HEADER SIGNALING PROTEIN 24-JAN-23 7FT9 TITLE SDCBP PANDDA ANALYSIS GROUP DEPOSITION -- THE PDZ DOMANS OF SDCBP IN TITLE 2 COMPLEX WITH Z45636695 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 7FT9 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. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 82379 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4245 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4973 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.4180 REMARK 3 BIN FREE R VALUE SET COUNT : 246 REMARK 3 BIN FREE R VALUE : 0.4160 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 : 93 REMARK 3 SOLVENT ATOMS : 306 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -15.48000 REMARK 3 B22 (A**2) : -4.59000 REMARK 3 B33 (A**2) : 20.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 7.59000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.030 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.029 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.792 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8143 ; 0.014 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 7092 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9886 ; 1.961 ; 1.638 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16390 ; 1.338 ; 1.593 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 962 ; 7.938 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 373 ;35.869 ;22.225 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1378 ;17.736 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 53 ;19.935 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 986 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8678 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1700 ; 0.003 ; 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): 4050 ; 2.638 ; 3.625 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3961 ; 2.661 ; 3.569 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4672 ; 3.800 ; 5.319 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): -29.127 2.953 -45.100 REMARK 3 T TENSOR REMARK 3 T11: 0.0825 T22: 0.0693 REMARK 3 T33: 0.1182 T12: 0.0213 REMARK 3 T13: 0.0289 T23: -0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.6299 L22: 0.1159 REMARK 3 L33: 0.2379 L12: -0.2533 REMARK 3 L13: -0.1737 L23: 0.1103 REMARK 3 S TENSOR REMARK 3 S11: 0.0100 S12: -0.0483 S13: -0.2323 REMARK 3 S21: -0.0354 S22: -0.0087 S23: 0.0892 REMARK 3 S31: -0.1280 S32: -0.0062 S33: -0.0013 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): -46.314 -14.459 -12.864 REMARK 3 T TENSOR REMARK 3 T11: 0.0351 T22: 0.0319 REMARK 3 T33: 0.0642 T12: -0.0057 REMARK 3 T13: -0.0146 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.5152 L22: 0.1748 REMARK 3 L33: 0.4629 L12: 0.1138 REMARK 3 L13: -0.0531 L23: -0.2699 REMARK 3 S TENSOR REMARK 3 S11: -0.0103 S12: 0.0908 S13: -0.0918 REMARK 3 S21: 0.0477 S22: -0.0120 S23: -0.0417 REMARK 3 S31: -0.0770 S32: 0.0374 S33: 0.0222 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): -3.204 1.936 -50.985 REMARK 3 T TENSOR REMARK 3 T11: 0.0341 T22: 0.0365 REMARK 3 T33: 0.0404 T12: 0.0014 REMARK 3 T13: -0.0034 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.2963 L22: 0.1864 REMARK 3 L33: 0.5301 L12: 0.0012 REMARK 3 L13: -0.0635 L23: 0.3081 REMARK 3 S TENSOR REMARK 3 S11: 0.0245 S12: -0.0407 S13: -0.0795 REMARK 3 S21: -0.0520 S22: 0.0065 S23: -0.0336 REMARK 3 S31: -0.0894 S32: 0.0076 S33: -0.0311 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): 9.308 -13.776 -5.207 REMARK 3 T TENSOR REMARK 3 T11: 0.0578 T22: 0.0246 REMARK 3 T33: 0.0507 T12: -0.0074 REMARK 3 T13: 0.0183 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 0.2306 L22: 0.1687 REMARK 3 L33: 0.3840 L12: 0.0824 REMARK 3 L13: -0.0763 L23: -0.2387 REMARK 3 S TENSOR REMARK 3 S11: 0.0306 S12: 0.0595 S13: -0.0303 REMARK 3 S21: 0.0531 S22: -0.0117 S23: 0.0253 REMARK 3 S31: -0.0391 S32: 0.0280 S33: -0.0189 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 7FT9 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_1001405318. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-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 : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 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 : 87561 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 80.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 2.59200 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 (%): 53.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 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 24.57600 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 O HOH B 469 O HOH B 477 2.12 REMARK 500 NH2 ARG C 197 O HOH C 401 2.17 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 B 197 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG C 229 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 PHE D 137 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG D 197 NE - CZ - NH1 ANGL. DEV. = -4.2 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 ASP A 120 -168.11 -76.49 REMARK 500 GLU A 184 -81.31 17.46 REMARK 500 LYS A 185 119.93 -160.91 REMARK 500 ARG A 193 57.63 37.55 REMARK 500 ARG A 281 83.83 87.34 REMARK 500 MET A 282 110.38 155.72 REMARK 500 PRO A 284 40.84 -67.30 REMARK 500 PHE B 154 127.02 -39.61 REMARK 500 ARG B 193 60.81 34.25 REMARK 500 ASN C 144 -13.08 80.94 REMARK 500 ASN C 144 49.34 32.18 REMARK 500 PHE C 182 18.31 -156.17 REMARK 500 LYS C 185 166.04 157.82 REMARK 500 ARG C 193 56.87 26.93 REMARK 500 SER C 205 -30.26 -39.19 REMARK 500 ARG C 281 27.29 82.26 REMARK 500 PHE D 154 126.93 -37.49 REMARK 500 ARG D 193 55.95 32.67 REMARK 500 REMARK 500 REMARK: NULL DBREF 7FT9 A 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FT9 B 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FT9 C 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FT9 D 106 298 UNP O00560 SDCB1_HUMAN 106 298 SEQADV 7FT9 SER A 104 UNP O00560 EXPRESSION TAG SEQADV 7FT9 MET A 105 UNP O00560 EXPRESSION TAG SEQADV 7FT9 SER B 104 UNP O00560 EXPRESSION TAG SEQADV 7FT9 MET B 105 UNP O00560 EXPRESSION TAG SEQADV 7FT9 SER C 104 UNP O00560 EXPRESSION TAG SEQADV 7FT9 MET C 105 UNP O00560 EXPRESSION TAG SEQADV 7FT9 SER D 104 UNP O00560 EXPRESSION TAG SEQADV 7FT9 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 4MB C 301 14 HET EDO C 302 4 HET EDO C 303 4 HET GLY C 304 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 DGL D-GLUTAMIC ACID HETNAM 4MB 4-[(METHYLSULFONYL)AMINO]BENZOIC ACID HETNAM GLY GLYCINE HETNAM SO4 SULFATE ION HETNAM ALA ALANINE HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 7(C2 H6 O2) FORMUL 8 DGL 2(C5 H9 N O4) FORMUL 9 4MB C8 H9 N O4 S FORMUL 12 GLY 2(C2 H5 N O2) FORMUL 15 SO4 3(O4 S 2-) FORMUL 18 ALA C3 H7 N O2 FORMUL 21 HOH *306(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 ILE A 279 1 8 HELIX 6 AA6 SER A 285 LEU A 290 1 6 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 ILE B 279 1 8 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 ASN C 230 1 6 HELIX 16 AB7 LYS C 250 THR C 260 1 11 HELIX 17 AB8 ALA C 272 LYS C 280 1 9 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 ALA D 181 1 12 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 4 ILE A 112 LEU A 117 0 SHEET 2 AA1 4 ILE A 186 ARG A 191 -1 O ILE A 186 N LEU A 117 SHEET 3 AA1 4 GLN A 157 ILE A 161 -1 N GLN A 157 O ARG A 191 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 GLN A 139 N ARG A 128 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 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 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 186 N LEU B 117 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 4 ARG B 197 HIS B 202 0 SHEET 2 AA7 4 VAL B 264 PRO B 271 -1 O ILE B 269 N ARG B 197 SHEET 3 AA7 4 HIS B 236 ILE B 241 -1 N GLU B 240 O THR B 268 SHEET 4 AA7 4 GLN B 244 ASN B 245 -1 O GLN B 244 N ILE B 241 SHEET 1 AA8 2 PHE B 211 LYS B 214 0 SHEET 2 AA8 2 LYS B 217 ILE B 221 -1 O THR B 219 N ILE B 212 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 190 N ARG C 113 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 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 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 CYS D 239 O THR D 268 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 CYS D 239 O THR D 268 SHEET 4 AB7 4 GLN D 244 ASN D 245 -1 O GLN D 244 N ILE D 241 CRYST1 80.845 49.152 115.021 90.00 95.03 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 0.012369 0.000000 0.001088 0.00000 SCALE2 0.000000 0.020345 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008728 0.00000