HEADER CELL INVASION 21-JUL-15 5CQ9 TITLE CRYSTAL STRUCTURE OF SOPD2, A TYPE III SECRETED VIRULENCE EFFECTOR TITLE 2 FROM SALMONELLA ENTERICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SECRETED EFFECTOR PROTEIN SOPD2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SALMONELLA OUTER PROTEIN D 2; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 11-MER PEPTIDE; COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM (STRAIN LT2 / SGSC1412 / SOURCE 3 ATCC 700720); SOURCE 4 ORGANISM_TAXID: 99287; SOURCE 5 STRAIN: LT2 / SGSC1412 / ATCC 700720; SOURCE 6 GENE: SOPD2, STM0972; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX-4T1; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 14 TYPHIMURIUM; SOURCE 15 ORGANISM_TAXID: 90371; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS T3SS EFFECTOR PROTEIN, STRUCTURAL GENOMICS, MONTREAL-KINGSTON KEYWDS 2 BACTERIAL STRUCTURAL GENOMICS INITIATIVE, BSGI, CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR R.SHI,M.CYGLER,MONTREAL-KINGSTON BACTERIAL STRUCTURAL GENOMICS AUTHOR 2 INITIATIVE (BSGI) REVDAT 5 27-SEP-23 5CQ9 1 REMARK REVDAT 4 08-JAN-20 5CQ9 1 REMARK REVDAT 3 13-SEP-17 5CQ9 1 REMARK REVDAT 2 16-SEP-15 5CQ9 1 JRNL REVDAT 1 09-SEP-15 5CQ9 0 JRNL AUTH V.M.D'COSTA,V.BRAUN,M.LANDEKIC,R.SHI,A.PROTEAU,L.MCDONALD, JRNL AUTH 2 M.CYGLER,S.GRINSTEIN,J.H.BRUMELL JRNL TITL SALMONELLA DISRUPTS HOST ENDOCYTIC TRAFFICKING BY JRNL TITL 2 SOPD2-MEDIATED INHIBITION OF RAB7. JRNL REF CELL REP V. 12 1508 2015 JRNL REFN ESSN 2211-1247 JRNL PMID 26299973 JRNL DOI 10.1016/J.CELREP.2015.07.063 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 15983 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) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.309 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 850 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4577 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 86.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.79000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -0.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.506 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.498 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 62.231 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 76 A 319 REMARK 3 ORIGIN FOR THE GROUP (A): 21.1611 1.3411 0.7862 REMARK 3 T TENSOR REMARK 3 T11: 0.0364 T22: 0.0687 REMARK 3 T33: 0.1479 T12: 0.0018 REMARK 3 T13: -0.0133 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.8330 L22: 2.3964 REMARK 3 L33: 1.2393 L12: 0.4032 REMARK 3 L13: 0.3583 L23: 1.1987 REMARK 3 S TENSOR REMARK 3 S11: -0.1105 S12: -0.0381 S13: 0.1305 REMARK 3 S21: -0.2485 S22: -0.0296 S23: 0.0369 REMARK 3 S31: -0.0947 S32: -0.1427 S33: 0.1401 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 76 B 319 REMARK 3 ORIGIN FOR THE GROUP (A): 3.0757 -67.1558 -22.4053 REMARK 3 T TENSOR REMARK 3 T11: 0.0189 T22: 0.0822 REMARK 3 T33: 0.1185 T12: -0.0175 REMARK 3 T13: 0.0167 T23: -0.0416 REMARK 3 L TENSOR REMARK 3 L11: 0.5379 L22: 1.5295 REMARK 3 L33: 3.4794 L12: 0.8258 REMARK 3 L13: 1.0379 L23: 1.3815 REMARK 3 S TENSOR REMARK 3 S11: 0.0486 S12: 0.0322 S13: -0.0138 REMARK 3 S21: 0.1259 S22: 0.0261 S23: -0.0298 REMARK 3 S31: 0.0513 S32: 0.0236 S33: -0.0747 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 36 A 62 REMARK 3 RESIDUE RANGE : B 36 B 63 REMARK 3 RESIDUE RANGE : D 15 D 25 REMARK 3 RESIDUE RANGE : C 16 C 24 REMARK 3 ORIGIN FOR THE GROUP (A): 20.6949 -34.9487 -14.4469 REMARK 3 T TENSOR REMARK 3 T11: 0.6693 T22: 0.6487 REMARK 3 T33: 0.8169 T12: -0.0434 REMARK 3 T13: 0.0377 T23: -0.0370 REMARK 3 L TENSOR REMARK 3 L11: 1.0592 L22: 0.3913 REMARK 3 L33: 0.1255 L12: -0.5636 REMARK 3 L13: -0.2864 L23: 0.1517 REMARK 3 S TENSOR REMARK 3 S11: -0.3914 S12: -0.3761 S13: -0.1151 REMARK 3 S21: 0.3011 S22: 0.2613 S23: -0.1662 REMARK 3 S31: 0.1533 S32: 0.1940 S33: 0.1301 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 5CQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000212025. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16873 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.73900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: 5CPC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CHES PH 9.5, 20% PEG 8000, REMARK 280 MICROBATCH, TEMPERATURE 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 44.90000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 MET A 1 REMARK 465 PRO A 2 REMARK 465 VAL A 3 REMARK 465 THR A 4 REMARK 465 LEU A 5 REMARK 465 SER A 6 REMARK 465 PHE A 7 REMARK 465 GLY A 8 REMARK 465 ASN A 9 REMARK 465 ARG A 10 REMARK 465 HIS A 11 REMARK 465 ASN A 12 REMARK 465 TYR A 13 REMARK 465 GLU A 14 REMARK 465 ILE A 15 REMARK 465 ASN A 16 REMARK 465 HIS A 17 REMARK 465 SER A 18 REMARK 465 ARG A 19 REMARK 465 LEU A 20 REMARK 465 ALA A 21 REMARK 465 ARG A 22 REMARK 465 LEU A 23 REMARK 465 MET A 24 REMARK 465 SER A 25 REMARK 465 PRO A 26 REMARK 465 ASP A 27 REMARK 465 LYS A 28 REMARK 465 GLU A 29 REMARK 465 GLU A 30 REMARK 465 ALA A 31 REMARK 465 LEU A 32 REMARK 465 TYR A 33 REMARK 465 MET A 34 REMARK 465 GLY A 35 REMARK 465 CYS A 63 REMARK 465 GLU A 64 REMARK 465 ARG A 65 REMARK 465 GLU A 66 REMARK 465 ASN A 67 REMARK 465 GLN A 68 REMARK 465 ALA A 69 REMARK 465 GLU A 70 REMARK 465 LEU A 71 REMARK 465 ASN A 72 REMARK 465 VAL A 73 REMARK 465 ASP A 74 REMARK 465 ILE A 75 REMARK 465 SER A 262 REMARK 465 SER A 263 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 VAL B 3 REMARK 465 THR B 4 REMARK 465 LEU B 5 REMARK 465 SER B 6 REMARK 465 PHE B 7 REMARK 465 GLY B 8 REMARK 465 ASN B 9 REMARK 465 ARG B 10 REMARK 465 HIS B 11 REMARK 465 ASN B 12 REMARK 465 TYR B 13 REMARK 465 GLU B 14 REMARK 465 ILE B 15 REMARK 465 ASN B 16 REMARK 465 HIS B 17 REMARK 465 SER B 18 REMARK 465 ARG B 19 REMARK 465 LEU B 20 REMARK 465 ALA B 21 REMARK 465 ARG B 22 REMARK 465 LEU B 23 REMARK 465 MET B 24 REMARK 465 SER B 25 REMARK 465 PRO B 26 REMARK 465 ASP B 27 REMARK 465 LYS B 28 REMARK 465 GLU B 29 REMARK 465 GLU B 30 REMARK 465 ALA B 31 REMARK 465 LEU B 32 REMARK 465 TYR B 33 REMARK 465 MET B 34 REMARK 465 GLY B 35 REMARK 465 GLU B 64 REMARK 465 ARG B 65 REMARK 465 GLU B 66 REMARK 465 ASN B 67 REMARK 465 GLN B 68 REMARK 465 ALA B 69 REMARK 465 GLU B 70 REMARK 465 LEU B 71 REMARK 465 ASN B 72 REMARK 465 VAL B 73 REMARK 465 ASP B 74 REMARK 465 ILE B 75 REMARK 465 SER B 263 REMARK 465 ASP B 264 REMARK 465 UNK C 25 REMARK 465 UNK C 26 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 59 CG CD1 CD2 REMARK 470 TRP B 37 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 37 CZ3 CH2 REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 LEU B 59 CG CD1 CD2 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 TRP A 37 -82.14 80.04 REMARK 500 CYS A 43 -73.90 -69.86 REMARK 500 ARG A 45 129.96 -34.18 REMARK 500 VAL A 55 13.01 -151.99 REMARK 500 ALA A 91 -53.17 -166.87 REMARK 500 ASN A 92 131.06 72.94 REMARK 500 PRO A 93 172.34 -46.30 REMARK 500 SER A 94 -24.87 71.59 REMARK 500 GLN A 107 17.85 53.32 REMARK 500 ASP A 115 -130.82 51.34 REMARK 500 TYR A 161 71.87 -119.39 REMARK 500 GLU A 166 160.04 -46.30 REMARK 500 PHE A 168 107.57 81.45 REMARK 500 GLN A 219 50.92 -143.07 REMARK 500 ASN A 224 113.48 -173.29 REMARK 500 SER A 260 114.82 -171.92 REMARK 500 GLU A 267 -81.60 -55.85 REMARK 500 SER A 274 0.22 -69.47 REMARK 500 SER A 312 -21.47 83.85 REMARK 500 MET A 317 161.95 -42.31 REMARK 500 THR B 46 -57.64 -29.54 REMARK 500 HIS B 47 -71.50 -71.94 REMARK 500 LYS B 48 -65.98 -23.24 REMARK 500 GLU B 54 -39.15 -28.70 REMARK 500 TYR B 57 -70.50 -53.10 REMARK 500 ALA B 91 174.99 170.66 REMARK 500 SER B 94 -29.69 83.88 REMARK 500 GLN B 107 18.13 58.68 REMARK 500 ASP B 115 43.76 38.20 REMARK 500 VAL B 118 102.97 -58.93 REMARK 500 GLU B 140 170.79 -58.81 REMARK 500 PRO B 162 -112.19 -53.16 REMARK 500 GLU B 163 13.70 -59.16 REMARK 500 LEU B 165 -61.50 -27.46 REMARK 500 PHE B 168 -49.79 -177.02 REMARK 500 ALA B 169 -152.38 167.11 REMARK 500 ASN B 170 -53.02 62.90 REMARK 500 MET B 220 -8.04 72.13 REMARK 500 SER B 260 -166.21 -169.49 REMARK 500 SER B 274 13.37 -69.26 REMARK 500 LYS B 311 -147.27 87.10 REMARK 500 CYS B 314 103.68 -162.99 REMARK 500 MET B 317 170.83 -49.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 55 LEU A 56 137.94 REMARK 500 GLY A 116 LYS A 117 -148.90 REMARK 500 VAL B 55 LEU B 56 142.04 REMARK 500 GLU B 163 LEU B 164 149.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CPC RELATED DB: PDB REMARK 900 5CPC CONTAINS THE STRUCTURE OF SOPD REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHOR BELIEVES THAT CHAIN C AND CHAIN D ARE PART OF THE SOPD2 REMARK 999 PROTEIN. THEY ARE BUILT BASED ON THE ELECTRON DENSITY MAPS BUT THE REMARK 999 SIDE CHAINS OF THESE TWO SEGMENTS ARE NOT CLEAR DUE TO THE POOR REMARK 999 QUALITY OF THE MAPS THEREFORE RESIDUES IDENTITY CAN NOT BE ASSIGNED REMARK 999 UNAMBIGUOUSLY. VERY LIKELY THESE ARE PART OF THE FLEXIBLE N- REMARK 999 TERMINAL (RESIDUES 1-35) SEGMENT, I.E., CHAIN C IS PART OF THE N- REMARK 999 TERMINAL OF CHAIN A AND CHAIN D IS PART OF THE N-TERMINAL OF CHAIN REMARK 999 B. DBREF 5CQ9 A 1 319 UNP Q8ZQC8 SOPD2_SALTY 1 319 DBREF 5CQ9 B 1 319 UNP Q8ZQC8 SOPD2_SALTY 1 319 DBREF 5CQ9 C 16 26 PDB 5CQ9 5CQ9 16 26 DBREF 5CQ9 D 15 25 PDB 5CQ9 5CQ9 15 25 SEQRES 1 A 319 MET PRO VAL THR LEU SER PHE GLY ASN ARG HIS ASN TYR SEQRES 2 A 319 GLU ILE ASN HIS SER ARG LEU ALA ARG LEU MET SER PRO SEQRES 3 A 319 ASP LYS GLU GLU ALA LEU TYR MET GLY VAL TRP ASP ARG SEQRES 4 A 319 PHE LYS ASP CYS PHE ARG THR HIS LYS LYS GLN GLU VAL SEQRES 5 A 319 LEU GLU VAL LEU TYR THR LEU ILE HIS GLY CYS GLU ARG SEQRES 6 A 319 GLU ASN GLN ALA GLU LEU ASN VAL ASP ILE THR GLY MET SEQRES 7 A 319 GLU LYS ILE HIS ALA PHE THR GLN LEU LYS GLU TYR ALA SEQRES 8 A 319 ASN PRO SER GLN GLN ASP ARG PHE VAL MET ARG PHE ASP SEQRES 9 A 319 MET ASN GLN THR GLN VAL LEU PHE GLU ILE ASP GLY LYS SEQRES 10 A 319 VAL ILE ASP LYS CYS ASN LEU HIS ARG LEU LEU ASN VAL SEQRES 11 A 319 SER GLU ASN CYS ILE PHE LYS VAL MET GLU GLU ASP GLU SEQRES 12 A 319 GLU GLU LEU PHE LEU LYS ILE CYS ILE LYS TYR GLY GLU SEQRES 13 A 319 LYS ILE SER ARG TYR PRO GLU LEU LEU GLU GLY PHE ALA SEQRES 14 A 319 ASN LYS LEU LYS ASP ALA VAL ASN GLU ASP ASP ASP VAL SEQRES 15 A 319 LYS ASP GLU VAL TYR LYS LEU MET ARG SER GLY GLU ASP SEQRES 16 A 319 ARG LYS MET GLU CYS VAL GLU TRP ASN GLY THR LEU THR SEQRES 17 A 319 GLU GLU GLU LYS ASN LYS LEU ARG CYS LEU GLN MET GLY SEQRES 18 A 319 SER PHE ASN ILE THR THR GLN PHE PHE LYS ILE GLY TYR SEQRES 19 A 319 TRP GLU LEU GLU GLY GLU VAL LEU PHE ASP MET VAL HIS SEQRES 20 A 319 PRO THR LEU SER TYR LEU LEU GLN ALA TYR LYS PRO SER SEQRES 21 A 319 LEU SER SER ASP LEU ILE GLU THR ASN THR MET LEU PHE SEQRES 22 A 319 SER ASP VAL LEU ASN LYS ASP TYR ASP ASP TYR GLN ASN SEQRES 23 A 319 ASN LYS ARG GLU ILE ASP ALA ILE LEU ARG ARG ILE TYR SEQRES 24 A 319 ARG SER HIS ASN ASN THR LEU PHE ILE SER GLU LYS SER SEQRES 25 A 319 SER CYS ARG ASN MET LEU ILE SEQRES 1 B 319 MET PRO VAL THR LEU SER PHE GLY ASN ARG HIS ASN TYR SEQRES 2 B 319 GLU ILE ASN HIS SER ARG LEU ALA ARG LEU MET SER PRO SEQRES 3 B 319 ASP LYS GLU GLU ALA LEU TYR MET GLY VAL TRP ASP ARG SEQRES 4 B 319 PHE LYS ASP CYS PHE ARG THR HIS LYS LYS GLN GLU VAL SEQRES 5 B 319 LEU GLU VAL LEU TYR THR LEU ILE HIS GLY CYS GLU ARG SEQRES 6 B 319 GLU ASN GLN ALA GLU LEU ASN VAL ASP ILE THR GLY MET SEQRES 7 B 319 GLU LYS ILE HIS ALA PHE THR GLN LEU LYS GLU TYR ALA SEQRES 8 B 319 ASN PRO SER GLN GLN ASP ARG PHE VAL MET ARG PHE ASP SEQRES 9 B 319 MET ASN GLN THR GLN VAL LEU PHE GLU ILE ASP GLY LYS SEQRES 10 B 319 VAL ILE ASP LYS CYS ASN LEU HIS ARG LEU LEU ASN VAL SEQRES 11 B 319 SER GLU ASN CYS ILE PHE LYS VAL MET GLU GLU ASP GLU SEQRES 12 B 319 GLU GLU LEU PHE LEU LYS ILE CYS ILE LYS TYR GLY GLU SEQRES 13 B 319 LYS ILE SER ARG TYR PRO GLU LEU LEU GLU GLY PHE ALA SEQRES 14 B 319 ASN LYS LEU LYS ASP ALA VAL ASN GLU ASP ASP ASP VAL SEQRES 15 B 319 LYS ASP GLU VAL TYR LYS LEU MET ARG SER GLY GLU ASP SEQRES 16 B 319 ARG LYS MET GLU CYS VAL GLU TRP ASN GLY THR LEU THR SEQRES 17 B 319 GLU GLU GLU LYS ASN LYS LEU ARG CYS LEU GLN MET GLY SEQRES 18 B 319 SER PHE ASN ILE THR THR GLN PHE PHE LYS ILE GLY TYR SEQRES 19 B 319 TRP GLU LEU GLU GLY GLU VAL LEU PHE ASP MET VAL HIS SEQRES 20 B 319 PRO THR LEU SER TYR LEU LEU GLN ALA TYR LYS PRO SER SEQRES 21 B 319 LEU SER SER ASP LEU ILE GLU THR ASN THR MET LEU PHE SEQRES 22 B 319 SER ASP VAL LEU ASN LYS ASP TYR ASP ASP TYR GLN ASN SEQRES 23 B 319 ASN LYS ARG GLU ILE ASP ALA ILE LEU ARG ARG ILE TYR SEQRES 24 B 319 ARG SER HIS ASN ASN THR LEU PHE ILE SER GLU LYS SER SEQRES 25 B 319 SER CYS ARG ASN MET LEU ILE SEQRES 1 C 11 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 1 D 11 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK HELIX 1 AA1 TRP A 37 ARG A 45 1 9 HELIX 2 AA2 HIS A 47 GLY A 62 1 16 HELIX 3 AA3 GLY A 77 TYR A 90 1 14 HELIX 4 AA4 GLN A 95 ASP A 97 5 3 HELIX 5 AA5 LEU A 124 LEU A 128 1 5 HELIX 6 AA6 GLU A 140 TYR A 161 1 22 HELIX 7 AA7 PRO A 162 LEU A 165 5 4 HELIX 8 AA8 ALA A 169 ASP A 179 1 11 HELIX 9 AA9 ASP A 179 ARG A 191 1 13 HELIX 10 AB1 THR A 208 LEU A 215 1 8 HELIX 11 AB2 ARG A 216 MET A 220 5 5 HELIX 12 AB3 HIS A 247 ALA A 256 1 10 HELIX 13 AB4 ILE A 266 PHE A 273 1 8 HELIX 14 AB5 PHE A 273 ASN A 287 1 15 HELIX 15 AB6 ASN A 287 HIS A 302 1 16 HELIX 16 AB7 TRP B 37 HIS B 61 1 25 HELIX 17 AB8 GLY B 77 TYR B 90 1 14 HELIX 18 AB9 LEU B 124 LEU B 128 1 5 HELIX 19 AC1 GLU B 140 TYR B 161 1 22 HELIX 20 AC2 ASN B 170 ASP B 179 1 10 HELIX 21 AC3 ASP B 179 ARG B 191 1 13 HELIX 22 AC4 THR B 208 LEU B 215 1 8 HELIX 23 AC5 ARG B 216 MET B 220 5 5 HELIX 24 AC6 ASN B 224 GLN B 228 5 5 HELIX 25 AC7 HIS B 247 ALA B 256 1 10 HELIX 26 AC8 ILE B 266 SER B 274 1 9 HELIX 27 AC9 VAL B 276 ASN B 287 1 12 HELIX 28 AD1 ASN B 287 HIS B 302 1 16 HELIX 29 AD2 UNK C 17 UNK C 24 1 8 HELIX 30 AD3 UNK D 16 UNK D 25 1 10 SHEET 1 AA1 3 PHE A 99 PHE A 103 0 SHEET 2 AA1 3 GLN A 109 ILE A 114 -1 O LEU A 111 N ARG A 102 SHEET 3 AA1 3 LYS A 117 ASN A 123 -1 O CYS A 122 N VAL A 110 SHEET 1 AA2 2 VAL A 201 GLU A 202 0 SHEET 2 AA2 2 ILE A 308 SER A 309 1 O SER A 309 N VAL A 201 SHEET 1 AA3 2 ILE A 232 LEU A 237 0 SHEET 2 AA3 2 GLU A 240 MET A 245 -1 O ASP A 244 N GLY A 233 SHEET 1 AA4 3 PHE B 99 PHE B 103 0 SHEET 2 AA4 3 GLN B 109 ILE B 114 -1 O LEU B 111 N ARG B 102 SHEET 3 AA4 3 LYS B 117 ASN B 123 -1 O ILE B 119 N PHE B 112 SHEET 1 AA5 2 VAL B 201 GLU B 202 0 SHEET 2 AA5 2 ILE B 308 SER B 309 1 O SER B 309 N VAL B 201 SHEET 1 AA6 2 ILE B 232 LEU B 237 0 SHEET 2 AA6 2 GLU B 240 MET B 245 -1 O LEU B 242 N TRP B 235 SSBOND 1 CYS B 200 CYS B 314 1555 1555 2.06 LINK C UNK C 16 N UNK C 17 1555 1555 1.33 LINK C UNK C 17 N UNK C 18 1555 1555 1.34 LINK C UNK C 18 N UNK C 19 1555 1555 1.33 LINK C UNK C 19 N UNK C 20 1555 1555 1.34 LINK C UNK C 20 N UNK C 21 1555 1555 1.33 LINK C UNK C 21 N UNK C 22 1555 1555 1.34 LINK C UNK C 22 N UNK C 23 1555 1555 1.34 LINK C UNK C 23 N UNK C 24 1555 1555 1.33 LINK C UNK D 15 N UNK D 16 1555 1555 1.34 LINK C UNK D 16 N UNK D 17 1555 1555 1.33 LINK C UNK D 17 N UNK D 18 1555 1555 1.33 LINK C UNK D 18 N UNK D 19 1555 1555 1.33 LINK C UNK D 19 N UNK D 20 1555 1555 1.33 LINK C UNK D 20 N UNK D 21 1555 1555 1.33 LINK C UNK D 21 N UNK D 22 1555 1555 1.33 LINK C UNK D 22 N UNK D 23 1555 1555 1.34 LINK C UNK D 23 N UNK D 24 1555 1555 1.34 LINK C UNK D 24 N UNK D 25 1555 1555 1.33 CRYST1 70.613 89.800 75.595 90.00 117.15 90.00 P 1 21 1 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 0.014162 0.000000 0.007261 0.00000 SCALE2 0.000000 0.011136 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014866 0.00000