HEADER SIGNALING PROTEIN 24-JAN-23 7FSV TITLE SDCBP PANDDA ANALYSIS GROUP DEPOSITION -- THE PDZ DOMANS OF SDCBP IN TITLE 2 COMPLEX WITH Z1454310449 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 7FSV 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. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 113.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 40814 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2098 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2923 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.4060 REMARK 3 BIN FREE R VALUE SET COUNT : 161 REMARK 3 BIN FREE R VALUE : 0.4450 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 : 129 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : -1.32000 REMARK 3 B33 (A**2) : 0.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.592 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.304 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.394 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 34.889 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 9738 ; 0.011 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 8122 ; 0.005 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11106 ; 1.633 ; 1.656 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18762 ; 1.198 ; 1.602 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1058 ; 8.014 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 382 ;35.292 ;22.330 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1573 ;17.945 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 50 ;20.889 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1128 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9485 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1888 ; 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): 4842 ; 1.596 ; 3.400 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4671 ; 1.622 ; 3.319 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5176 ; 2.924 ; 4.884 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 108 A 298 REMARK 3 RESIDUE RANGE : A 301 A 301 REMARK 3 ORIGIN FOR THE GROUP (A): -28.908 3.423 -45.252 REMARK 3 T TENSOR REMARK 3 T11: 0.1040 T22: 0.2809 REMARK 3 T33: 0.4110 T12: 0.0658 REMARK 3 T13: 0.0680 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 1.9446 L22: 0.0058 REMARK 3 L33: 0.5468 L12: 0.0349 REMARK 3 L13: -0.5609 L23: -0.0069 REMARK 3 S TENSOR REMARK 3 S11: 0.1084 S12: -0.0872 S13: -0.2322 REMARK 3 S21: 0.0009 S22: -0.0161 S23: 0.0348 REMARK 3 S31: -0.2252 S32: -0.1405 S33: -0.0923 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): -46.264 -14.834 -12.724 REMARK 3 T TENSOR REMARK 3 T11: 0.0213 T22: 0.2085 REMARK 3 T33: 0.5335 T12: -0.0215 REMARK 3 T13: 0.0087 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 0.7395 L22: 0.3560 REMARK 3 L33: 1.3786 L12: 0.0310 REMARK 3 L13: 0.1194 L23: -0.6408 REMARK 3 S TENSOR REMARK 3 S11: -0.0280 S12: 0.2291 S13: -0.1555 REMARK 3 S21: 0.0727 S22: -0.0196 S23: -0.1912 REMARK 3 S31: -0.1610 S32: 0.0222 S33: 0.0476 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): -3.004 2.313 -50.951 REMARK 3 T TENSOR REMARK 3 T11: 0.0701 T22: 0.2279 REMARK 3 T33: 0.3862 T12: -0.0235 REMARK 3 T13: 0.0743 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 0.6442 L22: 0.4977 REMARK 3 L33: 1.9563 L12: 0.2095 REMARK 3 L13: -0.2404 L23: 0.5654 REMARK 3 S TENSOR REMARK 3 S11: 0.0634 S12: -0.1087 S13: -0.1821 REMARK 3 S21: -0.1259 S22: -0.0324 S23: -0.1388 REMARK 3 S31: -0.2064 S32: 0.0731 S33: -0.0309 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): 9.207 -13.896 -5.160 REMARK 3 T TENSOR REMARK 3 T11: 0.0909 T22: 0.1646 REMARK 3 T33: 0.4024 T12: -0.0073 REMARK 3 T13: 0.0795 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.5588 L22: 0.5111 REMARK 3 L33: 0.7371 L12: 0.3844 REMARK 3 L13: -0.2278 L23: -0.5039 REMARK 3 S TENSOR REMARK 3 S11: 0.0482 S12: 0.1463 S13: -0.0130 REMARK 3 S21: 0.1376 S22: 0.0247 S23: 0.0906 REMARK 3 S31: -0.0870 S32: 0.0305 S33: -0.0729 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 7FSV 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_1001405304. 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 : 42971 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 113.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 1.48900 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 (%): 53.50 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 24.60400 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 D 444 O HOH D 459 1.93 REMARK 500 O HOH D 437 O HOH D 474 1.96 REMARK 500 NE2 GLN C 110 O HOH C 401 2.07 REMARK 500 O HOH B 424 O HOH B 466 2.10 REMARK 500 OD1 ASP B 292 OG1 THR B 294 2.13 REMARK 500 OD1 ASP A 292 OG1 THR A 294 2.16 REMARK 500 OE1 GLU A 235 O HOH A 401 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 120 CB ASP A 120 CG 0.139 REMARK 500 GLU B 235 CG GLU B 235 CD 0.132 REMARK 500 GLU B 235 CD GLU B 235 OE1 0.080 REMARK 500 GLU B 240 CG GLU B 240 CD 0.101 REMARK 500 PHE B 273 C PHE B 273 O 0.153 REMARK 500 PHE B 273 C PHE B 273 O 0.117 REMARK 500 THR D 234 C THR D 234 O 0.140 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 GLN A 110 30.08 -90.24 REMARK 500 PHE A 182 68.42 -63.31 REMARK 500 THR A 260 50.85 -92.97 REMARK 500 LYS A 280 134.43 -37.07 REMARK 500 ASP A 292 108.55 -55.46 REMARK 500 GLU B 107 109.72 -31.42 REMARK 500 ILE B 108 96.81 -65.23 REMARK 500 LYS B 109 88.26 -64.62 REMARK 500 GLN B 110 159.85 -42.87 REMARK 500 LYS B 119 136.20 -32.22 REMARK 500 ASN B 134 18.07 59.90 REMARK 500 ALA B 143 133.08 -36.44 REMARK 500 ARG B 193 63.30 21.69 REMARK 500 ASN B 242 27.71 48.70 REMARK 500 SER B 261 151.54 -46.69 REMARK 500 THR B 294 159.48 -49.95 REMARK 500 PHE C 182 -12.26 -142.18 REMARK 500 GLU C 184 -59.85 -169.77 REMARK 500 ASP C 204 -168.61 -69.23 REMARK 500 ASN C 242 56.63 33.90 REMARK 500 LYS C 280 155.19 -49.97 REMARK 500 ASP C 292 113.21 -39.68 REMARK 500 LYS D 109 141.02 -171.28 REMARK 500 ASP D 120 -161.82 -77.44 REMARK 500 ALA D 143 114.65 -37.99 REMARK 500 ARG D 193 59.00 36.54 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 GLY A 183 GLU A 184 149.56 REMARK 500 GLY C 111 ILE C 112 -142.14 REMARK 500 LEU D 127 ARG D 128 148.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 7FSV A 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSV B 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSV C 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 7FSV D 106 298 UNP O00560 SDCB1_HUMAN 106 298 SEQADV 7FSV SER A 104 UNP O00560 EXPRESSION TAG SEQADV 7FSV MET A 105 UNP O00560 EXPRESSION TAG SEQADV 7FSV SER B 104 UNP O00560 EXPRESSION TAG SEQADV 7FSV MET B 105 UNP O00560 EXPRESSION TAG SEQADV 7FSV SER C 104 UNP O00560 EXPRESSION TAG SEQADV 7FSV MET C 105 UNP O00560 EXPRESSION TAG SEQADV 7FSV SER D 104 UNP O00560 EXPRESSION TAG SEQADV 7FSV 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 UQS A 301 14 HET EDO A 302 4 HET UQS B 301 14 HET EDO B 302 4 HET EDO B 303 4 HET DGL B 304 10 HET UQS C 301 14 HET EDO C 302 4 HET EDO C 303 4 HET EDO C 304 4 HET GLY C 305 5 HET UQS D 301 14 HET EDO D 302 4 HET EDO D 303 4 HET SO4 D 304 5 HET ALA D 305 6 HET DGL D 306 10 HET GLY D 307 5 HETNAM UQS N-[(2-FLUOROPHENYL)METHYL]-1H-PYRAZOL-4-AMINE HETNAM EDO 1,2-ETHANEDIOL HETNAM DGL D-GLUTAMIC ACID HETNAM GLY GLYCINE HETNAM SO4 SULFATE ION HETNAM ALA ALANINE HETSYN EDO ETHYLENE GLYCOL FORMUL 5 UQS 4(C10 H10 F N3) FORMUL 6 EDO 8(C2 H6 O2) FORMUL 10 DGL 2(C5 H9 N O4) FORMUL 15 GLY 2(C2 H5 N O2) FORMUL 19 SO4 O4 S 2- FORMUL 20 ALA C3 H7 N O2 FORMUL 23 HOH *245(H2 O) HELIX 1 AA1 SER A 145 GLY A 151 1 7 HELIX 2 AA2 SER A 170 ALA A 181 1 12 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 ILE B 279 1 8 HELIX 12 AB3 ALA B 283 MET B 291 1 9 HELIX 13 AB4 SER C 145 GLY C 151 1 7 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 THR D 260 1 11 HELIX 23 AC5 ALA D 272 ILE D 279 1 8 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 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 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 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 GLY B 135 N ILE B 132 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 267 N ILE B 199 SHEET 3 AA7 4 HIS B 236 ILE B 241 -1 N ASN B 237 O MET B 270 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 5 ILE C 112 LEU C 117 0 SHEET 2 AA9 5 ILE C 186 ARG C 191 -1 O ILE C 186 N LEU C 117 SHEET 3 AA9 5 GLN C 157 ILE C 161 -1 N GLN C 157 O ARG C 191 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 ILE C 186 N LEU C 117 SHEET 3 AB1 4 GLN C 157 ILE C 161 -1 N GLN C 157 O ARG C 191 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 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 4 ILE D 112 LEU D 117 0 SHEET 2 AB4 4 ILE D 186 ARG D 191 -1 O ILE D 190 N ARG D 113 SHEET 3 AB4 4 GLN D 157 ILE D 161 -1 N GLN D 157 O ARG D 191 SHEET 4 AB4 4 GLU D 164 ASN D 165 -1 O GLU D 164 N ILE D 161 SHEET 1 AB5 2 LEU D 127 ILE D 132 0 SHEET 2 AB5 2 GLY D 135 VAL D 141 -1 O GLN D 139 N ARG D 128 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 ASN D 237 O MET D 270 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 80.911 49.208 114.396 90.00 95.35 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 0.012359 0.000000 0.001157 0.00000 SCALE2 0.000000 0.020322 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008780 0.00000