HEADER STRUCTURAL PROTEIN 21-DEC-04 1YBO TITLE CRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN WITH SYNDECAN TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTENIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SYNDECAN BINDING PROTEIN 1, MELANOMA DIFFERENTIATION COMPND 5 ASSOCIATED PROTEIN-9, MDA-9, SCAFFOLD PROTEIN PBP1, PRO-TGF-ALPHA COMPND 6 CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 18, TACIP18; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SYNDECAN-4; COMPND 10 CHAIN: C, D; COMPND 11 SYNONYM: AMPHIGLYCAN, SYND4, RYUDOCAN CORE PROTEIN; 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 GENE: SDCBP, MDA9, SYCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGST-PARALLEL-1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHESIZED PEPTIDE COORESPONDING TO THE C-TERMINUS SOURCE 14 OF SYNDECAN KEYWDS PDZ DOMAIN, SCAFFOLDING PROTEIN, ADHESION COMPLEX, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.GREMBECKA,D.R.COOPER,T.CIERPICKI,B.S.KANG,Y.DEVEDJIEV,Z.DEREWENDA REVDAT 6 23-AUG-23 1YBO 1 SEQADV REVDAT 5 11-OCT-17 1YBO 1 REMARK REVDAT 4 13-JUL-11 1YBO 1 VERSN REVDAT 3 24-FEB-09 1YBO 1 VERSN REVDAT 2 07-NOV-06 1YBO 1 JRNL REVDAT 1 10-JAN-06 1YBO 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 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. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 15391 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) : 0.193 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 800 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1068 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2580 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 190 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 25.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.25 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) : 1.05000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.280 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.189 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.260 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.868 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2613 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2423 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3520 ; 2.613 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5654 ; 1.484 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 333 ; 5.735 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;40.271 ;25.089 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 482 ;14.390 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;22.434 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 412 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2894 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 490 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 460 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2391 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1192 ; 0.159 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1562 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 166 ; 0.175 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.015 ; 0.200 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): 24 ; 0.118 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 55 ; 0.211 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.274 ; 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): 2164 ; 1.022 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 704 ; 0.093 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2684 ; 0.928 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1060 ; 1.477 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 836 ; 2.246 ; 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 : 4 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 111 A 195 REMARK 3 ORIGIN FOR THE GROUP (A): 55.7780 47.1690 35.1050 REMARK 3 T TENSOR REMARK 3 T11: -0.0785 T22: -0.0349 REMARK 3 T33: -0.0790 T12: -0.0016 REMARK 3 T13: -0.0194 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 4.7775 L22: 2.1453 REMARK 3 L33: 2.4920 L12: -0.5191 REMARK 3 L13: 0.5585 L23: -0.6667 REMARK 3 S TENSOR REMARK 3 S11: 0.0657 S12: 0.3130 S13: -0.2309 REMARK 3 S21: 0.1143 S22: -0.0476 S23: -0.1684 REMARK 3 S31: 0.0615 S32: 0.3268 S33: -0.0181 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 : C 1 C 6 REMARK 3 ORIGIN FOR THE GROUP (A): 44.3510 25.9530 46.4010 REMARK 3 T TENSOR REMARK 3 T11: -0.0103 T22: -0.0971 REMARK 3 T33: -0.0912 T12: 0.0268 REMARK 3 T13: 0.0067 T23: 0.0143 REMARK 3 L TENSOR REMARK 3 L11: 2.8328 L22: 2.7674 REMARK 3 L33: 2.0703 L12: -0.9323 REMARK 3 L13: -0.2846 L23: -0.7531 REMARK 3 S TENSOR REMARK 3 S11: 0.0822 S12: 0.0943 S13: -0.0397 REMARK 3 S21: -0.0777 S22: -0.0859 S23: -0.0871 REMARK 3 S31: 0.0560 S32: -0.0136 S33: 0.0037 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 : B 109 B 195 REMARK 3 ORIGIN FOR THE GROUP (A): 21.9500 36.0780 50.6150 REMARK 3 T TENSOR REMARK 3 T11: -0.0137 T22: -0.1066 REMARK 3 T33: -0.0418 T12: 0.0199 REMARK 3 T13: 0.0124 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 2.1351 L22: 2.4329 REMARK 3 L33: 1.5015 L12: -0.7243 REMARK 3 L13: -1.0101 L23: 0.3339 REMARK 3 S TENSOR REMARK 3 S11: 0.0697 S12: 0.0057 S13: -0.0027 REMARK 3 S21: 0.0243 S22: -0.0640 S23: 0.2181 REMARK 3 S31: -0.0695 S32: 0.0395 S33: -0.0058 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 3 D 6 REMARK 3 ORIGIN FOR THE GROUP (A): 33.2780 57.5030 38.4460 REMARK 3 T TENSOR REMARK 3 T11: -0.0393 T22: -0.0755 REMARK 3 T33: -0.0488 T12: 0.0139 REMARK 3 T13: 0.0297 T23: 0.0577 REMARK 3 L TENSOR REMARK 3 L11: 3.9619 L22: 2.1873 REMARK 3 L33: 1.8889 L12: -0.2591 REMARK 3 L13: -1.1889 L23: -0.5383 REMARK 3 S TENSOR REMARK 3 S11: 0.0162 S12: 0.3137 S13: 0.2628 REMARK 3 S21: 0.0159 S22: 0.1178 S23: 0.0973 REMARK 3 S31: -0.0740 S32: -0.2518 S33: -0.1340 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: NULL REMARK 4 REMARK 4 1YBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031350. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97960 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23083 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.3000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.310 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: 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% PEG 3350, 0.2M NH4CL, VAPOR REMARK 280 DIFFUSION, SITTING DROP 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 62.96050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.16100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.16100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.48025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.16100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.16100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 94.44075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.16100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.16100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.48025 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.16100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.16100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 94.44075 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 62.96050 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: THE DIMER IN THE ASSYMETRIC UNIT IS THE BIOLOGICAL 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: 3710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 GLY A 108 REMARK 465 ALA A 109 REMARK 465 MET A 110 REMARK 465 GLY B 108 REMARK 465 PHE B 273 REMARK 465 LEU C -10 REMARK 465 GLY C -9 REMARK 465 LYS C -8 REMARK 465 LYS C -7 REMARK 465 PRO C -6 REMARK 465 ILE C -5 REMARK 465 TYR C -4 REMARK 465 LYS C -3 REMARK 465 LYS C -2 REMARK 465 ALA C -1 REMARK 465 PRO C 0 REMARK 465 LEU D -10 REMARK 465 GLY D -9 REMARK 465 LYS D -8 REMARK 465 LYS D -7 REMARK 465 PRO D -6 REMARK 465 ILE D -5 REMARK 465 TYR D -4 REMARK 465 LYS D -3 REMARK 465 LYS D -2 REMARK 465 ALA D -1 REMARK 465 PRO D 0 REMARK 465 THR D 1 REMARK 465 ASN D 2 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 342 O HOH B 352 2.19 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 282 O HOH A 350 3645 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 ASP A 172 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 193 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 193 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 229 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP A 256 CB - CG - OD1 ANGL. DEV. = -8.2 DEGREES REMARK 500 ASP A 256 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 GLY A 262 C - N - CA ANGL. DEV. = -13.6 DEGREES REMARK 500 ASP B 122 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 128 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP B 133 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP B 156 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 156 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG B 197 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 197 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP B 204 CB - CG - OD1 ANGL. DEV. = 6.9 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 ASP A 122 -42.04 114.30 REMARK 500 LYS A 124 133.06 -8.62 REMARK 500 ASN A 134 18.83 56.54 REMARK 500 ARG A 193 77.11 2.10 REMARK 500 ARG B 193 78.42 2.15 REMARK 500 ASN C 2 45.92 -103.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 1YBO A 113 273 UNP O00560 SDCB1_HUMAN 113 273 DBREF 1YBO B 113 273 UNP O00560 SDCB1_HUMAN 113 273 DBREF 1YBO C -10 6 UNP P31431 SDC4_HUMAN 182 198 DBREF 1YBO D -10 6 UNP P31431 SDC4_HUMAN 182 198 SEQADV 1YBO GLY A 108 UNP O00560 CLONING ARTIFACT SEQADV 1YBO ALA A 109 UNP O00560 CLONING ARTIFACT SEQADV 1YBO MET A 110 UNP O00560 CLONING ARTIFACT SEQADV 1YBO ASP A 111 UNP O00560 CLONING ARTIFACT SEQADV 1YBO PRO A 112 UNP O00560 CLONING ARTIFACT SEQADV 1YBO GLY B 108 UNP O00560 CLONING ARTIFACT SEQADV 1YBO ALA B 109 UNP O00560 CLONING ARTIFACT SEQADV 1YBO MET B 110 UNP O00560 CLONING ARTIFACT SEQADV 1YBO ASP B 111 UNP O00560 CLONING ARTIFACT SEQADV 1YBO PRO B 112 UNP O00560 CLONING ARTIFACT 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 C 17 LEU GLY LYS LYS PRO ILE TYR LYS LYS ALA PRO THR ASN SEQRES 2 C 17 GLU PHE TYR ALA SEQRES 1 D 17 LEU GLY LYS LYS PRO ILE TYR LYS LYS ALA PRO THR ASN SEQRES 2 D 17 GLU PHE TYR ALA FORMUL 5 HOH *190(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 THR A 260 1 11 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 SER B 261 1 12 SHEET 1 A 5 ARG A 113 CYS A 118 0 SHEET 2 A 5 LYS A 185 ARG A 191 -1 O ILE A 186 N LEU A 117 SHEET 3 A 5 GLN A 157 ILE A 161 -1 N GLN A 157 O ARG A 191 SHEET 4 A 5 GLY A 135 VAL A 141 -1 N ILE A 136 O VAL A 158 SHEET 5 A 5 LEU A 127 ILE A 132 -1 N LYS A 130 O PHE A 137 SHEET 1 B 4 ARG A 113 CYS A 118 0 SHEET 2 B 4 LYS A 185 ARG A 191 -1 O ILE A 186 N LEU A 117 SHEET 3 B 4 GLN A 157 ILE A 161 -1 N GLN A 157 O ARG A 191 SHEET 4 B 4 GLU A 164 ASN A 165 -1 O GLU A 164 N ILE A 161 SHEET 1 C 4 ARG A 197 HIS A 202 0 SHEET 2 C 4 VAL A 264 PRO A 271 -1 O ILE A 267 N ILE A 199 SHEET 3 C 4 HIS A 236 ILE A 241 -1 N CYS A 239 O THR A 268 SHEET 4 C 4 GLN A 244 ASN A 245 -1 O GLN A 244 N ILE A 241 SHEET 1 D 6 ARG A 197 HIS A 202 0 SHEET 2 D 6 VAL A 264 PRO A 271 -1 O ILE A 267 N ILE A 199 SHEET 3 D 6 HIS A 236 ILE A 241 -1 N CYS A 239 O THR A 268 SHEET 4 D 6 LYS A 217 ILE A 221 -1 N ILE A 218 O HIS A 236 SHEET 5 D 6 PHE A 211 LYS A 214 -1 N ILE A 212 O SER A 220 SHEET 6 D 6 PHE C 4 ALA C 6 -1 O ALA C 6 N PHE A 211 SHEET 1 E 5 ARG B 113 CYS B 118 0 SHEET 2 E 5 LYS B 185 ARG B 191 -1 O ILE B 190 N ARG B 113 SHEET 3 E 5 GLN B 157 ILE B 161 -1 N GLN B 157 O ARG B 191 SHEET 4 E 5 GLY B 135 VAL B 141 -1 N ILE B 136 O VAL B 158 SHEET 5 E 5 LEU B 127 ILE B 132 -1 N ARG B 128 O GLN B 139 SHEET 1 F 4 ARG B 113 CYS B 118 0 SHEET 2 F 4 LYS B 185 ARG B 191 -1 O ILE B 190 N ARG B 113 SHEET 3 F 4 GLN B 157 ILE B 161 -1 N GLN B 157 O ARG B 191 SHEET 4 F 4 GLU B 164 ASN B 165 -1 O GLU B 164 N ILE B 161 SHEET 1 G 4 ARG B 197 HIS B 202 0 SHEET 2 G 4 VAL B 264 PRO B 271 -1 O ILE B 267 N ILE B 199 SHEET 3 G 4 HIS B 236 ILE B 241 -1 N ASN B 237 O MET B 270 SHEET 4 G 4 GLN B 244 ASN B 245 -1 O GLN B 244 N ILE B 241 SHEET 1 H 6 ARG B 197 HIS B 202 0 SHEET 2 H 6 VAL B 264 PRO B 271 -1 O ILE B 267 N ILE B 199 SHEET 3 H 6 HIS B 236 ILE B 241 -1 N ASN B 237 O MET B 270 SHEET 4 H 6 LYS B 217 ILE B 221 -1 N ILE B 218 O HIS B 236 SHEET 5 H 6 PHE B 211 LYS B 214 -1 N ILE B 212 O SER B 220 SHEET 6 H 6 PHE D 4 TYR D 5 -1 O PHE D 4 N PHE B 213 CISPEP 1 THR C 1 ASN C 2 0 -6.87 CRYST1 72.322 72.322 125.921 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 0.013827 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007941 0.00000 MASTER 449 0 0 8 38 0 0 6 2770 4 0 30 END