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