HEADER SIGNALING PROTEIN 24-JAN-23 7FSP TITLE SDCBP PANDDA ANALYSIS GROUP DEPOSITION -- THE PDZ DOMANS OF SDCBP IN TITLE 2 COMPLEX WITH Z1650168321 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 7FSP 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. 1.86 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 72084 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3707 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5224 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.3910 REMARK 3 BIN FREE R VALUE SET COUNT : 280 REMARK 3 BIN FREE R VALUE : 0.4050 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 : 98 REMARK 3 SOLVENT ATOMS : 371 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.58000 REMARK 3 B22 (A**2) : -1.01000 REMARK 3 B33 (A**2) : 1.25000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.72000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.152 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.159 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.533 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8907 ; 0.011 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 7690 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10406 ; 1.798 ; 1.645 REMARK 3 BOND ANGLES OTHERS (DEGREES): 17766 ; 1.316 ; 1.601 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1004 ; 7.877 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 361 ;35.806 ;22.798 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1489 ;16.203 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 47 ;17.618 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1065 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8921 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1697 ; 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): 4477 ; 2.118 ; 3.284 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4470 ; 2.117 ; 3.282 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4916 ; 3.465 ; 4.713 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): -28.718 3.052 -45.211 REMARK 3 T TENSOR REMARK 3 T11: 0.0746 T22: 0.2721 REMARK 3 T33: 0.0925 T12: 0.1125 REMARK 3 T13: 0.0304 T23: 0.0450 REMARK 3 L TENSOR REMARK 3 L11: 2.0279 L22: 0.0267 REMARK 3 L33: 0.2658 L12: -0.0907 REMARK 3 L13: -0.5816 L23: 0.0723 REMARK 3 S TENSOR REMARK 3 S11: 0.0845 S12: -0.0705 S13: -0.2827 REMARK 3 S21: -0.0415 S22: -0.0967 S23: -0.0031 REMARK 3 S31: -0.1124 S32: -0.1310 S33: 0.0121 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): -46.066 -14.954 -12.911 REMARK 3 T TENSOR REMARK 3 T11: 0.0222 T22: 0.1126 REMARK 3 T33: 0.2108 T12: -0.0202 REMARK 3 T13: -0.0017 T23: -0.0176 REMARK 3 L TENSOR REMARK 3 L11: 0.6558 L22: 0.3019 REMARK 3 L33: 0.6909 L12: 0.0988 REMARK 3 L13: -0.0797 L23: -0.4338 REMARK 3 S TENSOR REMARK 3 S11: -0.0345 S12: 0.1549 S13: -0.1667 REMARK 3 S21: 0.0697 S22: -0.0387 S23: -0.1257 REMARK 3 S31: -0.1159 S32: 0.0359 S33: 0.0732 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): -2.807 2.146 -50.873 REMARK 3 T TENSOR REMARK 3 T11: 0.0241 T22: 0.1273 REMARK 3 T33: 0.0962 T12: -0.0083 REMARK 3 T13: -0.0019 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.5391 L22: 0.2838 REMARK 3 L33: 0.9768 L12: 0.1490 REMARK 3 L13: -0.2695 L23: 0.3680 REMARK 3 S TENSOR REMARK 3 S11: 0.0490 S12: -0.0632 S13: -0.1306 REMARK 3 S21: -0.0528 S22: -0.0049 S23: -0.0723 REMARK 3 S31: -0.1436 S32: 0.0558 S33: -0.0441 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): 9.047 -13.642 -5.168 REMARK 3 T TENSOR REMARK 3 T11: 0.0503 T22: 0.0858 REMARK 3 T33: 0.1062 T12: -0.0107 REMARK 3 T13: 0.0079 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 0.3966 L22: 0.4267 REMARK 3 L33: 0.4249 L12: 0.1122 REMARK 3 L13: -0.0247 L23: -0.4129 REMARK 3 S TENSOR REMARK 3 S11: 0.0498 S12: 0.0603 S13: -0.0459 REMARK 3 S21: 0.0627 S22: 0.0028 S23: 0.0562 REMARK 3 S31: -0.0491 S32: 0.0241 S33: -0.0525 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 7FSP 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_1001405298. 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 : 75903 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 80.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 1.65100 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 (%): 53.51 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 24.75100 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 470 O HOH B 487 2.08 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 - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 THR B 198 CA - CB - OG1 ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG D 113 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG D 197 NE - CZ - NH1 ANGL. DEV. = -3.0 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 -60.79 -7.73 REMARK 500 LYS A 185 111.56 -162.21 REMARK 500 ARG A 193 64.65 26.44 REMARK 500 ASP A 292 105.77 -54.72 REMARK 500 ILE B 108 100.26 -58.18 REMARK 500 ARG B 193 63.32 20.97 REMARK 500 ASN C 144 56.80 30.41 REMARK 500 ARG C 193 60.21 24.91 REMARK 500 GLN D 110 -178.64 -48.79 REMARK 500 ASP D 120 -166.69 -77.42 REMARK 500 ALA D 143 118.12 -36.14 REMARK 500 ASN D 144 37.44 71.94 REMARK 500 ARG D 193 63.75 22.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 7FSP A 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSP B 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSP C 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSP D 106 298 UNP O00560 SDCB1_HUMAN 106 298 SEQADV 7FSP SER A 104 UNP O00560 EXPRESSION TAG SEQADV 7FSP MET A 105 UNP O00560 EXPRESSION TAG SEQADV 7FSP SER B 104 UNP O00560 EXPRESSION TAG SEQADV 7FSP MET B 105 UNP O00560 EXPRESSION TAG SEQADV 7FSP SER C 104 UNP O00560 EXPRESSION TAG SEQADV 7FSP MET C 105 UNP O00560 EXPRESSION TAG SEQADV 7FSP SER D 104 UNP O00560 EXPRESSION TAG SEQADV 7FSP 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 A 302 4 HET EDO B 301 4 HET EDO B 302 4 HET SO4 B 303 5 HET DGL B 304 10 HET EDO C 301 4 HET EDO C 302 4 HET SO4 C 303 5 HET GLY C 304 5 HET VW7 D 301 15 HET EDO D 302 4 HET EDO D 303 4 HET ALA D 304 6 HET DGL D 305 10 HET GLY D 306 5 HET GLY D 307 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM DGL D-GLUTAMIC ACID HETNAM GLY GLYCINE HETNAM VW7 N-(8-METHYL-1,2,3,4-TETRAHYDROQUINOLIN-5-YL)ACETAMIDE HETNAM ALA ALANINE HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 8(C2 H6 O2) FORMUL 9 SO4 2(O4 S 2-) FORMUL 10 DGL 2(C5 H9 N O4) FORMUL 14 GLY 3(C2 H5 N O2) FORMUL 15 VW7 C12 H16 N2 O FORMUL 18 ALA C3 H7 N O2 FORMUL 22 HOH *371(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 SER B 261 1 12 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 ASN C 230 1 6 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 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 VAL A 265 N MET A 201 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 VAL A 265 N MET A 201 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 GLN B 157 O ARG B 191 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 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 LYS B 214 O LYS B 217 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 5 ILE C 112 LEU C 117 0 SHEET 2 AA9 5 ILE C 186 ARG C 191 -1 O MET C 188 N VAL C 115 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 ILE C 112 LEU C 117 0 SHEET 2 AB1 4 ILE C 186 ARG C 191 -1 O MET C 188 N VAL C 115 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 GLU C 240 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 GLU C 240 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 186 N LEU D 117 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 ILE D 186 N LEU D 117 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 ILE D 267 N ILE D 199 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 ILE D 267 N ILE D 199 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 80.444 49.502 114.424 90.00 95.40 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 0.012431 0.000000 0.001175 0.00000 SCALE2 0.000000 0.020201 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008778 0.00000