PDB Short entry for 1NTE HEADER SIGNALING PROTEIN 29-JAN-03 1NTE TITLE CRYSTAL STRUCTURE ANALYSIS OF THE SECOND PDZ DOMAIN OF SYNTENIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTENIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ 2; 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SDCBP OR MDA9 OR SYCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGST-PARALLEL KEYWDS SYNTENIN, PDZ RECOGNITION, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.S.KANG,D.R.COOPER,Y.DEVEDJIEV,U.DEREWENDA,Z.S.DEREWENDA REVDAT 4 16-AUG-23 1NTE 1 REMARK SEQADV LINK REVDAT 3 02-MAY-12 1NTE 1 AUTHOR JRNL VERSN REVDAT 2 24-FEB-09 1NTE 1 VERSN REVDAT 1 15-JUL-03 1NTE 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. 1.24 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) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 15684 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) : 0.115 REMARK 3 R VALUE (WORKING SET) : 0.113 REMARK 3 FREE R VALUE : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 851 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) : 1.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.27 REMARK 3 REFLECTION IN BIN (WORKING SET) : 801 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1590 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.1970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 608 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : -0.18000 REMARK 3 B33 (A**2) : 0.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.26000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.027 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.603 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 632 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 590 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 851 ; 1.626 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1384 ; 1.885 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 81 ; 6.398 ; 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): 105 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 687 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 112 ; 0.019 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 115 ; 0.246 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 709 ; 0.252 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 364 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 108 ; 0.254 ; 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): 11 ; 0.103 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 46 ; 0.332 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 53 ; 0.184 ; 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): 406 ; 1.312 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 665 ; 1.956 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 226 ; 2.474 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 186 ; 3.372 ; 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): 632 ; 1.271 ; 2.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 176 ; 5.089 ; 2.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 625 ; 3.222 ; 2.000 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 1NTE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018184. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 12.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.3 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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 (%): 12.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 7.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 294K 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 21.28500 REMARK 290 SMTRY3 2 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: 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 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 100 O HOH A 124 1.65 REMARK 500 O O A 178 O HOH A 104 2.07 REMARK 500 O HOH A 104 O HOH A 155 2.08 REMARK 500 O HOH A 30 O HOH A 174 2.11 REMARK 500 O HOH A 89 O HOH A 173 2.13 REMARK 500 CD LYS A 250 O HOH A 151 2.14 REMARK 500 O HOH A 37 O HOH A 131 2.14 REMARK 500 O HOH A 131 O HOH A 146 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE O A 178 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 DBREF 1NTE A 197 273 UNP O00560 SDCB1_HUMAN 197 273 SEQADV 1NTE GLY A 192 UNP O00560 CLONING ARTIFACT SEQADV 1NTE ALA A 193 UNP O00560 CLONING ARTIFACT SEQADV 1NTE MET A 194 UNP O00560 CLONING ARTIFACT SEQADV 1NTE ASP A 195 UNP O00560 CLONING ARTIFACT SEQADV 1NTE PRO A 196 UNP O00560 CLONING ARTIFACT SEQRES 1 A 82 GLY ALA MET ASP PRO ARG THR ILE THR MET HIS LYS ASP SEQRES 2 A 82 SER THR GLY HIS VAL GLY PHE ILE PHE LYS ASN GLY LYS SEQRES 3 A 82 ILE THR SER ILE VAL LYS ASP SER SER ALA ALA ARG ASN SEQRES 4 A 82 GLY LEU LEU THR GLU HIS ASN ILE CYS GLU ILE ASN GLY SEQRES 5 A 82 GLN ASN VAL ILE GLY LEU LYS ASP SER GLN ILE ALA ASP SEQRES 6 A 82 ILE LEU SER THR SER GLY THR VAL VAL THR ILE THR ILE SEQRES 7 A 82 MET PRO ALA PHE HET O A 178 1 HETNAM O OXYGEN ATOM FORMUL 2 O O FORMUL 3 HOH *175(H2 O) HELIX 1 1 SER A 225 GLY A 231 1 7 HELIX 2 2 LYS A 250 SER A 261 1 12 SHEET 1 A 4 ARG A 197 HIS A 202 0 SHEET 2 A 4 VAL A 264 PRO A 271 -1 O ILE A 269 N ARG A 197 SHEET 3 A 4 HIS A 236 ILE A 241 -1 N ASN A 237 O MET A 270 SHEET 4 A 4 GLN A 244 ASN A 245 -1 O GLN A 244 N ILE A 241 SHEET 1 B 2 PHE A 211 LYS A 214 0 SHEET 2 B 2 LYS A 217 ILE A 221 -1 O LYS A 217 N LYS A 214 LINK O O A 178 SG BCYS A 239 1555 1555 1.20 SITE 1 AC1 4 HOH A 104 HOH A 155 CYS A 239 ASN A 245 CRYST1 25.292 42.570 31.038 90.00 108.71 90.00 P 1 21 1 2 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 0.039538 0.000000 0.013391 0.00000 SCALE2 0.000000 0.023491 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034016 0.00000