HEADER SIGNALING PROTEIN 22-NOV-02 1N99 TITLE CRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTENIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PDZ TANDEM; 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_STRAIN: D834; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGST-PARALLEL1 KEYWDS PDZ DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.S.KANG,D.R.COOPER,F.JELEN,Y.DEVEDJIEV,U.DEREWENDA,Z.DAUTER, AUTHOR 2 J.OTLEWSKI,Z.S.DEREWENDA REVDAT 4 21-DEC-22 1N99 1 SEQADV LINK REVDAT 3 13-JUL-11 1N99 1 VERSN REVDAT 2 24-FEB-09 1N99 1 VERSN REVDAT 1 15-APR-03 1N99 0 JRNL AUTH B.S.KANG,D.R.COOPER,F.JELEN,Y.DEVEDJIEV,U.DEREWENDA, JRNL AUTH 2 Z.DAUTER,J.OTLEWSKI,Z.S.DEREWENDA JRNL TITL PDZ TANDEM OF HUMAN SYNTENIN: CRYSTAL STRUCTURE AND JRNL TITL 2 FUNCTIONAL PROPERTIES JRNL REF STRUCTURE V. 11 459 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12679023 JRNL DOI 10.1016/S0969-2126(03)00052-2 REMARK 2 REMARK 2 RESOLUTION. 1.94 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21926 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1182 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) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1560 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2454 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 254 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 28.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.58000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : 2.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.62000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.178 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.308 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2454 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2280 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3315 ; 1.803 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5303 ; 0.874 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 323 ; 7.542 ; 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): 397 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2745 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 454 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 452 ; 0.247 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2743 ; 0.267 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1630 ; 0.094 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 310 ; 0.212 ; 0.500 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): 18 ; 0.134 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 53 ; 0.328 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.300 ; 0.500 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): 1599 ; 1.902 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2575 ; 3.060 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 855 ; 5.018 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 740 ; 7.528 ; 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 112 A 194 REMARK 3 ORIGIN FOR THE GROUP (A): 28.9410 -13.6970 9.7270 REMARK 3 T TENSOR REMARK 3 T11: 0.1062 T22: 0.1189 REMARK 3 T33: 0.0259 T12: -0.0302 REMARK 3 T13: 0.0481 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 2.4901 L22: 4.7488 REMARK 3 L33: 1.4838 L12: 1.6665 REMARK 3 L13: 0.5331 L23: 0.2066 REMARK 3 S TENSOR REMARK 3 S11: -0.1519 S12: 0.2056 S13: -0.1612 REMARK 3 S21: -0.2671 S22: 0.2494 S23: -0.2525 REMARK 3 S31: 0.1707 S32: -0.0105 S33: -0.0974 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 : A 197 A 271 REMARK 3 ORIGIN FOR THE GROUP (A): 5.7740 0.3000 12.9720 REMARK 3 T TENSOR REMARK 3 T11: 0.0389 T22: 0.0859 REMARK 3 T33: 0.0613 T12: -0.0169 REMARK 3 T13: -0.0015 T23: 0.0204 REMARK 3 L TENSOR REMARK 3 L11: 3.6759 L22: 3.8885 REMARK 3 L33: 2.1664 L12: -0.7084 REMARK 3 L13: -0.6635 L23: 1.5039 REMARK 3 S TENSOR REMARK 3 S11: -0.0284 S12: 0.2724 S13: -0.0987 REMARK 3 S21: -0.1093 S22: 0.1331 S23: 0.2292 REMARK 3 S31: -0.0011 S32: 0.0513 S33: -0.1047 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 112 B 194 REMARK 3 ORIGIN FOR THE GROUP (A): 14.8380 20.3460 25.4140 REMARK 3 T TENSOR REMARK 3 T11: 0.0837 T22: 0.0845 REMARK 3 T33: 0.0861 T12: -0.0097 REMARK 3 T13: 0.0148 T23: 0.0391 REMARK 3 L TENSOR REMARK 3 L11: 2.1459 L22: 2.0718 REMARK 3 L33: 2.1608 L12: 0.3090 REMARK 3 L13: 0.0446 L23: 0.9157 REMARK 3 S TENSOR REMARK 3 S11: -0.1679 S12: -0.0405 S13: 0.0489 REMARK 3 S21: 0.0659 S22: 0.1251 S23: -0.1026 REMARK 3 S31: -0.1562 S32: 0.0591 S33: 0.0429 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 : B 197 B 270 REMARK 3 ORIGIN FOR THE GROUP (A): 38.6120 7.4570 19.5710 REMARK 3 T TENSOR REMARK 3 T11: 0.0346 T22: 0.0374 REMARK 3 T33: 0.1476 T12: -0.0162 REMARK 3 T13: 0.0343 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 2.7931 L22: 2.7338 REMARK 3 L33: 1.3753 L12: 0.6351 REMARK 3 L13: 0.0926 L23: 0.2181 REMARK 3 S TENSOR REMARK 3 S11: 0.0748 S12: -0.0263 S13: 0.3832 REMARK 3 S21: 0.1843 S22: -0.0488 S23: -0.1048 REMARK 3 S31: 0.1073 S32: 0.0388 S33: -0.0261 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 1N99 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-02. REMARK 100 THE DEPOSITION ID IS D_1000017677. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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, 0.97133, 0.97900 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 : TRUNCATE, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23111 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, PEG4000, AMMONIUM REMARK 280 ACETATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 50.36350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.33900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.36350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.33900 REMARK 290 SMTRY3 4 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 300 REMARK: EACH MONOMER IS A 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MSE A 110 REMARK 465 ASP A 111 REMARK 465 GLY B 108 REMARK 465 ALA B 109 REMARK 465 PHE B 273 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 LYS A 214 CG CD CE NZ REMARK 470 GLN B 121 CB CG CD OE1 NE2 REMARK 470 LYS B 124 CG CD CE NZ REMARK 470 LYS B 214 CG CD CE NZ REMARK 470 LYS B 250 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 121 CG CD OE1 NE2 REMARK 480 LYS A 124 CD CE NZ REMARK 480 ARG A 128 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 176 CB CG CD CE NZ REMARK 480 PHE A 182 CG CD1 CD2 CE1 CE2 CZ REMARK 480 LYS A 217 CE NZ REMARK 480 LYS B 223 CG 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 O HOH B 388 O HOH B 400 2.01 REMARK 500 O HOH B 294 O HOH B 403 2.01 REMARK 500 CB ASN B 134 O HOH B 402 2.13 REMARK 500 O HOH A 397 O HOH B 286 2.13 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 N MSE B 110 O HOH B 312 2656 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 182 CB PHE A 182 CG -0.192 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 192 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 251 CB - CG - OD1 ANGL. DEV. = 5.8 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 90.47 -15.62 REMARK 500 ASP A 204 -148.34 -95.79 REMARK 500 THR A 206 3.77 -61.67 REMARK 500 ARG B 193 90.95 -8.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 205 THR A 206 147.65 REMARK 500 THR A 206 GLY A 207 -142.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 1N99 A 113 273 UNP O00560 SDCB1_HUMAN 113 273 DBREF 1N99 B 113 273 UNP O00560 SDCB1_HUMAN 113 273 SEQADV 1N99 GLY A 108 UNP O00560 CLONING ARTIFACT SEQADV 1N99 ALA A 109 UNP O00560 CLONING ARTIFACT SEQADV 1N99 MSE A 110 UNP O00560 CLONING ARTIFACT SEQADV 1N99 ASP A 111 UNP O00560 CLONING ARTIFACT SEQADV 1N99 PRO A 112 UNP O00560 CLONING ARTIFACT SEQADV 1N99 MSE A 188 UNP O00560 MET 188 MODIFIED RESIDUE SEQADV 1N99 MSE A 201 UNP O00560 MET 201 MODIFIED RESIDUE SEQADV 1N99 MSE A 270 UNP O00560 MET 270 MODIFIED RESIDUE SEQADV 1N99 GLY B 108 UNP O00560 CLONING ARTIFACT SEQADV 1N99 ALA B 109 UNP O00560 CLONING ARTIFACT SEQADV 1N99 MSE B 110 UNP O00560 CLONING ARTIFACT SEQADV 1N99 ASP B 111 UNP O00560 CLONING ARTIFACT SEQADV 1N99 PRO B 112 UNP O00560 CLONING ARTIFACT SEQADV 1N99 MSE B 188 UNP O00560 MET 188 MODIFIED RESIDUE SEQADV 1N99 MSE B 201 UNP O00560 MET 201 MODIFIED RESIDUE SEQADV 1N99 MSE B 270 UNP O00560 MET 270 MODIFIED RESIDUE SEQRES 1 A 166 GLY ALA MSE 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 MSE THR ILE ARG ASP ARG PRO PHE GLU ARG THR SEQRES 8 A 166 ILE THR MSE 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 MSE PRO ALA PHE SEQRES 1 B 166 GLY ALA MSE 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 MSE THR ILE ARG ASP ARG PRO PHE GLU ARG THR SEQRES 8 B 166 ILE THR MSE 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 MSE PRO ALA PHE MODRES 1N99 MSE A 188 MET SELENOMETHIONINE MODRES 1N99 MSE A 201 MET SELENOMETHIONINE MODRES 1N99 MSE A 270 MET SELENOMETHIONINE MODRES 1N99 MSE B 110 MET SELENOMETHIONINE MODRES 1N99 MSE B 188 MET SELENOMETHIONINE MODRES 1N99 MSE B 201 MET SELENOMETHIONINE MODRES 1N99 MSE B 270 MET SELENOMETHIONINE HET MSE A 188 8 HET MSE A 201 8 HET MSE A 270 8 HET MSE B 110 8 HET MSE B 188 8 HET MSE B 201 8 HET MSE B 270 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 7(C5 H11 N O2 SE) FORMUL 3 HOH *254(H2 O) HELIX 1 1 SER A 145 VAL A 150 1 6 HELIX 2 2 SER A 170 GLN A 180 1 11 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 ALA B 147 GLY B 151 5 5 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 ARG A 128 O GLN A 139 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 VAL A 265 N MSE A 201 SHEET 3 C 4 HIS A 236 ILE A 241 -1 N ASN A 237 O MSE A 270 SHEET 4 C 4 GLN A 244 ASN A 245 -1 O GLN A 244 N ILE A 241 SHEET 1 D 2 PHE A 211 LYS A 214 0 SHEET 2 D 2 LYS A 217 ILE A 221 -1 O THR A 219 N ILE A 212 SHEET 1 E 4 ARG B 113 LEU B 117 0 SHEET 2 E 4 ILE B 186 ARG B 191 -1 O ILE B 190 N ARG B 113 SHEET 3 E 4 GLN B 157 ILE B 161 -1 N GLN B 157 O ARG B 191 SHEET 4 E 4 GLU B 164 ASN B 165 -1 O GLU B 164 N ILE B 161 SHEET 1 F 2 LEU B 127 ILE B 132 0 SHEET 2 F 2 GLY B 135 VAL B 141 -1 O GLN B 139 N ARG B 128 SHEET 1 G 5 ARG B 197 HIS B 202 0 SHEET 2 G 5 VAL B 264 PRO B 271 -1 O VAL B 265 N MSE B 201 SHEET 3 G 5 HIS B 236 ILE B 241 -1 N ASN B 237 O MSE B 270 SHEET 4 G 5 LYS B 217 ILE B 221 -1 N ILE B 218 O HIS B 236 SHEET 5 G 5 PHE B 211 LYS B 214 -1 N LYS B 214 O LYS B 217 SHEET 1 H 4 ARG B 197 HIS B 202 0 SHEET 2 H 4 VAL B 264 PRO B 271 -1 O VAL B 265 N MSE B 201 SHEET 3 H 4 HIS B 236 ILE B 241 -1 N ASN B 237 O MSE B 270 SHEET 4 H 4 GLN B 244 ASN B 245 -1 O GLN B 244 N ILE B 241 LINK C THR A 187 N MSE A 188 1555 1555 1.33 LINK C MSE A 188 N THR A 189 1555 1555 1.34 LINK C THR A 200 N MSE A 201 1555 1555 1.32 LINK C MSE A 201 N HIS A 202 1555 1555 1.32 LINK C ILE A 269 N MSE A 270 1555 1555 1.31 LINK C MSE A 270 N PRO A 271 1555 1555 1.32 LINK C MSE B 110 N ASP B 111 1555 1555 1.32 LINK C THR B 187 N MSE B 188 1555 1555 1.33 LINK C MSE B 188 N THR B 189 1555 1555 1.33 LINK C THR B 200 N MSE B 201 1555 1555 1.32 LINK C MSE B 201 N HIS B 202 1555 1555 1.32 LINK C ILE B 269 N MSE B 270 1555 1555 1.31 LINK C MSE B 270 N PRO B 271 1555 1555 1.32 CRYST1 100.727 48.678 74.690 90.00 120.82 90.00 C 1 2 1 8 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 0.009928 0.000000 0.005922 0.00000 SCALE2 0.000000 0.020543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015590 0.00000