HEADER INHIBITOR 04-MAY-06 2CM9 TITLE THE COMPLEMENT INHIBITOR OMCI IN COMPLEX WITH RICINOLEIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OMCI; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: DOUBLE MUTATION TO PREVENT THE YEAST EXPRESSION SYSTEM COMPND 8 TO INTRODUCE GLYCOSYLATION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORNITHODOROS MOUBATA; SOURCE 3 ORGANISM_COMMON: SOFT TICK; SOURCE 4 ORGANISM_TAXID: 6938; SOURCE 5 EXPRESSION_SYSTEM: PICHIA METHANOLICA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 33166; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: PMAD11; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PMETALPHAC KEYWDS ORNITHODOROS MOUBATA, C5, TICK, OMCI, LIPOCALIN, INHIBITOR, KEYWDS 2 COMPLEMENT EXPDTA X-RAY DIFFRACTION AUTHOR P.ROVERSI,S.JOHNSON,O.LISSINA,G.C.PAESEN,W.BOLAND,M.A.NUNN,S.M.LEA REVDAT 4 13-DEC-23 2CM9 1 REMARK REVDAT 3 24-FEB-09 2CM9 1 VERSN REVDAT 2 22-MAY-07 2CM9 1 JRNL REVDAT 1 01-MAY-07 2CM9 0 JRNL AUTH P.ROVERSI,O.LISSINA,S.JOHNSON,N.AHMAT,G.C.PAESEN,K.PLOSS, JRNL AUTH 2 W.BOLAND,M.A.NUNN,S.M.LEA JRNL TITL THE STRUCTURE OF OMCI, A NOVEL LIPOCALIN INHIBITOR OF THE JRNL TITL 2 COMPLEMENT SYSTEM. JRNL REF J.MOL.BIOL. V. 369 784 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17445829 JRNL DOI 10.1016/J.JMB.2007.03.064 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5.6.1 REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6289 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1970 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1950 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.00 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 317 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1145 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 2.300 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.003 ; 2.000 ; 1198 REMARK 3 BOND ANGLES (DEGREES) : 0.625 ; 3.000 ; 1607 REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : 12.500; 1.000 ; 6 REMARK 3 TRIGONAL CARBON PLANES (A) : 0.004 ; 2.000 ; 41 REMARK 3 GENERAL PLANES (A) : 0.015 ; 5.000 ; 168 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 0.977 ; 20.000; 1199 REMARK 3 NON-BONDED CONTACTS (A) : 0.064 ; 5.000 ; 13 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : 0 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BABINET SCALING REMARK 3 KSOL : 0.50 REMARK 3 BSOL : 48.00 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TNT WAS RUN AGAINST MAXIMUM LIKELIHOOD REMARK 3 IN BUSTER-TNT VERSION 1.3.0 REMARK 4 REMARK 4 2CM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1290028657. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97923 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58577 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 38.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1QFT REMARK 200 REMARK 200 REMARK: AMORE WAS RUN ON THE CASPAR SERVER AT WWW.IGS.CNRS- MRS.FR REMARK 200 SLASH CASPR2 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000 0.1 M SODIUM ACETATE PH REMARK 280 4.6 0.2 M AMMONIUM ACETATE, PH 4.60 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 22.54500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.51500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.51500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.54500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 ASP A 19 REMARK 465 SER A 20 REMARK 465 GLU A 21 REMARK 465 SER A 22 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 LYS A 65 99.00 -69.97 REMARK 500 ASP A 67 -109.54 34.99 REMARK 500 LEU A 165 55.08 -99.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RCL A1169 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CM4 RELATED DB: PDB REMARK 900 THE COMPLEMENT INHIBITOR OMCI IN COMPLEX WITH RICINOLEIC ACID REMARK 999 REMARK 999 SEQUENCE REMARK 999 NO SIGNAL TAG 1-18 IN THIS CONSTRUCT MUTATIONS N78Q, N102Q DBREF 2CM9 A 19 168 UNP Q5YD59 Q5YD59_ORNMO 19 168 SEQADV 2CM9 GLN A 78 UNP Q5YD59 ASN 78 ENGINEERED MUTATION SEQADV 2CM9 GLN A 102 UNP Q5YD59 ASN 102 ENGINEERED MUTATION SEQRES 1 A 150 ASP SER GLU SER ASP CYS THR GLY SER GLU PRO VAL ASP SEQRES 2 A 150 ALA PHE GLN ALA PHE SER GLU GLY LYS GLU ALA TYR VAL SEQRES 3 A 150 LEU VAL ARG SER THR ASP PRO LYS ALA ARG ASP CYS LEU SEQRES 4 A 150 LYS GLY GLU PRO ALA GLY GLU LYS GLN ASP ASN THR LEU SEQRES 5 A 150 PRO VAL MET MET THR PHE LYS GLN GLY THR ASP TRP ALA SEQRES 6 A 150 SER THR ASP TRP THR PHE THR LEU ASP GLY ALA LYS VAL SEQRES 7 A 150 THR ALA THR LEU GLY GLN LEU THR GLN ASN ARG GLU VAL SEQRES 8 A 150 VAL TYR ASP SER GLN SER HIS HIS CYS HIS VAL ASP LYS SEQRES 9 A 150 VAL GLU LYS GLU VAL PRO ASP TYR GLU MET TRP MET LEU SEQRES 10 A 150 ASP ALA GLY GLY LEU GLU VAL GLU VAL GLU CYS CYS ARG SEQRES 11 A 150 GLN LYS LEU GLU GLU LEU ALA SER GLY ARG ASN GLN MET SEQRES 12 A 150 TYR PRO HIS LEU LYS ASP CYS HET RCL A1169 21 HET ACT A1170 4 HETNAM RCL RICINOLEIC ACID HETNAM ACT ACETATE ION FORMUL 2 RCL C18 H34 O3 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *44(H2 O) HELIX 1 1 ASP A 31 PHE A 36 1 6 HELIX 2 2 SER A 37 LYS A 40 5 4 HELIX 3 3 LEU A 140 ALA A 155 1 16 SHEET 1 AA10 TYR A 43 SER A 48 0 SHEET 2 AA10 ASP A 55 PRO A 61 -1 O LEU A 57 N LEU A 45 SHEET 3 AA10 THR A 69 GLN A 78 -1 O MET A 73 N GLU A 60 SHEET 4 AA10 ASP A 81 ASP A 92 -1 O ASP A 81 N GLN A 78 SHEET 5 AA10 LYS A 95 LEU A 100 -1 O LYS A 95 N ASP A 92 SHEET 6 AA10 LEU A 103 ASP A 112 -1 O LEU A 103 N LEU A 100 SHEET 7 AA10 CYS A 118 GLU A 124 -1 O VAL A 120 N VAL A 110 SHEET 8 AA10 ASP A 129 LEU A 135 -1 O ASP A 129 N VAL A 123 SHEET 9 AA10 TYR A 43 SER A 48 -1 O VAL A 44 N MET A 134 SHEET 10 AA10 TYR A 43 SER A 48 0 SSBOND 1 CYS A 24 CYS A 146 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 168 1555 1555 2.03 SSBOND 3 CYS A 118 CYS A 147 1555 1555 2.03 CISPEP 1 GLU A 28 PRO A 29 0 -1.63 SITE 1 AC1 6 GLU A 108 LYS A 122 GLU A 124 LEU A 140 SITE 2 AC1 6 VAL A 142 GLU A 143 SITE 1 AC2 12 PHE A 36 ARG A 54 LEU A 57 VAL A 72 SITE 2 AC2 12 TRP A 87 PHE A 89 GLN A 105 ARG A 107 SITE 3 AC2 12 HIS A 119 ASP A 121 TRP A 133 HOH A2035 CRYST1 45.090 54.000 55.030 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 0.022177 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018170 0.00000