE,C.BRANNEN,E.A.ORTLUND,L.LEBIODA,J.M.SODETZ REVDAT 4 20-OCT-21 2OVD 1 REMARK SEQADV REVDAT 3 18-OCT-17 2OVD 1 REMARK REVDAT 2 24-FEB-09 2OVD 1 VERSN REVDAT 1 22-MAY-07 2OVD 0 JRNL AUTH B.CHISWELL,L.L.LOVELACE,C.BRANNEN,E.A.ORTLUND,L.LEBIODA, JRNL AUTH 2 J.M.SODETZ JRNL TITL STRUCTURAL FEATURES OF THE LIGAND BINDING SITE ON HUMAN JRNL TITL 2 COMPLEMENT PROTEIN C8GAMMA: A MEMBER OF THE LIPOCALIN FAMILY JRNL REF BIOCHIM.BIOPHYS.ACTA V.1774 637 2007 JRNL REFN ISSN 0006-3002 JRNL PMID 17452033 JRNL DOI 10.1016/J.BBAPAP.2007.03.004 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 500.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1149.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 15376 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1516 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 30 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 275 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 36 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 199 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.82000 REMARK 3 B22 (A**2) : 3.16400 REMARK 3 B33 (A**2) : -1.34400 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.153 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.083 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.471 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.637 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.154 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 56.68 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 : CNS_TOPPAR:PROTEIN_REP.PARAMHICUP REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : LIGAND.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOPHICUP REMARK 3 TOPOLOGY FILE 2 : CNS_TOPPAR:DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CNS_TOPPAR:ION.TOP REMARK 3 TOPOLOGY FILE 5 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91963 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18059 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.33500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 43.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE AND 25-27% PEG REMARK 280 4000. SODIUM LAURATE (SIGMA) WAS SOLUBILIZED IN METHANOL/WATER REMARK 280 AND USED TO PREPARE A 0.9 MM SOLUTION IN 0.1M IMIDAZOLE REMARK 280 CONTAINING 32% PEG 4000, PH 7.0, PH 4.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 290K 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 21.04050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.41800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.76950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.41800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.04050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.76950 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 ALA A 10 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 49 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 ALA A 52 132.33 67.41 REMARK 500 ARG A 97 105.38 -169.74 REMARK 500 ALA A 108 -119.43 -93.80 REMARK 500 THR A 110 142.23 -173.81 REMARK 500 TYR A 112 -27.54 62.38 REMARK 500 SER A 114 -37.39 -145.58 REMARK 500 GLU A 169 33.86 -152.48 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 DAO A 190 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IW2 RELATED DB: PDB REMARK 900 RELATED ID: 1LF7 RELATED DB: PDB REMARK 900 RELATED ID: 2OVA RELATED DB: PDB REMARK 900 RELATED ID: 2OVE RELATED DB: PDB DBREF 2OVD A 1 182 UNP Q14CU0 Q14CU0_HUMAN 21 202 SEQADV 2OVD ALA A 40 UNP Q14CU0 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 ALA 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 HET DAO A 190 14 HETNAM DAO LAURIC ACID FORMUL 2 DAO C12 H24 O2 FORMUL 3 HOH *199(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 A 6 ILE A 159 TYR A 161 0 SHEET 2 A 6 GLY A 29 GLY A 37 -1 N VAL A 36 O PHE A 160 SHEET 3 A 6 THR A 54 GLN A 60 -1 O LEU A 55 N TRP A 31 SHEET 4 A 6 ALA A 63 LEU A 72 -1 O ALA A 65 N ALA A 58 SHEET 5 A 6 ILE A 75 ASP A 85 -1 O GLN A 81 N VAL A 66 SHEET 6 A 6 VAL A 176 ASP A 178 1 O LEU A 177 N GLN A 78 SHEET 1 B 8 ILE A 159 TYR A 161 0 SHEET 2 B 8 GLY A 29 GLY A 37 -1 N VAL A 36 O PHE A 160 SHEET 3 B 8 GLN A 125 ALA A 132 -1 O VAL A 128 N GLY A 37 SHEET 4 B 8 PHE A 115 ARG A 122 -1 N LEU A 118 O LYS A 129 SHEET 5 B 8 VAL A 103 THR A 110 -1 N GLU A 109 O VAL A 117 SHEET 6 B 8 ARG A 91 LEU A 94 -1 N PHE A 92 O VAL A 105 SHEET 7 B 8 ILE A 75 ASP A 85 -1 N GLY A 84 O LEU A 93 SHEET 8 B 8 VAL A 176 ASP A 178 1 O LEU A 177 N GLN A 78 SSBOND 1 CYS A 76 CYS A 168 1555 1555 2.04 CISPEP 1 LEU A 135 PRO A 136 0 0.40 SITE 1 AC1 5 TYR A 83 LEU A 120 ARG A 122 LYS A 129 SITE 2 AC1 5 TYR A 131 CRYST1 42.081 59.539 70.836 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 0.023764 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016796 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014117 0.00000