PDB Short entry for 1V1T HEADER CELL ADHESION 23-APR-04 1V1T TITLE CRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN IN COMPLEX WITH TITLE 2 TNEYKV PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTENIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PDZ TANDEM, RESIDUES 108-273; COMPND 5 SYNONYM: SYNDECAN BINDING PROTEIN 1, MELANOMA DIFFERENTIATION COMPND 6 ASSOCIATED PROTEIN-9, MDA-9, SCAFFOLD PROTEIN PBP1, PRO-TGF-ALPHA COMPND 7 CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 18, TACIP18; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TNEYKV PEPTIDE; COMPND 11 CHAIN: S, T; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGST-PARALLEL1; SOURCE 10 OTHER_DETAILS: GENE, SDCBP OR MDA9 OR SYCL; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS CELL ADHESION, ADHESION-COMPLEX, PDZ DOMAIN, SCAFFOLDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.GREMBECKA,T.CIERPICKI,Y.DEVEDJIEV,D.R.COOPER,U.DEREWENDA, AUTHOR 2 Z.S.DEREWENDA REVDAT 7 13-DEC-23 1V1T 1 REMARK REVDAT 6 09-OCT-19 1V1T 1 SOURCE REVDAT 5 30-JAN-19 1V1T 1 REMARK REVDAT 4 30-MAY-12 1V1T 1 AUTHOR REMARK VERSN FORMUL REVDAT 3 24-FEB-09 1V1T 1 VERSN REVDAT 2 22-MAR-06 1V1T 1 SOURCE JRNL REVDAT 1 14-JUN-05 1V1T 0 JRNL AUTH J.GREMBECKA,T.CIERPICKI,Y.DEVEDJIEV,U.DEREWENDA,B.S.KANG, JRNL AUTH 2 J.H.BUSHWELLER,Z.S.DEREWENDA JRNL TITL THE BINDING OF THE PDZ TANDEM OF SYNTENIN TO TARGET JRNL TITL 2 PROTEINS. JRNL REF BIOCHEMISTRY V. 45 3674 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16533050 JRNL DOI 10.1021/BI052225Y REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 30277 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 993 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2232 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2576 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 281 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.53000 REMARK 3 B22 (A**2) : -0.53000 REMARK 3 B33 (A**2) : 1.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.265 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.895 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2616 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2419 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3518 ; 1.475 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5653 ; 0.833 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 332 ; 5.813 ; 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): 412 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2888 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 479 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 480 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2898 ; 0.250 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1689 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 203 ; 0.175 ; 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 ; 0.164 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 78 ; 0.320 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.191 ; 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): 1660 ; 1.504 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2679 ; 2.428 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 956 ; 3.632 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 839 ; 5.613 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 1V1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-04. REMARK 100 THE DEPOSITION ID IS D_1290015043. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97912 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34079 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.700 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): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M NH4CL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 62.83800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.17050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.17050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.41900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.17050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.17050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 94.25700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.17050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.17050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.41900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.17050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.17050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 94.25700 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 62.83800 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 300 REMARK: PROTEIN CHAINS A AND B FORM A DIMERIC REMARK 300 COMPLEX, BUTSINCE EACH OF THESE IS IN COMPLEX REMARK 300 WITH A PEPTIDE(CHAINS S AND T), THIS ENTRY HAS REMARK 300 BEEN CLASSIFIED AS A TETRAMERIC ASSEMBLY. 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, S, T 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 GLY A 108 REMARK 465 ALA A 109 REMARK 465 GLY B 108 REMARK 465 ALA B 109 REMARK 465 MET B 110 REMARK 465 PHE B 273 REMARK 465 THR S 1 REMARK 465 THR T 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 A 2034 O HOH A 2035 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 O HOH A 2003 O HOH B 2116 7556 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 193 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 256 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 172 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 229 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ARG A 193 80.40 -1.76 REMARK 500 ASP B 120 -155.06 -75.49 REMARK 500 ARG B 193 73.74 13.44 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 BEZ A 1274 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N99 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN REMARK 900 RELATED ID: 1NTE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF THE SECOND PDZ DOMAIN OFSYNTENIN 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: 1OBY 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 THE PDZ TANDEM OF SYNTENIN WITH REMARK 900 AN INTERLEUKIN 5 RECEPTOR ALPHA PEPTIDE. DBREF 1V1T A 108 112 PDB 1V1T 1V1T 108 112 DBREF 1V1T A 113 273 UNP O00560 SDB1_HUMAN 113 273 DBREF 1V1T B 108 112 PDB 1V1T 1V1T 108 112 DBREF 1V1T B 113 273 UNP O00560 SDB1_HUMAN 113 273 DBREF 1V1T S 1 6 PDB 1V1T 1V1T 1 6 DBREF 1V1T T 1 6 PDB 1V1T 1V1T 1 6 SEQRES 1 A 166 GLY ALA MET ASP PRO ARG GLU VAL ILE LEU CYS LYS ASP SEQRES 2 A 166 GLN ASP GLY LYS ILE GLY LEU ARG LEU LYS SER ILE ASP SEQRES 3 A 166 ASN GLY ILE PHE VAL GLN LEU VAL GLN ALA ASN SER PRO SEQRES 4 A 166 ALA SER LEU VAL GLY LEU ARG PHE GLY ASP GLN VAL LEU SEQRES 5 A 166 GLN ILE ASN GLY GLU ASN CYS ALA GLY TRP SER SER ASP SEQRES 6 A 166 LYS ALA HIS LYS VAL LEU LYS GLN ALA PHE GLY GLU LYS SEQRES 7 A 166 ILE THR MET THR ILE ARG ASP ARG PRO PHE GLU ARG THR SEQRES 8 A 166 ILE THR MET HIS LYS ASP SER THR GLY HIS VAL GLY PHE SEQRES 9 A 166 ILE PHE LYS ASN GLY LYS ILE THR SER ILE VAL LYS ASP SEQRES 10 A 166 SER SER ALA ALA ARG ASN GLY LEU LEU THR GLU HIS ASN SEQRES 11 A 166 ILE CYS GLU ILE ASN GLY GLN ASN VAL ILE GLY LEU LYS SEQRES 12 A 166 ASP SER GLN ILE ALA ASP ILE LEU SER THR SER GLY THR SEQRES 13 A 166 VAL VAL THR ILE THR ILE MET PRO ALA PHE SEQRES 1 B 166 GLY ALA MET ASP PRO ARG GLU VAL ILE LEU CYS LYS ASP SEQRES 2 B 166 GLN ASP GLY LYS ILE GLY LEU ARG LEU LYS SER ILE ASP SEQRES 3 B 166 ASN GLY ILE PHE VAL GLN LEU VAL GLN ALA ASN SER PRO SEQRES 4 B 166 ALA SER LEU VAL GLY LEU ARG PHE GLY ASP GLN VAL LEU SEQRES 5 B 166 GLN ILE ASN GLY GLU ASN CYS ALA GLY TRP SER SER ASP SEQRES 6 B 166 LYS ALA HIS LYS VAL LEU LYS GLN ALA PHE GLY GLU LYS SEQRES 7 B 166 ILE THR MET THR ILE ARG ASP ARG PRO PHE GLU ARG THR SEQRES 8 B 166 ILE THR MET HIS LYS ASP SER THR GLY HIS VAL GLY PHE SEQRES 9 B 166 ILE PHE LYS ASN GLY LYS ILE THR SER ILE VAL LYS ASP SEQRES 10 B 166 SER SER ALA ALA ARG ASN GLY LEU LEU THR GLU HIS ASN SEQRES 11 B 166 ILE CYS GLU ILE ASN GLY GLN ASN VAL ILE GLY LEU LYS SEQRES 12 B 166 ASP SER GLN ILE ALA ASP ILE LEU SER THR SER GLY THR SEQRES 13 B 166 VAL VAL THR ILE THR ILE MET PRO ALA PHE SEQRES 1 S 6 THR ASN GLU TYR LYS VAL SEQRES 1 T 6 THR ASN GLU TYR LYS VAL HET BEZ A1274 9 HETNAM BEZ BENZOIC ACID FORMUL 5 BEZ C7 H6 O2 FORMUL 6 HOH *281(H2 O) HELIX 1 1 SER A 145 VAL A 150 1 6 HELIX 2 2 SER A 170 ALA A 181 1 12 HELIX 3 3 SER A 225 ASN A 230 1 6 HELIX 4 4 LYS A 250 SER A 261 1 12 HELIX 5 5 SER B 145 VAL B 150 1 6 HELIX 6 6 SER B 170 ALA B 181 1 12 HELIX 7 7 SER B 225 ASN B 230 1 6 HELIX 8 8 LYS B 250 THR B 260 1 11 SHEET 1 AA 5 ARG A 113 CYS A 118 0 SHEET 2 AA 5 LYS A 185 ARG A 191 -1 O ILE A 186 N LEU A 117 SHEET 3 AA 5 GLN A 157 ILE A 161 -1 O GLN A 157 N ARG A 191 SHEET 4 AA 5 GLY A 135 VAL A 141 -1 O ILE A 136 N VAL A 158 SHEET 5 AA 5 LEU A 127 ILE A 132 -1 O ARG A 128 N GLN A 139 SHEET 1 AB 4 ARG A 113 CYS A 118 0 SHEET 2 AB 4 LYS A 185 ARG A 191 -1 O ILE A 186 N LEU A 117 SHEET 3 AB 4 GLN A 157 ILE A 161 -1 O GLN A 157 N ARG A 191 SHEET 4 AB 4 GLU A 164 ASN A 165 -1 O GLU A 164 N ILE A 161 SHEET 1 AC 6 ARG A 197 HIS A 202 0 SHEET 2 AC 6 VAL A 264 PRO A 271 -1 O VAL A 265 N MET A 201 SHEET 3 AC 6 HIS A 236 ILE A 241 -1 O ASN A 237 N MET A 270 SHEET 4 AC 6 LYS A 217 ILE A 221 -1 N ILE A 218 O HIS A 236 SHEET 5 AC 6 PHE A 211 LYS A 214 -1 O ILE A 212 N THR A 219 SHEET 6 AC 6 TYR T 4 VAL T 6 -1 O TYR T 4 N PHE A 213 SHEET 1 AD 4 ARG A 197 HIS A 202 0 SHEET 2 AD 4 VAL A 264 PRO A 271 -1 O VAL A 265 N MET A 201 SHEET 3 AD 4 HIS A 236 ILE A 241 -1 O ASN A 237 N MET A 270 SHEET 4 AD 4 GLN A 244 ASN A 245 -1 O GLN A 244 N ILE A 241 SHEET 1 BA 4 ARG B 113 CYS B 118 0 SHEET 2 BA 4 LYS B 185 ARG B 191 -1 O ILE B 186 N LEU B 117 SHEET 3 BA 4 GLN B 157 ILE B 161 -1 O GLN B 157 N ARG B 191 SHEET 4 BA 4 GLU B 164 ASN B 165 -1 O GLU B 164 N ILE B 161 SHEET 1 BB 2 LEU B 127 ILE B 132 0 SHEET 2 BB 2 GLY B 135 VAL B 141 -1 O GLY B 135 N ILE B 132 SHEET 1 BC 6 ARG B 197 HIS B 202 0 SHEET 2 BC 6 VAL B 264 PRO B 271 -1 O VAL B 265 N MET B 201 SHEET 3 BC 6 HIS B 236 ILE B 241 -1 O ASN B 237 N MET B 270 SHEET 4 BC 6 LYS B 217 ILE B 221 -1 N ILE B 218 O HIS B 236 SHEET 5 BC 6 PHE B 211 LYS B 214 -1 O ILE B 212 N THR B 219 SHEET 6 BC 6 TYR S 4 VAL S 6 -1 O TYR S 4 N PHE B 213 SHEET 1 BD 4 ARG B 197 HIS B 202 0 SHEET 2 BD 4 VAL B 264 PRO B 271 -1 O VAL B 265 N MET B 201 SHEET 3 BD 4 HIS B 236 ILE B 241 -1 O ASN B 237 N MET B 270 SHEET 4 BD 4 GLN B 244 ASN B 245 -1 O GLN B 244 N ILE B 241 SITE 1 AC1 9 ASP A 120 GLY A 126 ASN A 144 SER A 145 SITE 2 AC1 9 PRO A 146 HIS A 202 SER A 226 ARG A 229 SITE 3 AC1 9 ASN A 230 CRYST1 72.341 72.341 125.676 90.00 90.00 90.00 P 41 21 2 16 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 0.013823 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007957 0.00000