HEADER SIGNALING PROTEIN 24-JAN-23 7FSX TITLE SDCBP PANDDA ANALYSIS GROUP DEPOSITION -- THE PDZ DOMANS OF SDCBP IN TITLE 2 COMPLEX WITH Z1328078283 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 1 15-FEB-23 7FSX 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. 1.91 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 114.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 67272 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3446 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) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4865 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3550 REMARK 3 BIN FREE R VALUE SET COUNT : 246 REMARK 3 BIN FREE R VALUE : 0.3750 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 : 118 REMARK 3 SOLVENT ATOMS : 391 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.28000 REMARK 3 B22 (A**2) : -0.42000 REMARK 3 B33 (A**2) : 1.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.54000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.181 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.157 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.556 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8643 ; 0.012 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 7604 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10248 ; 1.868 ; 1.652 REMARK 3 BOND ANGLES OTHERS (DEGREES): 17588 ; 1.336 ; 1.612 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 995 ; 8.040 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 349 ;36.912 ;22.808 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1477 ;17.394 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;17.541 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1042 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8750 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1686 ; 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): 4352 ; 2.005 ; 3.224 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4229 ; 2.032 ; 3.178 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4849 ; 3.284 ; 4.637 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): -28.591 3.154 -45.517 REMARK 3 T TENSOR REMARK 3 T11: 0.0154 T22: 0.1531 REMARK 3 T33: 0.0615 T12: -0.0013 REMARK 3 T13: 0.0068 T23: 0.0253 REMARK 3 L TENSOR REMARK 3 L11: 1.8895 L22: 0.0079 REMARK 3 L33: 0.8038 L12: 0.0221 REMARK 3 L13: -1.0652 L23: 0.0229 REMARK 3 S TENSOR REMARK 3 S11: 0.1378 S12: 0.0642 S13: -0.0104 REMARK 3 S21: 0.0020 S22: -0.0378 S23: -0.0130 REMARK 3 S31: -0.0875 S32: -0.1554 S33: -0.1001 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 106 B 298 REMARK 3 RESIDUE RANGE : B 301 B 301 REMARK 3 ORIGIN FOR THE GROUP (A): -46.169 -14.589 -13.012 REMARK 3 T TENSOR REMARK 3 T11: 0.0431 T22: 0.0727 REMARK 3 T33: 0.0869 T12: -0.0168 REMARK 3 T13: -0.0029 T23: -0.0280 REMARK 3 L TENSOR REMARK 3 L11: 0.7089 L22: 0.2634 REMARK 3 L33: 0.8797 L12: 0.2335 REMARK 3 L13: -0.2462 L23: -0.4594 REMARK 3 S TENSOR REMARK 3 S11: -0.0273 S12: 0.1460 S13: -0.2048 REMARK 3 S21: 0.0621 S22: -0.0150 S23: -0.0685 REMARK 3 S31: -0.1236 S32: 0.0571 S33: 0.0423 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 106 C 298 REMARK 3 RESIDUE RANGE : C 301 C 301 REMARK 3 ORIGIN FOR THE GROUP (A): -2.610 1.389 -51.049 REMARK 3 T TENSOR REMARK 3 T11: 0.0703 T22: 0.0670 REMARK 3 T33: 0.0284 T12: 0.0100 REMARK 3 T13: 0.0081 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.6148 L22: 0.1785 REMARK 3 L33: 1.1790 L12: 0.1967 REMARK 3 L13: -0.1649 L23: 0.2961 REMARK 3 S TENSOR REMARK 3 S11: 0.0762 S12: -0.0326 S13: -0.1067 REMARK 3 S21: -0.0123 S22: -0.0360 S23: -0.0605 REMARK 3 S31: -0.0774 S32: -0.0251 S33: -0.0402 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 108 D 298 REMARK 3 ORIGIN FOR THE GROUP (A): 9.265 -13.591 -5.187 REMARK 3 T TENSOR REMARK 3 T11: 0.0885 T22: 0.0341 REMARK 3 T33: 0.0471 T12: 0.0009 REMARK 3 T13: 0.0162 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.3896 L22: 0.3681 REMARK 3 L33: 0.5761 L12: 0.1313 REMARK 3 L13: -0.0842 L23: -0.4416 REMARK 3 S TENSOR REMARK 3 S11: 0.0250 S12: 0.0920 S13: -0.0441 REMARK 3 S21: 0.0749 S22: -0.0009 S23: 0.0331 REMARK 3 S31: -0.0571 S32: 0.0309 S33: -0.0241 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 7FSX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1001405306. 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 : 70825 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 114.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 1.19200 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 (%): 53.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 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 24.76800 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 NH2 ARG C 229 O HOH C 401 1.99 REMARK 500 NH2 ARG D 197 O HOH D 401 2.00 REMARK 500 O HOH A 411 O HOH A 448 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 197 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 197 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG C 128 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG D 153 CG - CD - NE ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG D 153 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES 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 GLU A 184 -53.52 -19.05 REMARK 500 LYS A 185 112.47 -169.26 REMARK 500 ARG A 193 57.55 32.74 REMARK 500 LYS A 223 133.38 -37.80 REMARK 500 ARG A 281 4.92 81.27 REMARK 500 CYS B 118 117.84 -167.83 REMARK 500 ARG B 193 58.40 27.93 REMARK 500 ASP C 120 -162.82 -75.89 REMARK 500 ARG C 193 59.07 27.16 REMARK 500 ASN C 242 47.65 39.18 REMARK 500 ARG C 281 21.11 81.98 REMARK 500 GLN D 110 81.68 -50.48 REMARK 500 ASN D 144 35.37 70.12 REMARK 500 ARG D 193 63.05 28.61 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 PHE A 182 GLY A 183 149.27 REMARK 500 GLY C 111 ILE C 112 -149.10 REMARK 500 REMARK 500 REMARK: NULL DBREF 7FSX A 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSX B 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSX C 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSX D 106 298 UNP O00560 SDCB1_HUMAN 106 298 SEQADV 7FSX SER A 104 UNP O00560 EXPRESSION TAG SEQADV 7FSX MET A 105 UNP O00560 EXPRESSION TAG SEQADV 7FSX SER B 104 UNP O00560 EXPRESSION TAG SEQADV 7FSX MET B 105 UNP O00560 EXPRESSION TAG SEQADV 7FSX SER C 104 UNP O00560 EXPRESSION TAG SEQADV 7FSX MET C 105 UNP O00560 EXPRESSION TAG SEQADV 7FSX SER D 104 UNP O00560 EXPRESSION TAG SEQADV 7FSX 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 I8A B 301 15 HET EDO B 302 4 HET EDO B 303 4 HET DGL B 304 10 HET I8A C 301 15 HET EDO C 302 4 HET EDO C 303 4 HET EDO C 304 4 HET SO4 C 305 5 HET GLY C 306 5 HET EDO D 301 4 HET EDO D 302 4 HET SO4 D 303 5 HET SO4 D 304 5 HET SO4 D 305 5 HET ALA D 306 6 HET DGL D 307 10 HET GLY D 308 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM I8A N-(CYCLOPROPYLMETHYL)-2,2,3,3-TETRAMETHYLAZETIDINE-1- HETNAM 2 I8A CARBOXAMIDE HETNAM DGL D-GLUTAMIC ACID HETNAM SO4 SULFATE ION HETNAM GLY GLYCINE HETNAM ALA ALANINE HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 8(C2 H6 O2) FORMUL 6 I8A 2(C12 H22 N2 O) FORMUL 9 DGL 2(C5 H9 N O4) FORMUL 14 SO4 4(O4 S 2-) FORMUL 15 GLY 2(C2 H5 N O2) FORMUL 21 ALA C3 H7 N O2 FORMUL 24 HOH *391(H2 O) HELIX 1 AA1 SER A 145 VAL A 150 1 6 HELIX 2 AA2 SER A 170 ALA A 181 1 12 HELIX 3 AA3 SER A 225 ASN A 230 1 6 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 ALA B 181 1 12 HELIX 9 AA9 SER B 225 ASN B 230 1 6 HELIX 10 AB1 LYS B 250 THR B 260 1 11 HELIX 11 AB2 ALA B 272 LYS B 280 1 9 HELIX 12 AB3 ALA B 283 MET B 291 1 9 HELIX 13 AB4 SER C 145 VAL C 150 1 6 HELIX 14 AB5 SER C 170 ALA C 181 1 12 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 ASN D 230 1 6 HELIX 22 AC4 LYS D 250 SER D 261 1 12 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 5 ILE A 112 LEU A 117 0 SHEET 2 AA1 5 ILE A 186 ARG A 191 -1 O ILE A 186 N LEU A 117 SHEET 3 AA1 5 GLN A 157 ILE A 161 -1 N LEU A 159 O THR A 189 SHEET 4 AA1 5 GLY A 135 VAL A 141 -1 N ILE A 136 O VAL A 158 SHEET 5 AA1 5 LEU A 127 ILE A 132 -1 N LYS A 130 O PHE A 137 SHEET 1 AA2 4 ILE A 112 LEU A 117 0 SHEET 2 AA2 4 ILE A 186 ARG A 191 -1 O ILE A 186 N LEU A 117 SHEET 3 AA2 4 GLN A 157 ILE A 161 -1 N LEU A 159 O THR A 189 SHEET 4 AA2 4 GLU A 164 ASN A 165 -1 O GLU A 164 N ILE A 161 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 267 N ILE A 199 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 THR A 219 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 267 N ILE A 199 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 5 ILE B 112 LEU B 117 0 SHEET 2 AA5 5 ILE B 186 ARG B 191 -1 O ILE B 186 N LEU B 117 SHEET 3 AA5 5 GLN B 157 ILE B 161 -1 N GLN B 157 O ARG B 191 SHEET 4 AA5 5 GLY B 135 VAL B 141 -1 N ILE B 136 O VAL B 158 SHEET 5 AA5 5 LEU B 127 ILE B 132 -1 N LYS B 130 O PHE B 137 SHEET 1 AA6 4 ILE B 112 LEU B 117 0 SHEET 2 AA6 4 ILE B 186 ARG B 191 -1 O ILE B 186 N LEU B 117 SHEET 3 AA6 4 GLN B 157 ILE B 161 -1 N GLN B 157 O ARG B 191 SHEET 4 AA6 4 GLU B 164 ASN B 165 -1 O GLU B 164 N ILE B 161 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 CYS B 239 O THR B 268 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 CYS B 239 O THR B 268 SHEET 4 AA8 4 GLN B 244 ASN B 245 -1 O GLN B 244 N ILE B 241 SHEET 1 AA9 4 ILE C 112 LEU C 117 0 SHEET 2 AA9 4 ILE C 186 ARG C 191 -1 O ILE C 186 N LEU C 117 SHEET 3 AA9 4 GLN C 157 ILE C 161 -1 N GLN C 157 O ARG C 191 SHEET 4 AA9 4 GLU C 164 ASN C 165 -1 O GLU C 164 N ILE C 161 SHEET 1 AB1 2 LEU C 127 ILE C 132 0 SHEET 2 AB1 2 GLY C 135 VAL C 141 -1 O PHE C 137 N LYS C 130 SHEET 1 AB2 5 ARG C 197 HIS C 202 0 SHEET 2 AB2 5 VAL C 264 PRO C 271 -1 O ILE C 269 N ARG C 197 SHEET 3 AB2 5 HIS C 236 ILE C 241 -1 N ASN C 237 O MET C 270 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 ILE C 269 N ARG C 197 SHEET 3 AB3 4 HIS C 236 ILE C 241 -1 N ASN C 237 O MET C 270 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 MET D 188 N VAL D 115 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 LYS D 130 O PHE D 137 SHEET 1 AB5 4 ILE D 112 LEU D 117 0 SHEET 2 AB5 4 ILE D 186 ARG D 191 -1 O MET D 188 N VAL D 115 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 5 ARG D 197 HIS D 202 0 SHEET 2 AB6 5 VAL D 264 PRO D 271 -1 O VAL D 265 N MET D 201 SHEET 3 AB6 5 HIS D 236 ILE D 241 -1 N ASN D 237 O MET D 270 SHEET 4 AB6 5 LYS D 217 ILE D 221 -1 N ILE D 218 O HIS D 236 SHEET 5 AB6 5 PHE D 211 LYS D 214 -1 N ILE D 212 O THR D 219 SHEET 1 AB7 4 ARG D 197 HIS D 202 0 SHEET 2 AB7 4 VAL D 264 PRO D 271 -1 O VAL D 265 N MET D 201 SHEET 3 AB7 4 HIS D 236 ILE D 241 -1 N ASN D 237 O MET D 270 SHEET 4 AB7 4 GLN D 244 ASN D 245 -1 O GLN D 244 N ILE D 241 CRYST1 80.629 49.536 115.265 90.00 95.43 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 0.012402 0.000000 0.001180 0.00000 SCALE2 0.000000 0.020187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008715 0.00000