HEADER SIGNALING PROTEIN 24-JAN-23 7FSR TITLE SDCBP PANDDA ANALYSIS GROUP DEPOSITION -- THE PDZ DOMANS OF SDCBP IN TITLE 2 COMPLEX WITH Z54615640 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTENIN-1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: MELANOMA DIFFERENTIATION-ASSOCIATED PROTEIN 9,MDA-9,PRO-TGF- COMPND 5 ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 18,TACIP18,SCAFFOLD COMPND 6 PROTEIN PBP1,SYNDECAN-BINDING PROTEIN 1; COMPND 7 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: SDCBP, MDA9, SYCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.J.BRADSHAW,V.L.KATIS,C.BOUNTRA,F.VON DELFT,P.E.BRENNAN REVDAT 2 22-MAY-24 7FSR 1 REMARK REVDAT 1 15-FEB-23 7FSR 0 JRNL AUTH W.J.BRADSHAW,V.L.KATIS,C.BOUNTRA,F.VON DELFT,P.E.BRENNAN JRNL TITL SDCBP PANDDA ANALYSIS GROUP DEPOSITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 113.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 38950 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1985 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) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2770 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.3970 REMARK 3 BIN FREE R VALUE SET COUNT : 135 REMARK 3 BIN FREE R VALUE : 0.4500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5908 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 97 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.03000 REMARK 3 B22 (A**2) : -3.02000 REMARK 3 B33 (A**2) : 3.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.582 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.298 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.349 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.454 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 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): 9281 ; 0.008 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 7873 ; 0.002 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10813 ; 1.616 ; 1.643 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18259 ; 1.193 ; 1.597 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1067 ; 8.054 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 364 ;36.030 ;23.352 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1534 ;18.447 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;18.239 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1108 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9350 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1744 ; 0.002 ; 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): 4750 ; 2.253 ; 4.829 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4595 ; 2.287 ; 4.777 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5173 ; 4.006 ; 7.053 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 : 4 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 108 A 298 REMARK 3 ORIGIN FOR THE GROUP (A): -28.926 3.091 -45.107 REMARK 3 T TENSOR REMARK 3 T11: 0.0434 T22: 0.1761 REMARK 3 T33: 0.1851 T12: 0.0387 REMARK 3 T13: 0.0378 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 1.9105 L22: 0.0661 REMARK 3 L33: 0.8846 L12: -0.2115 REMARK 3 L13: -0.5806 L23: 0.2302 REMARK 3 S TENSOR REMARK 3 S11: 0.1149 S12: -0.0407 S13: -0.2392 REMARK 3 S21: -0.0435 S22: -0.0680 S23: 0.0181 REMARK 3 S31: -0.1805 S32: -0.2063 S33: -0.0469 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 106 B 298 REMARK 3 ORIGIN FOR THE GROUP (A): -46.335 -14.790 -12.893 REMARK 3 T TENSOR REMARK 3 T11: 0.0129 T22: 0.1457 REMARK 3 T33: 0.2741 T12: -0.0223 REMARK 3 T13: 0.0021 T23: -0.0190 REMARK 3 L TENSOR REMARK 3 L11: 0.6563 L22: 0.3206 REMARK 3 L33: 0.8269 L12: 0.1575 REMARK 3 L13: -0.0623 L23: -0.4634 REMARK 3 S TENSOR REMARK 3 S11: -0.0037 S12: 0.1871 S13: -0.1805 REMARK 3 S21: 0.0515 S22: -0.0325 S23: -0.1396 REMARK 3 S31: -0.0885 S32: 0.0488 S33: 0.0362 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 106 C 298 REMARK 3 ORIGIN FOR THE GROUP (A): -3.004 2.255 -50.821 REMARK 3 T TENSOR REMARK 3 T11: 0.1022 T22: 0.1021 REMARK 3 T33: 0.1817 T12: -0.0621 REMARK 3 T13: 0.0663 T23: -0.0343 REMARK 3 L TENSOR REMARK 3 L11: 0.6840 L22: 0.3415 REMARK 3 L33: 1.9884 L12: -0.0211 REMARK 3 L13: -0.2946 L23: 0.7594 REMARK 3 S TENSOR REMARK 3 S11: 0.1422 S12: -0.1241 S13: -0.1257 REMARK 3 S21: -0.1192 S22: 0.0449 S23: -0.1223 REMARK 3 S31: -0.2484 S32: 0.0928 S33: -0.1871 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 108 D 298 REMARK 3 RESIDUE RANGE : D 301 D 301 REMARK 3 ORIGIN FOR THE GROUP (A): 9.265 -13.999 -5.329 REMARK 3 T TENSOR REMARK 3 T11: 0.0346 T22: 0.0879 REMARK 3 T33: 0.2059 T12: 0.0222 REMARK 3 T13: 0.0203 T23: -0.0148 REMARK 3 L TENSOR REMARK 3 L11: 0.3520 L22: 1.0103 REMARK 3 L33: 0.6739 L12: 0.1942 REMARK 3 L13: -0.1167 L23: -0.5188 REMARK 3 S TENSOR REMARK 3 S11: 0.0626 S12: 0.1230 S13: -0.0295 REMARK 3 S21: 0.1109 S22: -0.0180 S23: 0.1280 REMARK 3 S31: 0.0108 S32: 0.0969 S33: -0.0446 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 7FSR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1001405300. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9179 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40973 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 113.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 1.37100 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 8BLU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MORPHEUS AMINO ACIDS, 100 MM REMARK 280 MORPHEUS BUFFER SYSTEM 1, 43% MORPHEUS PRECIPITANT MIX 3, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 24.74650 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, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 104 REMARK 465 MET A 105 REMARK 465 ALA A 106 REMARK 465 GLU A 107 REMARK 465 SER B 104 REMARK 465 MET B 105 REMARK 465 SER C 104 REMARK 465 MET C 105 REMARK 465 SER D 104 REMARK 465 MET D 105 REMARK 465 ALA D 106 REMARK 465 GLU D 107 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 NH1 ARG D 197 O HOH D 401 2.14 REMARK 500 O ASN D 215 O HOH D 402 2.15 REMARK 500 O HOH C 435 O HOH C 437 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 119 124.98 -37.64 REMARK 500 ASP A 120 -173.69 -69.73 REMARK 500 ASN A 144 -2.96 77.12 REMARK 500 ALA A 167 117.29 -34.82 REMARK 500 PHE A 182 36.15 -68.22 REMARK 500 ARG A 193 66.68 16.20 REMARK 500 ARG A 281 50.39 84.46 REMARK 500 MET A 282 91.16 -169.76 REMARK 500 ASN B 134 17.02 59.57 REMARK 500 ARG B 193 64.32 23.12 REMARK 500 ASP B 224 50.69 36.96 REMARK 500 PRO B 284 -24.99 -33.46 REMARK 500 GLU C 107 116.69 173.20 REMARK 500 ASN C 144 50.00 36.45 REMARK 500 PHE C 182 -13.83 -146.00 REMARK 500 ARG C 193 63.80 16.49 REMARK 500 ASP C 204 -174.79 -61.81 REMARK 500 THR C 206 0.31 -67.01 REMARK 500 LYS C 214 118.00 -167.44 REMARK 500 ASP C 224 3.78 82.43 REMARK 500 PRO C 296 -76.51 -73.56 REMARK 500 ASP D 120 -163.57 -71.76 REMARK 500 ALA D 143 118.44 -36.71 REMARK 500 ASN D 144 0.65 82.43 REMARK 500 ARG D 193 59.79 31.32 REMARK 500 ASP D 204 -165.17 -73.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 424 DISTANCE = 6.48 ANGSTROMS DBREF 7FSR A 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSR B 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSR C 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSR D 106 298 UNP O00560 SDCB1_HUMAN 106 298 SEQADV 7FSR SER A 104 UNP O00560 EXPRESSION TAG SEQADV 7FSR MET A 105 UNP O00560 EXPRESSION TAG SEQADV 7FSR SER B 104 UNP O00560 EXPRESSION TAG SEQADV 7FSR MET B 105 UNP O00560 EXPRESSION TAG SEQADV 7FSR SER C 104 UNP O00560 EXPRESSION TAG SEQADV 7FSR MET C 105 UNP O00560 EXPRESSION TAG SEQADV 7FSR SER D 104 UNP O00560 EXPRESSION TAG SEQADV 7FSR MET D 105 UNP O00560 EXPRESSION TAG SEQRES 1 A 195 SER MET ALA GLU ILE LYS GLN GLY ILE ARG GLU VAL ILE SEQRES 2 A 195 LEU CYS LYS ASP GLN ASP GLY LYS ILE GLY LEU ARG LEU SEQRES 3 A 195 LYS SER ILE ASP ASN GLY ILE PHE VAL GLN LEU VAL GLN SEQRES 4 A 195 ALA ASN SER PRO ALA SER LEU VAL GLY LEU ARG PHE GLY SEQRES 5 A 195 ASP GLN VAL LEU GLN ILE ASN GLY GLU ASN CYS ALA GLY SEQRES 6 A 195 TRP SER SER ASP LYS ALA HIS LYS VAL LEU LYS GLN ALA SEQRES 7 A 195 PHE GLY GLU LYS ILE THR MET THR ILE ARG ASP ARG PRO SEQRES 8 A 195 PHE GLU ARG THR ILE THR MET HIS LYS ASP SER THR GLY SEQRES 9 A 195 HIS VAL GLY PHE ILE PHE LYS ASN GLY LYS ILE THR SER SEQRES 10 A 195 ILE VAL LYS ASP SER SER ALA ALA ARG ASN GLY LEU LEU SEQRES 11 A 195 THR GLU HIS ASN ILE CYS GLU ILE ASN GLY GLN ASN VAL SEQRES 12 A 195 ILE GLY LEU LYS ASP SER GLN ILE ALA ASP ILE LEU SER SEQRES 13 A 195 THR SER GLY THR VAL VAL THR ILE THR ILE MET PRO ALA SEQRES 14 A 195 PHE ILE PHE GLU HIS ILE ILE LYS ARG MET ALA PRO SER SEQRES 15 A 195 ILE MET LYS SER LEU MET ASP HIS THR ILE PRO GLU VAL SEQRES 1 B 195 SER MET ALA GLU ILE LYS GLN GLY ILE ARG GLU VAL ILE SEQRES 2 B 195 LEU CYS LYS ASP GLN ASP GLY LYS ILE GLY LEU ARG LEU SEQRES 3 B 195 LYS SER ILE ASP ASN GLY ILE PHE VAL GLN LEU VAL GLN SEQRES 4 B 195 ALA ASN SER PRO ALA SER LEU VAL GLY LEU ARG PHE GLY SEQRES 5 B 195 ASP GLN VAL LEU GLN ILE ASN GLY GLU ASN CYS ALA GLY SEQRES 6 B 195 TRP SER SER ASP LYS ALA HIS LYS VAL LEU LYS GLN ALA SEQRES 7 B 195 PHE GLY GLU LYS ILE THR MET THR ILE ARG ASP ARG PRO SEQRES 8 B 195 PHE GLU ARG THR ILE THR MET HIS LYS ASP SER THR GLY SEQRES 9 B 195 HIS VAL GLY PHE ILE PHE LYS ASN GLY LYS ILE THR SER SEQRES 10 B 195 ILE VAL LYS ASP SER SER ALA ALA ARG ASN GLY LEU LEU SEQRES 11 B 195 THR GLU HIS ASN ILE CYS GLU ILE ASN GLY GLN ASN VAL SEQRES 12 B 195 ILE GLY LEU LYS ASP SER GLN ILE ALA ASP ILE LEU SER SEQRES 13 B 195 THR SER GLY THR VAL VAL THR ILE THR ILE MET PRO ALA SEQRES 14 B 195 PHE ILE PHE GLU HIS ILE ILE LYS ARG MET ALA PRO SER SEQRES 15 B 195 ILE MET LYS SER LEU MET ASP HIS THR ILE PRO GLU VAL SEQRES 1 C 195 SER MET ALA GLU ILE LYS GLN GLY ILE ARG GLU VAL ILE SEQRES 2 C 195 LEU CYS LYS ASP GLN ASP GLY LYS ILE GLY LEU ARG LEU SEQRES 3 C 195 LYS SER ILE ASP ASN GLY ILE PHE VAL GLN LEU VAL GLN SEQRES 4 C 195 ALA ASN SER PRO ALA SER LEU VAL GLY LEU ARG PHE GLY SEQRES 5 C 195 ASP GLN VAL LEU GLN ILE ASN GLY GLU ASN CYS ALA GLY SEQRES 6 C 195 TRP SER SER ASP LYS ALA HIS LYS VAL LEU LYS GLN ALA SEQRES 7 C 195 PHE GLY GLU LYS ILE THR MET THR ILE ARG ASP ARG PRO SEQRES 8 C 195 PHE GLU ARG THR ILE THR MET HIS LYS ASP SER THR GLY SEQRES 9 C 195 HIS VAL GLY PHE ILE PHE LYS ASN GLY LYS ILE THR SER SEQRES 10 C 195 ILE VAL LYS ASP SER SER ALA ALA ARG ASN GLY LEU LEU SEQRES 11 C 195 THR GLU HIS ASN ILE CYS GLU ILE ASN GLY GLN ASN VAL SEQRES 12 C 195 ILE GLY LEU LYS ASP SER GLN ILE ALA ASP ILE LEU SER SEQRES 13 C 195 THR SER GLY THR VAL VAL THR ILE THR ILE MET PRO ALA SEQRES 14 C 195 PHE ILE PHE GLU HIS ILE ILE LYS ARG MET ALA PRO SER SEQRES 15 C 195 ILE MET LYS SER LEU MET ASP HIS THR ILE PRO GLU VAL SEQRES 1 D 195 SER MET ALA GLU ILE LYS GLN GLY ILE ARG GLU VAL ILE SEQRES 2 D 195 LEU CYS LYS ASP GLN ASP GLY LYS ILE GLY LEU ARG LEU SEQRES 3 D 195 LYS SER ILE ASP ASN GLY ILE PHE VAL GLN LEU VAL GLN SEQRES 4 D 195 ALA ASN SER PRO ALA SER LEU VAL GLY LEU ARG PHE GLY SEQRES 5 D 195 ASP GLN VAL LEU GLN ILE ASN GLY GLU ASN CYS ALA GLY SEQRES 6 D 195 TRP SER SER ASP LYS ALA HIS LYS VAL LEU LYS GLN ALA SEQRES 7 D 195 PHE GLY GLU LYS ILE THR MET THR ILE ARG ASP ARG PRO SEQRES 8 D 195 PHE GLU ARG THR ILE THR MET HIS LYS ASP SER THR GLY SEQRES 9 D 195 HIS VAL GLY PHE ILE PHE LYS ASN GLY LYS ILE THR SER SEQRES 10 D 195 ILE VAL LYS ASP SER SER ALA ALA ARG ASN GLY LEU LEU SEQRES 11 D 195 THR GLU HIS ASN ILE CYS GLU ILE ASN GLY GLN ASN VAL SEQRES 12 D 195 ILE GLY LEU LYS ASP SER GLN ILE ALA ASP ILE LEU SER SEQRES 13 D 195 THR SER GLY THR VAL VAL THR ILE THR ILE MET PRO ALA SEQRES 14 D 195 PHE ILE PHE GLU HIS ILE ILE LYS ARG MET ALA PRO SER SEQRES 15 D 195 ILE MET LYS SER LEU MET ASP HIS THR ILE PRO GLU VAL HET EDO A 301 4 HET EDO B 301 4 HET EDO B 302 4 HET DGL B 303 10 HET EDO C 301 4 HET EDO C 302 4 HET EDO C 303 4 HET GLY C 304 5 HET YFN D 301 14 HET EDO D 302 4 HET EDO D 303 4 HET SO4 D 304 5 HET SO4 D 305 5 HET SO4 D 306 5 HET ALA D 307 6 HET DGL D 308 10 HET GLY D 309 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM DGL D-GLUTAMIC ACID HETNAM GLY GLYCINE HETNAM YFN N-[(3S)-3-METHYL-1,1-DIOXO-1LAMBDA~6~-THIOLAN-3- HETNAM 2 YFN YL]CYCLOPROPANECARBOXAMIDE HETNAM SO4 SULFATE ION HETNAM ALA ALANINE HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 8(C2 H6 O2) FORMUL 8 DGL 2(C5 H9 N O4) FORMUL 12 GLY 2(C2 H5 N O2) FORMUL 13 YFN C9 H15 N O3 S FORMUL 16 SO4 3(O4 S 2-) FORMUL 19 ALA C3 H7 N O2 FORMUL 22 HOH *246(H2 O) HELIX 1 AA1 SER A 145 VAL A 150 1 6 HELIX 2 AA2 SER A 170 LYS A 179 1 10 HELIX 3 AA3 SER A 225 GLY A 231 1 7 HELIX 4 AA4 LYS A 250 THR A 260 1 11 HELIX 5 AA5 ALA A 272 LYS A 280 1 9 HELIX 6 AA6 ALA A 283 MET A 291 1 9 HELIX 7 AA7 SER B 145 VAL B 150 1 6 HELIX 8 AA8 SER B 170 GLN B 180 1 11 HELIX 9 AA9 SER B 225 ASN B 230 1 6 HELIX 10 AB1 LYS B 250 SER B 261 1 12 HELIX 11 AB2 ALA B 272 LYS B 280 1 9 HELIX 12 AB3 ALA B 283 LEU B 290 1 8 HELIX 13 AB4 SER C 145 VAL C 150 1 6 HELIX 14 AB5 SER C 170 GLN C 180 1 11 HELIX 15 AB6 SER C 225 GLY C 231 1 7 HELIX 16 AB7 LYS C 250 THR C 260 1 11 HELIX 17 AB8 ALA C 272 ILE C 279 1 8 HELIX 18 AB9 ALA C 283 MET C 291 1 9 HELIX 19 AC1 SER D 145 VAL D 150 1 6 HELIX 20 AC2 SER D 170 GLN D 180 1 11 HELIX 21 AC3 SER D 225 GLY D 231 1 7 HELIX 22 AC4 LYS D 250 THR D 260 1 11 HELIX 23 AC5 ALA D 272 LYS D 280 1 9 HELIX 24 AC6 ALA D 283 MET D 291 1 9 SHEET 1 AA1 4 ILE A 112 LEU A 117 0 SHEET 2 AA1 4 ILE A 186 ARG A 191 -1 O ILE A 190 N ARG A 113 SHEET 3 AA1 4 GLN A 157 ILE A 161 -1 N LEU A 159 O THR A 189 SHEET 4 AA1 4 GLU A 164 ASN A 165 -1 O GLU A 164 N ILE A 161 SHEET 1 AA2 2 LEU A 127 ILE A 132 0 SHEET 2 AA2 2 GLY A 135 VAL A 141 -1 O PHE A 137 N LYS A 130 SHEET 1 AA3 5 ARG A 197 HIS A 202 0 SHEET 2 AA3 5 VAL A 264 PRO A 271 -1 O ILE A 269 N ARG A 197 SHEET 3 AA3 5 HIS A 236 ILE A 241 -1 N CYS A 239 O THR A 268 SHEET 4 AA3 5 LYS A 217 ILE A 221 -1 N ILE A 218 O HIS A 236 SHEET 5 AA3 5 PHE A 211 LYS A 214 -1 N ILE A 212 O SER A 220 SHEET 1 AA4 4 ARG A 197 HIS A 202 0 SHEET 2 AA4 4 VAL A 264 PRO A 271 -1 O ILE A 269 N ARG A 197 SHEET 3 AA4 4 HIS A 236 ILE A 241 -1 N CYS A 239 O THR A 268 SHEET 4 AA4 4 GLN A 244 ASN A 245 -1 O GLN A 244 N ILE A 241 SHEET 1 AA5 4 ILE B 112 LEU B 117 0 SHEET 2 AA5 4 ILE B 186 ARG B 191 -1 O ILE B 190 N ARG B 113 SHEET 3 AA5 4 GLN B 157 ILE B 161 -1 N LEU B 159 O THR B 189 SHEET 4 AA5 4 GLU B 164 ASN B 165 -1 O GLU B 164 N ILE B 161 SHEET 1 AA6 2 LEU B 127 ILE B 132 0 SHEET 2 AA6 2 GLY B 135 VAL B 141 -1 O PHE B 137 N LYS B 130 SHEET 1 AA7 5 ARG B 197 HIS B 202 0 SHEET 2 AA7 5 VAL B 264 PRO B 271 -1 O VAL B 265 N MET B 201 SHEET 3 AA7 5 HIS B 236 ILE B 241 -1 N ASN B 237 O MET B 270 SHEET 4 AA7 5 LYS B 217 ILE B 221 -1 N ILE B 218 O HIS B 236 SHEET 5 AA7 5 PHE B 211 LYS B 214 -1 N ILE B 212 O THR B 219 SHEET 1 AA8 4 ARG B 197 HIS B 202 0 SHEET 2 AA8 4 VAL B 264 PRO B 271 -1 O VAL B 265 N MET B 201 SHEET 3 AA8 4 HIS B 236 ILE B 241 -1 N ASN B 237 O MET B 270 SHEET 4 AA8 4 GLN B 244 ASN B 245 -1 O GLN B 244 N ILE B 241 SHEET 1 AA9 5 ARG C 113 LEU C 117 0 SHEET 2 AA9 5 ILE C 186 ARG C 191 -1 O ILE C 190 N ARG C 113 SHEET 3 AA9 5 GLN C 157 ILE C 161 -1 N LEU C 159 O THR C 189 SHEET 4 AA9 5 GLY C 135 VAL C 141 -1 N ILE C 136 O VAL C 158 SHEET 5 AA9 5 LEU C 127 ILE C 132 -1 N LYS C 130 O PHE C 137 SHEET 1 AB1 4 ARG C 113 LEU C 117 0 SHEET 2 AB1 4 ILE C 186 ARG C 191 -1 O ILE C 190 N ARG C 113 SHEET 3 AB1 4 GLN C 157 ILE C 161 -1 N LEU C 159 O THR C 189 SHEET 4 AB1 4 GLU C 164 ASN C 165 -1 O GLU C 164 N ILE C 161 SHEET 1 AB2 5 ARG C 197 HIS C 202 0 SHEET 2 AB2 5 VAL C 264 PRO C 271 -1 O VAL C 265 N MET C 201 SHEET 3 AB2 5 HIS C 236 ILE C 241 -1 N CYS C 239 O THR C 268 SHEET 4 AB2 5 LYS C 217 ILE C 221 -1 N ILE C 218 O HIS C 236 SHEET 5 AB2 5 PHE C 211 LYS C 214 -1 N ILE C 212 O THR C 219 SHEET 1 AB3 4 ARG C 197 HIS C 202 0 SHEET 2 AB3 4 VAL C 264 PRO C 271 -1 O VAL C 265 N MET C 201 SHEET 3 AB3 4 HIS C 236 ILE C 241 -1 N CYS C 239 O THR C 268 SHEET 4 AB3 4 GLN C 244 ASN C 245 -1 O GLN C 244 N ILE C 241 SHEET 1 AB4 5 ILE D 112 LEU D 117 0 SHEET 2 AB4 5 ILE D 186 ARG D 191 -1 O ILE D 190 N ARG D 113 SHEET 3 AB4 5 GLN D 157 ILE D 161 -1 N LEU D 159 O THR D 189 SHEET 4 AB4 5 GLY D 135 VAL D 141 -1 N ILE D 136 O VAL D 158 SHEET 5 AB4 5 LEU D 127 ILE D 132 -1 N ILE D 132 O GLY D 135 SHEET 1 AB5 4 ILE D 112 LEU D 117 0 SHEET 2 AB5 4 ILE D 186 ARG D 191 -1 O ILE D 190 N ARG D 113 SHEET 3 AB5 4 GLN D 157 ILE D 161 -1 N LEU D 159 O THR D 189 SHEET 4 AB5 4 GLU D 164 ASN D 165 -1 O GLU D 164 N ILE D 161 SHEET 1 AB6 4 ARG D 197 HIS D 202 0 SHEET 2 AB6 4 VAL D 264 PRO D 271 -1 O ILE D 269 N ARG D 197 SHEET 3 AB6 4 HIS D 236 ILE D 241 -1 N CYS D 239 O THR D 268 SHEET 4 AB6 4 GLN D 244 ASN D 245 -1 O GLN D 244 N ILE D 241 SHEET 1 AB7 2 PHE D 211 LYS D 214 0 SHEET 2 AB7 2 LYS D 217 ILE D 221 -1 O THR D 219 N ILE D 212 CRYST1 80.965 49.493 114.060 90.00 95.37 90.00 P 1 21 1 8 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 0.012351 0.000000 0.001162 0.00000 SCALE2 0.000000 0.020205 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008806 0.00000