PDB Short entry for 2V90 HEADER PROTEIN BINDING 16-AUG-07 2V90 TITLE CRYSTAL STRUCTURE OF THE 3RD PDZ DOMAIN OF INTESTINE- AND KIDNEY- TITLE 2 ENRICHED PDZ DOMAIN IKEPP (PDZD3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PDZ DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 FRAGMENT: PDZ DOMAIN, RESIDUES 246-335; COMPND 5 SYNONYM: PDZ DOMAIN-CONTAINING PROTEIN 2, INTESTINAL AND KIDNEY- COMPND 6 ENRICHED PDZ PROTEIN, INTESTINE- AND KIDNEY-ENRICHED PDZ DOMAIN COMPND 7 IKEPP; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: R3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC-BSA4 KEYWDS PDZD3, MEMBRANE, PDZ DOMAIN, PROTEIN-BINDING, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.UPPENBERG,C.GILEADI,C.PHILLIPS,J.ELKINS,G.BUNKOCZI,C.COOPER, AUTHOR 2 A.C.W.PIKE,E.SALAH,E.UGOCHUKWU,C.H.ARROWSMITH,A.EDWARDS,M.SUNDSTROM, AUTHOR 3 J.WEIGELT,D.A.DOYLE REVDAT 6 13-DEC-23 2V90 1 REMARK REVDAT 5 04-MAR-20 2V90 1 REMARK REVDAT 4 28-FEB-18 2V90 1 SOURCE REVDAT 3 13-JUL-11 2V90 1 VERSN REVDAT 2 24-FEB-09 2V90 1 VERSN REVDAT 1 28-AUG-07 2V90 0 JRNL AUTH J.UPPENBERG,C.GILEADI,C.PHILLIPS,J.ELKINS,G.BUNKOCZI, JRNL AUTH 2 C.COOPER,A.C.W.PIKE,E.SALAH,E.UGOCHUKWU,C.H.ARROWSMITH, JRNL AUTH 3 A.EDWARDS,M.SUNDSTROM,J.WEIGELT,D.A.DOYLE JRNL TITL CRYSTAL STRUCTURE OF THE 3RD PDZ DOMAIN OF INTESTINE- AND JRNL TITL 2 KIDNEY-ENRICHED PDZ DOMAIN IKEPP (PDZD3) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0034 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 34206 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1798 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2477 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4213 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 388 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.64000 REMARK 3 B22 (A**2) : 0.19000 REMARK 3 B33 (A**2) : 0.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.59000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.216 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.184 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4320 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3042 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5825 ; 1.475 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7415 ; 0.923 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 560 ; 6.891 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 189 ;34.090 ;24.233 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 738 ;14.858 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;21.960 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 625 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4886 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 816 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 720 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3059 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1965 ; 0.165 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2520 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 282 ; 0.170 ; 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): 40 ; 0.259 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 103 ; 0.250 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 41 ; 0.153 ; 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): 2885 ; 3.276 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4429 ; 4.324 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1597 ; 7.078 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1396 ; 9.687 ;11.000 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C D E F REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 3 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 244 A 267 5 REMARK 3 1 B 244 B 267 5 REMARK 3 1 C 244 C 267 5 REMARK 3 1 D 244 D 267 5 REMARK 3 1 E 244 E 267 5 REMARK 3 1 F 244 F 267 5 REMARK 3 2 A 275 A 299 5 REMARK 3 2 B 275 B 299 5 REMARK 3 2 C 275 C 299 5 REMARK 3 2 D 275 D 299 5 REMARK 3 2 E 275 E 299 5 REMARK 3 2 F 275 F 299 5 REMARK 3 3 A 300 A 332 5 REMARK 3 3 B 300 B 332 5 REMARK 3 3 C 300 C 332 5 REMARK 3 3 D 300 D 332 5 REMARK 3 3 E 300 E 332 5 REMARK 3 3 F 300 F 332 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 458 ; 0.22 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 458 ; 0.20 ; 0.00 REMARK 3 MEDIUM POSITIONAL 1 C (A): 458 ; 0.17 ; 0.00 REMARK 3 MEDIUM POSITIONAL 1 D (A): 458 ; 0.20 ; 0.00 REMARK 3 MEDIUM POSITIONAL 1 E (A): 458 ; 0.24 ; 0.00 REMARK 3 MEDIUM POSITIONAL 1 F (A): 458 ; 0.28 ; 0.00 REMARK 3 LOOSE POSITIONAL 1 A (A): 522 ; 0.52 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 B (A): 522 ; 0.58 ; 0.01 REMARK 3 LOOSE POSITIONAL 1 C (A): 522 ; 0.40 ; 0.00 REMARK 3 LOOSE POSITIONAL 1 D (A): 522 ; 0.41 ; 0.00 REMARK 3 LOOSE POSITIONAL 1 E (A): 522 ; 0.51 ; 0.00 REMARK 3 LOOSE POSITIONAL 1 F (A): 522 ; 0.62 ; 0.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 458 ; 1.35 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 458 ; 1.23 ; 0.00 REMARK 3 MEDIUM THERMAL 1 C (A**2): 458 ; 1.19 ; 0.00 REMARK 3 MEDIUM THERMAL 1 D (A**2): 458 ; 1.17 ; 0.00 REMARK 3 MEDIUM THERMAL 1 E (A**2): 458 ; 1.11 ; 0.00 REMARK 3 MEDIUM THERMAL 1 F (A**2): 458 ; 1.15 ; 0.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 522 ; 1.23 ; 10.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 522 ; 1.15 ; 0.02 REMARK 3 LOOSE THERMAL 1 C (A**2): 522 ; 1.26 ; 0.00 REMARK 3 LOOSE THERMAL 1 D (A**2): 522 ; 1.16 ; 0.00 REMARK 3 LOOSE THERMAL 1 E (A**2): 522 ; 1.19 ; 0.00 REMARK 3 LOOSE THERMAL 1 F (A**2): 522 ; 1.12 ; 0.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 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 244 A 339 REMARK 3 ORIGIN FOR THE GROUP (A): 5.2995 -41.8697 -9.6254 REMARK 3 T TENSOR REMARK 3 T11: -0.0210 T22: -0.0803 REMARK 3 T33: -0.0702 T12: -0.0306 REMARK 3 T13: 0.0058 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 3.4807 L22: 1.0563 REMARK 3 L33: 0.6207 L12: -0.1868 REMARK 3 L13: -0.2934 L23: -0.2742 REMARK 3 S TENSOR REMARK 3 S11: 0.1687 S12: -0.2304 S13: 0.0532 REMARK 3 S21: 0.1656 S22: -0.0877 S23: -0.0234 REMARK 3 S31: 0.0417 S32: -0.0337 S33: -0.0809 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 244 B 339 REMARK 3 ORIGIN FOR THE GROUP (A): 24.7695 7.0052 19.6598 REMARK 3 T TENSOR REMARK 3 T11: -0.0122 T22: -0.0680 REMARK 3 T33: -0.0683 T12: -0.0278 REMARK 3 T13: 0.0207 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 3.0706 L22: 1.1388 REMARK 3 L33: 1.2009 L12: 0.3280 REMARK 3 L13: 0.0924 L23: 0.2339 REMARK 3 S TENSOR REMARK 3 S11: 0.1567 S12: -0.2553 S13: 0.1195 REMARK 3 S21: 0.2491 S22: -0.1393 S23: 0.0433 REMARK 3 S31: 0.0110 S32: -0.0693 S33: -0.0174 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 244 C 339 REMARK 3 ORIGIN FOR THE GROUP (A): 23.7061 -21.5426 1.9500 REMARK 3 T TENSOR REMARK 3 T11: -0.0386 T22: -0.0500 REMARK 3 T33: -0.0192 T12: 0.0087 REMARK 3 T13: -0.0177 T23: -0.0275 REMARK 3 L TENSOR REMARK 3 L11: 3.3846 L22: 1.5008 REMARK 3 L33: 0.7576 L12: -0.5972 REMARK 3 L13: -0.2844 L23: 0.1992 REMARK 3 S TENSOR REMARK 3 S11: -0.0078 S12: -0.0800 S13: -0.3736 REMARK 3 S21: 0.2709 S22: 0.0279 S23: -0.1230 REMARK 3 S31: 0.1497 S32: 0.0288 S33: -0.0201 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 244 D 339 REMARK 3 ORIGIN FOR THE GROUP (A): 42.5827 27.2955 31.6913 REMARK 3 T TENSOR REMARK 3 T11: 0.0129 T22: -0.0652 REMARK 3 T33: -0.0588 T12: 0.0052 REMARK 3 T13: -0.0304 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 3.3111 L22: 2.2305 REMARK 3 L33: 1.0788 L12: -0.9149 REMARK 3 L13: -0.5183 L23: 0.8506 REMARK 3 S TENSOR REMARK 3 S11: -0.0142 S12: -0.1475 S13: -0.2936 REMARK 3 S21: 0.3336 S22: 0.0264 S23: -0.1596 REMARK 3 S31: 0.1467 S32: 0.1002 S33: -0.0122 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 244 E 339 REMARK 3 ORIGIN FOR THE GROUP (A): 5.6602 -12.6624 -3.8867 REMARK 3 T TENSOR REMARK 3 T11: -0.0519 T22: -0.0444 REMARK 3 T33: -0.0551 T12: 0.0249 REMARK 3 T13: 0.0076 T23: -0.0379 REMARK 3 L TENSOR REMARK 3 L11: 2.7214 L22: 0.9487 REMARK 3 L33: 1.5781 L12: -0.3478 REMARK 3 L13: 0.9577 L23: 0.1659 REMARK 3 S TENSOR REMARK 3 S11: -0.0155 S12: 0.1338 S13: 0.0797 REMARK 3 S21: -0.0223 S22: -0.0865 S23: 0.0371 REMARK 3 S31: -0.0951 S32: -0.0824 S33: 0.1019 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 244 F 339 REMARK 3 ORIGIN FOR THE GROUP (A): 24.4390 36.1391 25.7232 REMARK 3 T TENSOR REMARK 3 T11: 0.0221 T22: -0.0174 REMARK 3 T33: -0.0493 T12: 0.0325 REMARK 3 T13: -0.0158 T23: -0.0282 REMARK 3 L TENSOR REMARK 3 L11: 3.2220 L22: 0.8533 REMARK 3 L33: 1.4356 L12: -0.3194 REMARK 3 L13: 1.2404 L23: 0.3897 REMARK 3 S TENSOR REMARK 3 S11: 0.0595 S12: 0.1987 S13: 0.1127 REMARK 3 S21: -0.0673 S22: -0.1346 S23: 0.0731 REMARK 3 S31: -0.1336 S32: -0.0896 S33: 0.0751 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. REMARK 4 REMARK 4 2V90 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1290033471. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03315 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36079 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1G9O REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M (NH4)2SO4, 0.1M BIS-TRIS, PH=5.5, REMARK 280 PH 5.5 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 48.97500 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, E 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, F 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 244 REMARK 465 SER B 244 REMARK 465 SER C 244 REMARK 465 MET C 245 REMARK 465 LYS C 246 REMARK 465 SER D 244 REMARK 465 MET D 245 REMARK 465 LYS D 246 REMARK 465 SER E 244 REMARK 465 SER F 244 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU C 253 CD OE1 OE2 REMARK 470 GLU D 311 CD OE1 OE2 REMARK 470 ASP D 334 CG OD1 OD2 REMARK 470 MET E 245 CG SD CE REMARK 470 LYS E 246 CD CE NZ REMARK 470 GLN E 257 CG CD OE1 NE2 REMARK 470 MET F 245 CG SD CE REMARK 470 LYS F 246 CD CE NZ 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 OE2 GLU F 312 O HOH F 2047 2.14 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 335 55.94 -95.66 REMARK 500 ARG B 335 57.78 -91.75 REMARK 500 ARG F 335 45.71 -104.67 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 A1340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1341 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE LAST 4 RESIDUES (GLU336-VAL339) IS A COMMON PDZ-BINDING REMARK 999 SEQUENCE ENGINEERED AT THE C-TERMINUS OF THE PROTEIN TO PROMOTE REMARK 999 MACROMOLECULAR CONTACTS. THE FIRST TWO RESIDUES BELONG TO A REMARK 999 CLEAVED HIS-TAG LINKER DBREF 2V90 A 244 245 PDB 2V90 2V90 244 245 DBREF 2V90 A 246 335 UNP Q86UT5 PDZD3_HUMAN 246 335 DBREF 2V90 A 336 339 PDB 2V90 2V90 336 339 DBREF 2V90 B 244 245 PDB 2V90 2V90 244 245 DBREF 2V90 B 246 335 UNP Q86UT5 PDZD3_HUMAN 246 335 DBREF 2V90 B 336 339 PDB 2V90 2V90 336 339 DBREF 2V90 C 244 245 PDB 2V90 2V90 244 245 DBREF 2V90 C 246 335 UNP Q86UT5 PDZD3_HUMAN 246 335 DBREF 2V90 C 336 339 PDB 2V90 2V90 336 339 DBREF 2V90 D 244 245 PDB 2V90 2V90 244 245 DBREF 2V90 D 246 335 UNP Q86UT5 PDZD3_HUMAN 246 335 DBREF 2V90 D 336 339 PDB 2V90 2V90 336 339 DBREF 2V90 E 244 245 PDB 2V90 2V90 244 245 DBREF 2V90 E 246 335 UNP Q86UT5 PDZD3_HUMAN 246 335 DBREF 2V90 E 336 339 PDB 2V90 2V90 336 339 DBREF 2V90 F 244 245 PDB 2V90 2V90 244 245 DBREF 2V90 F 246 335 UNP Q86UT5 PDZD3_HUMAN 246 335 DBREF 2V90 F 336 339 PDB 2V90 2V90 336 339 SEQRES 1 A 96 SER MET LYS PRO ARG CYS LEU HIS LEU GLU LYS GLY PRO SEQRES 2 A 96 GLN GLY PHE GLY PHE LEU LEU ARG GLU GLU LYS GLY LEU SEQRES 3 A 96 ASP GLY ARG PRO GLY GLN PHE LEU TRP GLU VAL ASP PRO SEQRES 4 A 96 GLY LEU PRO ALA LYS LYS ALA GLY MET GLN ALA GLY ASP SEQRES 5 A 96 ARG LEU VAL ALA VAL ALA GLY GLU SER VAL GLU GLY LEU SEQRES 6 A 96 GLY HIS GLU GLU THR VAL SER ARG ILE GLN GLY GLN GLY SEQRES 7 A 96 SER CYS VAL SER LEU THR VAL VAL ASP PRO GLU ALA ASP SEQRES 8 A 96 ARG GLU THR SER VAL SEQRES 1 B 96 SER MET LYS PRO ARG CYS LEU HIS LEU GLU LYS GLY PRO SEQRES 2 B 96 GLN GLY PHE GLY PHE LEU LEU ARG GLU GLU LYS GLY LEU SEQRES 3 B 96 ASP GLY ARG PRO GLY GLN PHE LEU TRP GLU VAL ASP PRO SEQRES 4 B 96 GLY LEU PRO ALA LYS LYS ALA GLY MET GLN ALA GLY ASP SEQRES 5 B 96 ARG LEU VAL ALA VAL ALA GLY GLU SER VAL GLU GLY LEU SEQRES 6 B 96 GLY HIS GLU GLU THR VAL SER ARG ILE GLN GLY GLN GLY SEQRES 7 B 96 SER CYS VAL SER LEU THR VAL VAL ASP PRO GLU ALA ASP SEQRES 8 B 96 ARG GLU THR SER VAL SEQRES 1 C 96 SER MET LYS PRO ARG CYS LEU HIS LEU GLU LYS GLY PRO SEQRES 2 C 96 GLN GLY PHE GLY PHE LEU LEU ARG GLU GLU LYS GLY LEU SEQRES 3 C 96 ASP GLY ARG PRO GLY GLN PHE LEU TRP GLU VAL ASP PRO SEQRES 4 C 96 GLY LEU PRO ALA LYS LYS ALA GLY MET GLN ALA GLY ASP SEQRES 5 C 96 ARG LEU VAL ALA VAL ALA GLY GLU SER VAL GLU GLY LEU SEQRES 6 C 96 GLY HIS GLU GLU THR VAL SER ARG ILE GLN GLY GLN GLY SEQRES 7 C 96 SER CYS VAL SER LEU THR VAL VAL ASP PRO GLU ALA ASP SEQRES 8 C 96 ARG GLU THR SER VAL SEQRES 1 D 96 SER MET LYS PRO ARG CYS LEU HIS LEU GLU LYS GLY PRO SEQRES 2 D 96 GLN GLY PHE GLY PHE LEU LEU ARG GLU GLU LYS GLY LEU SEQRES 3 D 96 ASP GLY ARG PRO GLY GLN PHE LEU TRP GLU VAL ASP PRO SEQRES 4 D 96 GLY LEU PRO ALA LYS LYS ALA GLY MET GLN ALA GLY ASP SEQRES 5 D 96 ARG LEU VAL ALA VAL ALA GLY GLU SER VAL GLU GLY LEU SEQRES 6 D 96 GLY HIS GLU GLU THR VAL SER ARG ILE GLN GLY GLN GLY SEQRES 7 D 96 SER CYS VAL SER LEU THR VAL VAL ASP PRO GLU ALA ASP SEQRES 8 D 96 ARG GLU THR SER VAL SEQRES 1 E 96 SER MET LYS PRO ARG CYS LEU HIS LEU GLU LYS GLY PRO SEQRES 2 E 96 GLN GLY PHE GLY PHE LEU LEU ARG GLU GLU LYS GLY LEU SEQRES 3 E 96 ASP GLY ARG PRO GLY GLN PHE LEU TRP GLU VAL ASP PRO SEQRES 4 E 96 GLY LEU PRO ALA LYS LYS ALA GLY MET GLN ALA GLY ASP SEQRES 5 E 96 ARG LEU VAL ALA VAL ALA GLY GLU SER VAL GLU GLY LEU SEQRES 6 E 96 GLY HIS GLU GLU THR VAL SER ARG ILE GLN GLY GLN GLY SEQRES 7 E 96 SER CYS VAL SER LEU THR VAL VAL ASP PRO GLU ALA ASP SEQRES 8 E 96 ARG GLU THR SER VAL SEQRES 1 F 96 SER MET LYS PRO ARG CYS LEU HIS LEU GLU LYS GLY PRO SEQRES 2 F 96 GLN GLY PHE GLY PHE LEU LEU ARG GLU GLU LYS GLY LEU SEQRES 3 F 96 ASP GLY ARG PRO GLY GLN PHE LEU TRP GLU VAL ASP PRO SEQRES 4 F 96 GLY LEU PRO ALA LYS LYS ALA GLY MET GLN ALA GLY ASP SEQRES 5 F 96 ARG LEU VAL ALA VAL ALA GLY GLU SER VAL GLU GLY LEU SEQRES 6 F 96 GLY HIS GLU GLU THR VAL SER ARG ILE GLN GLY GLN GLY SEQRES 7 F 96 SER CYS VAL SER LEU THR VAL VAL ASP PRO GLU ALA ASP SEQRES 8 F 96 ARG GLU THR SER VAL HET SO4 A1340 5 HET SO4 B1340 5 HET SO4 B1341 5 HETNAM SO4 SULFATE ION FORMUL 7 SO4 3(O4 S 2-) FORMUL 10 HOH *388(H2 O) HELIX 1 1 LEU A 284 ALA A 289 1 6 HELIX 2 2 GLY A 309 GLY A 319 1 11 HELIX 3 3 LEU B 284 ALA B 289 1 6 HELIX 4 4 GLY B 309 GLY B 319 1 11 HELIX 5 5 LEU C 284 ALA C 289 1 6 HELIX 6 6 GLY C 309 GLY C 319 1 11 HELIX 7 7 LEU D 284 ALA D 289 1 6 HELIX 8 8 GLY D 309 GLY D 319 1 11 HELIX 9 9 LEU E 284 ALA E 289 1 6 HELIX 10 10 GLY E 309 GLY E 319 1 11 HELIX 11 11 LEU F 284 ALA F 289 1 6 HELIX 12 12 GLY F 309 GLY F 319 1 11 SHEET 1 AA 5 ARG A 248 GLU A 253 0 SHEET 2 AA 5 CYS A 323 VAL A 329 -1 O VAL A 324 N LEU A 252 SHEET 3 AA 5 ASP A 295 VAL A 300 -1 O ARG A 296 N VAL A 329 SHEET 4 AA 5 PRO A 273 VAL A 280 -1 O GLN A 275 N LEU A 297 SHEET 5 AA 5 PHE A 261 LYS A 267 -1 O LEU A 262 N TRP A 278 SHEET 1 AB 4 ARG A 248 GLU A 253 0 SHEET 2 AB 4 CYS A 323 VAL A 329 -1 O VAL A 324 N LEU A 252 SHEET 3 AB 4 ASP A 295 VAL A 300 -1 O ARG A 296 N VAL A 329 SHEET 4 AB 4 GLU A 303 SER A 304 -1 O GLU A 303 N VAL A 300 SHEET 1 BA 5 ARG B 248 GLU B 253 0 SHEET 2 BA 5 CYS B 323 VAL B 329 -1 O VAL B 324 N LEU B 252 SHEET 3 BA 5 ARG B 296 VAL B 300 -1 O ARG B 296 N VAL B 329 SHEET 4 BA 5 PRO B 273 VAL B 280 -1 O GLN B 275 N LEU B 297 SHEET 5 BA 5 PHE B 261 LYS B 267 -1 O LEU B 262 N TRP B 278 SHEET 1 BB 4 ARG B 248 GLU B 253 0 SHEET 2 BB 4 CYS B 323 VAL B 329 -1 O VAL B 324 N LEU B 252 SHEET 3 BB 4 ARG B 296 VAL B 300 -1 O ARG B 296 N VAL B 329 SHEET 4 BB 4 GLU B 303 SER B 304 -1 O GLU B 303 N VAL B 300 SHEET 1 CA 4 ARG C 248 GLU C 253 0 SHEET 2 CA 4 CYS C 323 VAL C 329 -1 O VAL C 324 N LEU C 252 SHEET 3 CA 4 ARG C 296 VAL C 300 -1 O ARG C 296 N VAL C 329 SHEET 4 CA 4 GLU C 303 SER C 304 -1 O GLU C 303 N VAL C 300 SHEET 1 CB 3 PRO C 273 VAL C 280 0 SHEET 2 CB 3 PHE C 261 LYS C 267 -1 O LEU C 262 N TRP C 278 SHEET 3 CB 3 GLU E 336 VAL E 339 -1 O THR E 337 N LEU C 263 SHEET 1 CC 3 GLU C 336 VAL C 339 0 SHEET 2 CC 3 PHE E 261 LYS E 267 -1 O PHE E 261 N VAL C 339 SHEET 3 CC 3 PRO E 273 VAL E 280 -1 O GLY E 274 N GLU E 266 SHEET 1 DA 4 ARG D 248 GLU D 253 0 SHEET 2 DA 4 CYS D 323 VAL D 329 -1 O VAL D 324 N LEU D 252 SHEET 3 DA 4 ARG D 296 VAL D 300 -1 O ARG D 296 N VAL D 329 SHEET 4 DA 4 GLU D 303 SER D 304 -1 O GLU D 303 N VAL D 300 SHEET 1 DB 3 PRO D 273 VAL D 280 0 SHEET 2 DB 3 PHE D 261 LYS D 267 -1 O LEU D 262 N TRP D 278 SHEET 3 DB 3 GLU F 336 VAL F 339 -1 O THR F 337 N LEU D 263 SHEET 1 DC 3 GLU D 336 VAL D 339 0 SHEET 2 DC 3 PHE F 261 LYS F 267 -1 O PHE F 261 N VAL D 339 SHEET 3 DC 3 PRO F 273 VAL F 280 -1 O GLY F 274 N GLU F 266 SHEET 1 EA 4 ARG E 248 GLU E 253 0 SHEET 2 EA 4 CYS E 323 VAL E 329 -1 O VAL E 324 N LEU E 252 SHEET 3 EA 4 ARG E 296 VAL E 300 -1 O ARG E 296 N VAL E 329 SHEET 4 EA 4 GLU E 303 SER E 304 -1 O GLU E 303 N VAL E 300 SHEET 1 FA 4 ARG F 248 GLU F 253 0 SHEET 2 FA 4 CYS F 323 VAL F 329 -1 O VAL F 324 N LEU F 252 SHEET 3 FA 4 ARG F 296 VAL F 300 -1 O ARG F 296 N VAL F 329 SHEET 4 FA 4 GLU F 303 SER F 304 -1 O GLU F 303 N VAL F 300 SITE 1 AC1 5 GLY A 268 LEU A 269 ASP A 270 HOH A2073 SITE 2 AC1 5 HOH A2074 SITE 1 AC2 6 GLY B 268 LEU B 269 ASP B 270 SO4 B1341 SITE 2 AC2 6 HOH B2063 HOH B2064 SITE 1 AC3 4 GLY B 268 ARG B 296 SO4 B1340 HOH B2065 CRYST1 48.150 97.950 59.500 90.00 99.59 90.00 P 1 21 1 12 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 0.020768 0.000000 0.003509 0.00000 SCALE2 0.000000 0.010209 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017045 0.00000 MTRIX1 1 0.999960 -0.006190 0.005780 19.25825 1 MTRIX2 1 0.006320 0.999720 -0.022630 48.58855 1 MTRIX3 1 -0.005640 0.022660 0.999730 30.25384 1 MTRIX1 2 -0.999960 0.007900 -0.004990 29.15355 1 MTRIX2 2 0.000350 -0.502090 -0.864820 -51.12002 1 MTRIX3 2 -0.009330 -0.864780 0.502060 -29.03732 1 MTRIX1 3 -0.999770 0.019700 -0.008000 48.38662 1 MTRIX2 3 -0.002930 -0.500120 -0.865950 -2.11191 1 MTRIX3 3 -0.021060 -0.865730 0.500060 0.71022 1 MTRIX1 4 0.999940 -0.007200 0.008770 0.23440 1 MTRIX2 4 -0.011310 -0.573580 0.819070 -28.58708 1 MTRIX3 4 -0.000870 -0.819120 -0.573620 -43.79194 1 MTRIX1 5 0.999960 -0.003920 0.008020 19.18380 1 MTRIX2 5 -0.008810 -0.577480 0.816350 20.06012 1 MTRIX3 5 0.001430 -0.816390 -0.577500 -14.01673 1