HEADER SIGNALING PROTEIN 10-NOV-22 8BLU TITLE THE PDZ DOMAINS OF HUMAN SDCBP 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS APO, CYTOSOLIC, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.J.BRADSHAW,V.L.KATIS,M.DANIEL-MOZO,C.BOUNTRA,F.VON DELFT, AUTHOR 2 P.E.BRENNAN REVDAT 2 31-JAN-24 8BLU 1 REMARK REVDAT 1 30-NOV-22 8BLU 0 JRNL AUTH W.J.BRADSHAW,V.L.KATIS,M.DANIEL-MOZO,C.BOUNTRA,F.VON DELFT, JRNL AUTH 2 P.E.BRENNAN JRNL TITL THE PDZ DOMAINS OF HUMAN SDCBP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 147639 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.392 REMARK 3 FREE R VALUE TEST SET COUNT : 2055 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10667 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4110 REMARK 3 BIN FREE R VALUE SET COUNT : 177 REMARK 3 BIN FREE R VALUE : 0.3850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5950 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 121 REMARK 3 SOLVENT ATOMS : 774 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.93300 REMARK 3 B22 (A**2) : 1.16900 REMARK 3 B33 (A**2) : 0.67100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.63000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.074 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.082 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6448 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 6233 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8716 ; 1.727 ; 1.641 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14610 ; 0.581 ; 1.570 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 859 ; 7.112 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 38 ; 8.349 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1252 ;13.695 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1026 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7237 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1163 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1183 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 135 ; 0.203 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3097 ; 0.162 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 575 ; 0.187 ; 0.200 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): 3219 ; 3.252 ; 3.229 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3219 ; 3.251 ; 3.230 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4026 ; 4.369 ; 4.827 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4027 ; 4.372 ; 4.828 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3229 ; 4.661 ; 3.642 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3227 ; 4.658 ; 3.642 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4647 ; 6.538 ; 5.287 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4648 ; 6.537 ; 5.287 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 : 6 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 106 A 297 NULL REMARK 3 1 A 106 A 297 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 2 A 106 A 298 NULL REMARK 3 2 A 106 A 298 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 3 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 3 A 106 A 298 NULL REMARK 3 3 A 106 A 298 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 NCS GROUP NUMBER : 4 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 4 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 4 A 106 A 297 NULL REMARK 3 4 A 106 A 297 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 NCS GROUP NUMBER : 5 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 5 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 5 A 106 A 297 NULL REMARK 3 5 A 106 A 297 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 NCS GROUP NUMBER : 6 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 6 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 6 A 106 A 298 NULL REMARK 3 6 A 106 A 298 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8BLU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 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) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 147705 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 68.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 26.00 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 18.90 REMARK 200 R MERGE FOR SHELL (I) : 5.44600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1N99 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 50 MM MES, 100 MM REMARK 280 MORPHEUS AMINO ACID MIX, 8.3% PEG 8000, 16.6% ETHYLENE GLYCOL, REMARK 280 PH 6.7, 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 24.79400 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 SER C 104 REMARK 465 MET C 105 REMARK 465 SER D 104 REMARK 465 MET D 105 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 443 O HOH D 586 1.97 REMARK 500 O HOH B 676 O HOH B 737 2.03 REMARK 500 O1 GOL B 303 O HOH B 601 2.13 REMARK 500 OD1 ASP D 256 O HOH D 401 2.14 REMARK 500 O HOH B 736 O HOH B 757 2.14 REMARK 500 O ASP C 172 O2 EDO C 303 2.14 REMARK 500 O GLY C 111 O HOH C 401 2.14 REMARK 500 OD1 ASP C 256 O HOH C 402 2.15 REMARK 500 O HOH D 421 O HOH D 470 2.15 REMARK 500 O HOH A 425 O HOH A 518 2.17 REMARK 500 O LEU C 290 O HOH C 403 2.17 REMARK 500 O GLY D 111 O HOH D 402 2.17 REMARK 500 OE2 GLU D 164 O HOH D 403 2.18 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. = -4.2 DEGREES REMARK 500 ARG B 128 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 191 CG - CD - NE ANGL. DEV. = 14.8 DEGREES REMARK 500 ARG B 197 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG B 197 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 229 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG C 197 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG D 193 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG D 197 NE - CZ - NH1 ANGL. DEV. = -4.7 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 PHE A 182 123.43 -35.11 REMARK 500 ARG A 193 62.61 28.60 REMARK 500 ARG B 193 60.14 33.32 REMARK 500 PHE C 182 22.28 -151.77 REMARK 500 ARG C 193 62.18 30.89 REMARK 500 ARG D 193 64.73 31.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 191 0.11 SIDE CHAIN REMARK 500 ARG D 128 0.08 SIDE CHAIN REMARK 500 ARG D 191 0.08 SIDE CHAIN REMARK 500 ASP D 192 0.07 SIDE CHAIN REMARK 500 ARG D 197 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8BLU A 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 8BLU B 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 8BLU C 106 298 UNP O00560 SDCB1_HUMAN 106 298 DBREF 8BLU D 106 298 UNP O00560 SDCB1_HUMAN 106 298 SEQADV 8BLU SER A 104 UNP O00560 EXPRESSION TAG SEQADV 8BLU MET A 105 UNP O00560 EXPRESSION TAG SEQADV 8BLU SER B 104 UNP O00560 EXPRESSION TAG SEQADV 8BLU MET B 105 UNP O00560 EXPRESSION TAG SEQADV 8BLU SER C 104 UNP O00560 EXPRESSION TAG SEQADV 8BLU MET C 105 UNP O00560 EXPRESSION TAG SEQADV 8BLU SER D 104 UNP O00560 EXPRESSION TAG SEQADV 8BLU 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 SO4 A 303 5 HET EDO B 301 4 HET EDO B 302 4 HET GOL B 303 6 HET SO4 B 304 5 HET DGL B 305 10 HET MES B 306 12 HET EDO C 301 4 HET EDO C 302 4 HET EDO C 303 4 HET GLY C 304 5 HET GLY C 305 5 HET GLY C 306 5 HET EDO D 301 4 HET EDO D 302 4 HET GOL D 303 6 HET SO4 D 304 5 HET GLY D 305 5 HET DGL D 306 10 HET ALA D 307 6 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM DGL D-GLUTAMIC ACID HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM GLY GLYCINE HETNAM ALA ALANINE HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 EDO 9(C2 H6 O2) FORMUL 7 SO4 3(O4 S 2-) FORMUL 10 GOL 2(C3 H8 O3) FORMUL 12 DGL 2(C5 H9 N O4) FORMUL 13 MES C6 H13 N O4 S FORMUL 17 GLY 4(C2 H5 N O2) FORMUL 26 ALA C3 H7 N O2 FORMUL 27 HOH *774(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 SER A 261 1 12 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 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 GLN C 180 1 11 HELIX 15 AB6 SER C 225 ASN C 230 1 6 HELIX 16 AB7 LYS C 250 SER C 261 1 12 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 ILE D 279 1 8 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 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 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 LEU B 159 O THR B 189 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 LEU B 159 O THR B 189 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 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 267 N ILE C 199 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 ILE C 267 N ILE C 199 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 4 ILE D 112 CYS D 118 0 SHEET 2 AB4 4 LYS D 185 ARG D 191 -1 O ILE D 186 N LEU D 117 SHEET 3 AB4 4 GLN D 157 ILE D 161 -1 N LEU D 159 O THR D 189 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 PHE D 137 N LYS D 130 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 79.603 49.588 118.194 90.00 93.93 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 0.012562 0.000000 0.000863 0.00000 SCALE2 0.000000 0.020166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008481 0.00000