HEADER PROTEIN BINDING 26-JUL-18 6E7E TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF INCA SOLUBLE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INCLUSION MEMBRANE PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SOLUBLE DOMAIN (UNP RESIDUES 87-246); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLAMYDIA TRACHOMATIS; SOURCE 3 ORGANISM_TAXID: 813; SOURCE 4 GENE: INCA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE FUSION, CHLAMYDIA, SNARE-LIKE PROTEIN, INCLUSION, PROTEIN KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.CINGOLANI,F.PAUMET REVDAT 3 13-MAR-24 6E7E 1 REMARK REVDAT 2 04-DEC-19 6E7E 1 REMARK REVDAT 1 10-JUL-19 6E7E 0 JRNL AUTH G.CINGOLANI,M.MCCAULEY,A.LOBLEY,A.J.BRYER,J.WESOLOWSKI, JRNL AUTH 2 D.L.GRECO,R.K.LOKAREDDY,E.RONZONE,J.R.PERILLA,F.PAUMET JRNL TITL STRUCTURAL BASIS FOR THE HOMOTYPIC FUSION OF CHLAMYDIAL JRNL TITL 2 INCLUSIONS BY THE SNARE-LIKE PROTEIN INCA. JRNL REF NAT COMMUN V. 10 2747 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31227715 JRNL DOI 10.1038/S41467-019-10806-9 REMARK 2 REMARK 2 RESOLUTION. 1.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0241 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 50533 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2010 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) : 1.12 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1971 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 47.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1376 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : -0.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.034 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.035 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.022 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.021 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1396 ; 0.012 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1298 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1875 ; 1.649 ; 1.634 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3018 ; 1.671 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 168 ; 4.556 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;31.385 ;22.561 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 272 ;12.340 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;14.610 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 182 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1543 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 291 ; 0.001 ; 0.020 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): 675 ; 1.239 ; 1.281 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 674 ; 1.223 ; 1.280 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 842 ; 1.688 ; 1.933 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 843 ; 1.690 ; 1.935 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 721 ; 2.271 ; 1.759 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 722 ; 2.269 ; 1.761 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1034 ; 2.734 ; 2.491 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1706 ; 3.523 ;17.887 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1640 ; 3.043 ;16.665 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2694 ; 2.189 ; 3.000 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.10 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6E7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000235818. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0-8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52606 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 47.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 55.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29800 REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, PH REMARK 280 8.0, 20% W/V PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 24.41100 REMARK 290 SMTRY3 2 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 DBREF 6E7E A 87 246 UNP Q50FQ0 Q50FQ0_CHLTH 87 246 SEQADV 6E7E ALA A 86 UNP Q50FQ0 EXPRESSION TAG SEQADV 6E7E ALA A 211 UNP Q50FQ0 VAL 211 ENGINEERED MUTATION SEQADV 6E7E ALA A 212 UNP Q50FQ0 VAL 212 ENGINEERED MUTATION SEQADV 6E7E LEU A 247 UNP Q50FQ0 EXPRESSION TAG SEQADV 6E7E GLU A 248 UNP Q50FQ0 EXPRESSION TAG SEQADV 6E7E HIS A 249 UNP Q50FQ0 EXPRESSION TAG SEQADV 6E7E HIS A 250 UNP Q50FQ0 EXPRESSION TAG SEQADV 6E7E HIS A 251 UNP Q50FQ0 EXPRESSION TAG SEQADV 6E7E HIS A 252 UNP Q50FQ0 EXPRESSION TAG SEQADV 6E7E HIS A 253 UNP Q50FQ0 EXPRESSION TAG SEQADV 6E7E HIS A 254 UNP Q50FQ0 EXPRESSION TAG SEQRES 1 A 169 ALA THR ALA ASN LEU HIS LEU TYR GLN ASP LEU GLN ARG SEQRES 2 A 169 GLU VAL GLY SER LEU LYS GLU ILE ASN PHE MET LEU SER SEQRES 3 A 169 VAL LEU GLN LYS GLU PHE LEU HIS LEU SER LYS GLU PHE SEQRES 4 A 169 ALA THR THR SER LYS ASP LEU SER ALA VAL SER GLN ASP SEQRES 5 A 169 PHE TYR SER CYS LEU GLN GLY PHE ARG ASP ASN TYR LYS SEQRES 6 A 169 GLY PHE GLU SER LEU LEU ASP GLU TYR LYS ASN SER THR SEQRES 7 A 169 GLU GLU MET ARG LYS LEU PHE SER GLN GLU ILE ILE ALA SEQRES 8 A 169 ASP LEU LYS GLY SER VAL ALA SER LEU ARG GLU GLU ILE SEQRES 9 A 169 ARG PHE LEU THR PRO LEU ALA GLU GLU VAL ARG ARG LEU SEQRES 10 A 169 ALA HIS ASN GLN GLN SER LEU THR ALA ALA ILE GLU GLU SEQRES 11 A 169 LEU LYS THR ILE ARG ASP SER LEU ARG ASP GLU ILE GLY SEQRES 12 A 169 GLN LEU SER GLN LEU SER LYS THR LEU THR SER GLN ILE SEQRES 13 A 169 ALA LEU GLN ARG LYS LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *197(H2 O) HELIX 1 AA1 ALA A 88 PHE A 124 1 37 HELIX 2 AA2 SER A 128 GLN A 143 1 16 HELIX 3 AA3 GLY A 144 ASN A 148 5 5 HELIX 4 AA4 TYR A 149 TYR A 159 1 11 HELIX 5 AA5 THR A 163 LYS A 168 1 6 HELIX 6 AA6 SER A 171 THR A 193 1 23 HELIX 7 AA7 PRO A 194 ASN A 205 1 12 HELIX 8 AA8 LEU A 209 HIS A 251 1 43 HELIX 9 AA9 HIS A 252 HIS A 254 5 3 CRYST1 38.323 48.822 41.738 90.00 103.91 90.00 P 1 21 1 2 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 0.026094 0.000000 0.006462 0.00000 SCALE2 0.000000 0.020483 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024683 0.00000