PDB Short entry for 1OBY HEADER CELL ADHESION 31-JAN-03 1OBY TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF PDZ2 OF SYNTENIN WITH A SYNDECAN-4 TITLE 2 PEPTIDE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTENIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PDZ2, RESIDUES 197-270; COMPND 5 SYNONYM: SYNDECAN BINDING PROTEIN 1, MELANOMA DIFFERENTIATION COMPND 6 ASSOCIATED PROTEIN-9, MDA-9, SCAFFOLD PROTEIN PBP1, TACIP18, PRO-TGF- COMPND 7 ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 18; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SYNDECAN-4; COMPND 11 CHAIN: P, Q; COMPND 12 FRAGMENT: LAST 6 RESIDUES, RESIDUES 193-198; COMPND 13 SYNONYM: AMPHIGLYCAN, SYND4, RYUDOCAN CORE PROTEIN; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ATCC: 72537; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGST-PARALLEL1; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS CELL ADHESION, ADHESION-COMPLEX, PDZ DOMAIN, SIGNAL TRANSDUCTION, KEYWDS 2 NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.S.KANG,D.R.COOPER,Y.DEVEDJIEV,U.DEREWENDA,Z.S.DEREWENDA REVDAT 5 16-OCT-19 1OBY 1 REMARK REVDAT 4 08-MAY-19 1OBY 1 REMARK REVDAT 3 24-FEB-09 1OBY 1 VERSN REVDAT 2 14-OCT-03 1OBY 1 TITLE REVDAT 1 11-JUL-03 1OBY 0 JRNL AUTH B.S.KANG,D.R.COOPER,Y.DEVEDJIEV,U.DEREWENDA,Z.S.DEREWENDA JRNL TITL MOLECULAR ROOTS OF DEGENERATE SPECIFICITY IN SYNTENIN'S PDZ2 JRNL TITL 2 DOMAIN: REASSESSMENT OF THE PDZ RECOGNITION PARADIGM JRNL REF STRUCTURE V. 11 845 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12842047 JRNL DOI 10.1016/S0969-2126(03)00125-4 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 12001 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.600 REMARK 3 FREE R VALUE TEST SET COUNT : 985 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 739 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.05000 REMARK 3 B22 (A**2) : 0.44000 REMARK 3 B33 (A**2) : -1.70000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.68000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.155 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.147 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.107 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.645 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1235 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1118 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1663 ; 1.815 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2610 ; 0.941 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 156 ; 5.762 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 205 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1342 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 222 ; 0.015 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 227 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1273 ; 0.257 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 732 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 96 ; 0.247 ; 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): 28 ; 0.668 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 72 ; 0.366 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.251 ; 0.200 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): 787 ; 1.120 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1275 ; 2.005 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 448 ; 3.160 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 388 ; 5.005 ; 4.500 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 : 2 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 197 A 270 REMARK 3 ORIGIN FOR THE GROUP (A): 8.5350 0.0330 11.4090 REMARK 3 T TENSOR REMARK 3 T11: 0.0839 T22: 0.1013 REMARK 3 T33: 0.0164 T12: 0.0029 REMARK 3 T13: -0.0046 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 1.3204 L22: 2.7056 REMARK 3 L33: 4.8398 L12: 0.5960 REMARK 3 L13: -1.7543 L23: -0.6148 REMARK 3 S TENSOR REMARK 3 S11: -0.0471 S12: -0.0468 S13: -0.0891 REMARK 3 S21: -0.1466 S22: -0.0233 S23: -0.0417 REMARK 3 S31: -0.1767 S32: 0.1682 S33: 0.0705 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 197 B 270 REMARK 3 ORIGIN FOR THE GROUP (A): 8.8390 30.5630 12.2190 REMARK 3 T TENSOR REMARK 3 T11: 0.1082 T22: 0.1033 REMARK 3 T33: 0.0164 T12: -0.0029 REMARK 3 T13: 0.0412 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 1.1031 L22: 1.8190 REMARK 3 L33: 4.9443 L12: -0.6378 REMARK 3 L13: 1.2035 L23: -0.6651 REMARK 3 S TENSOR REMARK 3 S11: -0.0677 S12: -0.0325 S13: 0.0211 REMARK 3 S21: 0.0309 S22: -0.1043 S23: -0.0475 REMARK 3 S31: 0.2779 S32: 0.0963 S33: 0.1720 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 1OBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1290012083. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46421 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.570 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1N99 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SITTING DROP WITH 0.1 M HEPES, PH 6.8, REMARK 280 1.6 M AMMONIUM SULFATE, 20 MM COCL2, AND 0.2 MGSO4, PH 6.80, REMARK 280 VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.16850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.22050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.16850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.22050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P, Q 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2034 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 MOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. REMARK 400 MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELETAL REMARK 400 TRANSCRIPTION PROTEINS OR SIGNALING COMPONENTS. ALSO SEEMS REMARK 400 TO COUPLE FACTOR SOX4 TO THE IL-5 RECEPTOR (IL5RA) REMARK 400 REMARK 400 MOL_ID 2: CELL SURFACE PROTEOGLYCAN CONTAINING HEPARAN REMARK 400 SULFATE 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 GLY A 192 REMARK 465 ALA A 193 REMARK 465 MET A 194 REMARK 465 ASP A 195 REMARK 465 GLY B 192 REMARK 465 ALA B 193 REMARK 465 MET B 194 REMARK 465 ASP B 195 REMARK 465 PRO B 196 REMARK 465 THR P 1 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 2025 O HOH B 2060 1.94 REMARK 500 O HOH B 2015 O HOH B 2039 2.07 REMARK 500 O HOH B 2003 O HOH B 2063 2.15 REMARK 500 O HOH A 2003 O HOH A 2055 2.16 REMARK 500 O HOH A 2017 O HOH A 2018 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 S SO4 A 1271 O4 SO4 A 1271 2555 1.11 REMARK 500 O4 SO4 A 1271 O4 SO4 A 1271 2555 1.26 REMARK 500 O2 SO4 A 1271 O4 SO4 A 1271 2555 1.31 REMARK 500 O1 SO4 A 1271 O3 SO4 A 1271 2555 1.53 REMARK 500 S SO4 A 1271 O3 SO4 A 1271 2555 1.56 REMARK 500 O3 SO4 A 1271 O3 SO4 A 1271 2555 1.67 REMARK 500 O3 SO4 A 1271 O4 SO4 A 1271 2555 2.16 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 229 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP B 224 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1271 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1272 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1271 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NTE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF THE SECOND PDZ DOMAIN OF SYNTENIN REMARK 900 RELATED ID: 1OBX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF PDZ2 OF SYNTENIN WITH AN REMARK 900 INTERLEUKIN 5 RECEPTOR ALPHA PEPTIDE. REMARK 900 RELATED ID: 1OBZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF PDZ TANDEM OF SYNTENIN WITH AN REMARK 900 INTERLEUKIN 5 RECEPTOR ALPHA PEPTIDE REMARK 900 RELATED ID: 1EJP RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMICDOMAIN REMARK 900 RELATED ID: 1EJQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN IN REMARK 900 THE PRESENCE OF PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE DBREF 1OBY A 192 196 PDB 1OBY 1OBY 192 196 DBREF 1OBY A 197 270 UNP O00560 SDB1_HUMAN 197 270 DBREF 1OBY B 192 196 PDB 1OBY 1OBY 192 196 DBREF 1OBY B 197 270 UNP O00560 SDB1_HUMAN 197 270 DBREF 1OBY P 1 6 UNP P31431 SDC4_HUMAN 193 198 DBREF 1OBY Q 1 6 UNP P31431 SDC4_HUMAN 193 198 SEQRES 1 A 79 GLY ALA MET ASP PRO ARG THR ILE THR MET HIS LYS ASP SEQRES 2 A 79 SER THR GLY HIS VAL GLY PHE ILE PHE LYS ASN GLY LYS SEQRES 3 A 79 ILE THR SER ILE VAL LYS ASP SER SER ALA ALA ARG ASN SEQRES 4 A 79 GLY LEU LEU THR GLU HIS ASN ILE CYS GLU ILE ASN GLY SEQRES 5 A 79 GLN ASN VAL ILE GLY LEU LYS ASP SER GLN ILE ALA ASP SEQRES 6 A 79 ILE LEU SER THR SER GLY THR VAL VAL THR ILE THR ILE SEQRES 7 A 79 MET SEQRES 1 B 79 GLY ALA MET ASP PRO ARG THR ILE THR MET HIS LYS ASP SEQRES 2 B 79 SER THR GLY HIS VAL GLY PHE ILE PHE LYS ASN GLY LYS SEQRES 3 B 79 ILE THR SER ILE VAL LYS ASP SER SER ALA ALA ARG ASN SEQRES 4 B 79 GLY LEU LEU THR GLU HIS ASN ILE CYS GLU ILE ASN GLY SEQRES 5 B 79 GLN ASN VAL ILE GLY LEU LYS ASP SER GLN ILE ALA ASP SEQRES 6 B 79 ILE LEU SER THR SER GLY THR VAL VAL THR ILE THR ILE SEQRES 7 B 79 MET SEQRES 1 P 6 THR ASN GLU PHE TYR ALA SEQRES 1 Q 6 THR ASN GLU PHE TYR ALA HET SO4 A1271 5 HET SO4 A1272 5 HET SO4 B1271 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 3(O4 S 2-) FORMUL 8 HOH *145(H2 O) HELIX 1 1 SER A 225 GLY A 231 1 7 HELIX 2 2 LYS A 250 SER A 261 1 12 HELIX 3 3 SER B 225 GLY B 231 1 7 HELIX 4 4 LYS B 250 SER B 261 1 12 SHEET 1 AA 4 ARG A 197 HIS A 202 0 SHEET 2 AA 4 VAL A 264 MET A 270 -1 O VAL A 265 N MET A 201 SHEET 3 AA 4 ASN A 237 ILE A 241 -1 O ASN A 237 N MET A 270 SHEET 4 AA 4 GLN A 244 ASN A 245 -1 O GLN A 244 N ILE A 241 SHEET 1 AB 3 LYS A 217 ILE A 221 0 SHEET 2 AB 3 PHE A 211 LYS A 214 -1 O ILE A 212 N THR A 219 SHEET 3 AB 3 PHE P 4 ALA P 6 -1 O PHE P 4 N PHE A 213 SHEET 1 BA 6 THR B 198 HIS B 202 0 SHEET 2 BA 6 VAL B 264 MET B 270 -1 O VAL B 265 N MET B 201 SHEET 3 BA 6 HIS B 236 ILE B 241 -1 O ASN B 237 N MET B 270 SHEET 4 BA 6 LYS B 217 ILE B 221 -1 N ILE B 218 O HIS B 236 SHEET 5 BA 6 PHE B 211 LYS B 214 -1 O ILE B 212 N THR B 219 SHEET 6 BA 6 PHE Q 4 ALA Q 6 -1 O PHE Q 4 N PHE B 213 SHEET 1 BB 4 THR B 198 HIS B 202 0 SHEET 2 BB 4 VAL B 264 MET B 270 -1 O VAL B 265 N MET B 201 SHEET 3 BB 4 HIS B 236 ILE B 241 -1 O ASN B 237 N MET B 270 SHEET 4 BB 4 GLN B 244 ASN B 245 -1 O GLN B 244 N ILE B 241 SITE 1 AC1 5 PRO A 196 ARG A 197 LEU A 233 HIS A 236 SITE 2 AC1 5 MET A 270 SITE 1 AC2 8 HIS A 202 SER A 226 ARG A 229 ASN A 230 SITE 2 AC2 8 HOH A2008 HOH A2060 LYS B 250 GLN B 253 SITE 1 AC3 6 ASN A 242 SER A 261 GLY A 262 ASN B 215 SITE 2 AC3 6 LYS B 217 HOH B2022 CRYST1 58.337 54.441 50.219 90.00 98.65 90.00 C 1 2 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 0.017142 0.000000 0.002609 0.00000 SCALE2 0.000000 0.018368 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020142 0.00000