HEADER MEMBRANE PROTEIN 04-JAN-11 2Y44 TITLE CRYSTAL STRUCTURE OF GARP FROM TRYPANOSOMA CONGOLENSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMIC ACID/ALANINE-RICH PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ECTODOMAIN, RESIDUES 40-224; COMPND 5 SYNONYM: GARP; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA CONGOLENSE; SOURCE 3 ORGANISM_TAXID: 5692; SOURCE 4 STRAIN: IL3000; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1 KEYWDS MEMBRANE PROTEIN, SURFACE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.C.LOVELESS,J.W.MASON,T.SAKURAI,N.INOUE,M.RAZAVI,T.W.PEARSON, AUTHOR 2 M.J.BOULANGER REVDAT 3 21-NOV-12 2Y44 1 SEQADV REVDAT 2 15-JUN-11 2Y44 1 SOURCE REVDAT JRNL REMARK REVDAT 1 30-MAR-11 2Y44 0 JRNL AUTH B.C.LOVELESS,J.W.MASON,T.SAKURAI,N.INOUE,M.RAZAVI, JRNL AUTH 2 T.W.PEARSON,M.J.BOULANGER JRNL TITL STRUCTURAL CHARACTERIZATION AND EPITOPE MAPPING OF JRNL TITL 2 THE GLUTAMIC ACID/ALANINE-RICH PROTEIN FROM JRNL TITL 3 TRYPANOSOMA CONGOLENSE: DEFINING ASSEMBLY ON THE JRNL TITL 4 PARASITE CELL SURFACE. JRNL REF J.BIOL.CHEM. V. 286 20658 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21471223 JRNL DOI 10.1074/JBC.M111.218941 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 93.10 REMARK 3 NUMBER OF REFLECTIONS : 19462 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 + TEST SET) : 0.20176 REMARK 3 R VALUE (WORKING SET) : 0.19923 REMARK 3 FREE R VALUE : 0.25085 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.2 REMARK 3 FREE R VALUE TEST SET COUNT : 1059 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.650 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.693 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1331 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.334 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.381 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1344 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.995 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02 REMARK 3 B22 (A**2) : 0.00 REMARK 3 B33 (A**2) : 0.00 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.01 REMARK 3 B23 (A**2) : 0.01 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.125 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.171 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1364 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1836 ; 1.402 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 182 ; 4.847 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;32.841 ;24.655 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 248 ;16.106 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;17.595 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 220 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 995 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 914 ; 1.481 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1440 ; 2.544 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 450 ; 4.611 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 396 ; 7.595 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2Y44 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JAN-11. REMARK 100 THE PDBE ID CODE IS EBI-46894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20523 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.65 REMARK 200 RESOLUTION RANGE LOW (A) : 34.62 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 7.86 REMARK 200 R MERGE (I) : 0.09 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.90 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.85 REMARK 200 R MERGE FOR SHELL (I) : 0.45 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: PISA 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2109 O HOH A 2202 1.84 REMARK 500 OE2 GLU A 194 O HOH A 2223 1.89 REMARK 500 OE1 GLU A 221 O HOH A 2249 1.95 REMARK 500 NE2 GLN A 45 O HOH A 2006 2.04 REMARK 500 O HOH A 2060 O HOH A 2061 2.14 REMARK 500 OE2 GLU A 153 O HOH A 2179 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2016 O HOH A 2125 1544 2.15 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 IOD A1228 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1229 REMARK 999 REMARK 999 SEQUENCE REMARK 999 GENE CLONED FROM A SPECIFIC STRAIN AND WITH THE KNOWN LEVEL REMARK 999 OF POLYMORPHISM IN THIS FAMILY OF GENES, THERE IS NO EXACT REMARK 999 SEQUENCE PUBLISHED. HOWEVER, SEQUENCES FROM SEVERAL CLONES REMARK 999 (SEVERAL PCR REACTIONS) INDICATE THAT DIFFERENCES IN SEQUENCE REMARK 999 ARE SIMPLY ONE OF THE MANY POLYMORPHISMS. THUS THERE IS REMARK 999 ONLY A "LOOSE" SEQUENCE REFERENCE CROSS-REFERENCE POSSIBLE. DBREF 2Y44 A 40 224 UNP Q9U0E1 Q9U0E1_TRYCO 40 224 SEQADV 2Y44 THR A 98 UNP Q9U0E1 ALA 98 SEE REMARK 999 SEQADV 2Y44 A UNP Q9U0E1 LYS 150 DELETION SEQADV 2Y44 TYR A 218 UNP Q9U0E1 SER 218 SEE REMARK 999 SEQRES 1 A 184 LYS VAL GLU GLU VAL GLN THR MET CYS ASP VAL ALA ARG SEQRES 2 A 184 GLN LEU ARG ALA LEU GLU THR ALA SER GLN SER ALA VAL SEQRES 3 A 184 ALA ALA VAL VAL SER SER ALA ARG GLU ALA SER GLU ALA SEQRES 4 A 184 LYS GLU ARG ALA GLU LYS ALA VAL GLU ARG ALA LYS SER SEQRES 5 A 184 LYS LYS ARG GLY VAL ASP THR ALA THR GLU ALA ALA ALA SEQRES 6 A 184 ARG ALA ALA ALA ALA ALA GLN ARG ALA GLU THR VAL VAL SEQRES 7 A 184 SER ASP ALA ARG LYS HIS ALA ALA ASP LEU THR ALA ALA SEQRES 8 A 184 SER LYS ASP ALA ILE GLU THR THR ASP GLU SER LEU ARG SEQRES 9 A 184 LEU LEU ALA THR OCS GLU ALA ASP GLU PRO ILE ARG THR SEQRES 10 A 184 ALA ALA LYS LYS CYS THR GLY ALA ALA ALA GLU VAL THR SEQRES 11 A 184 SER LYS SER LEU GLU SER ALA PHE ASP ALA LEU ALA GLU SEQRES 12 A 184 LEU LEU PRO ASP GLY ALA ASP ASP ILE ARG GLU HIS GLY SEQRES 13 A 184 ALA VAL PHE VAL LYS GLY LEU LYS SER LEU GLU ASP ASP SEQRES 14 A 184 VAL ARG THR ALA GLY GLU ALA LYS TYR GLU ALA GLU LYS SEQRES 15 A 184 ALA GLU MODRES 2Y44 OCS A 148 CYS CYSTEINESULFONIC ACID HET OCS A 148 9 HET IOD A1225 1 HET IOD A1226 1 HET IOD A1227 1 HET IOD A1228 1 HET GOL A1229 6 HETNAM OCS CYSTEINESULFONIC ACID HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN FORMUL 1 OCS C3 H7 N O5 S FORMUL 2 IOD 4(I 1-) FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *255(H2 O) HELIX 1 1 LYS A 40 ALA A 56 1 17 HELIX 2 2 ALA A 56 LYS A 93 1 38 HELIX 3 3 GLY A 95 THR A 147 1 53 HELIX 4 4 ASP A 152 LYS A 161 1 10 HELIX 5 5 THR A 170 LEU A 185 1 16 HELIX 6 6 GLY A 188 GLU A 224 1 37 SSBOND 1 CYS A 48 CYS A 162 1555 1555 2.06 LINK C THR A 147 N OCS A 148 1555 1555 1.33 LINK C OCS A 148 N GLU A 149 1555 1555 1.33 SITE 1 AC1 1 LYS A 160 SITE 1 AC2 5 ARG A 105 THR A 163 GLY A 164 HOH A2247 SITE 2 AC2 5 HOH A2255 CRYST1 36.184 37.795 40.680 106.17 111.75 99.50 P 1 1 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 0.027637 0.004625 0.013718 0.00000 SCALE2 0.000000 0.026826 0.010710 0.00000 SCALE3 0.000000 0.000000 0.028497 0.00000