HEADER IMMUNE SYSTEM 18-JUL-17 5WI8 TITLE CRYSTAL STRUCTURE OF MURINE 4-1BB FROM HEK293T CELLS IN P21 SPACE TITLE 2 GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 9; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: 4-1BB LIGAND RECEPTOR,T-CELL ANTIGEN 4-1BB; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TNFRSF9, CD137, ILA, LY63; SOURCE 6 EXPRESSION_SYSTEM: MAMMALIAN EXPRESSION VECTOR PCDNA3-N-HA-LIC; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1758149 KEYWDS TUMOR NECROSIS FACTOR, APOPTOSIS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR D.M.ZAJONC,A.BITRA REVDAT 3 29-JUL-20 5WI8 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 31-OCT-18 5WI8 1 JRNL REVDAT 1 20-DEC-17 5WI8 0 JRNL AUTH A.BITRA,T.DOUKOV,J.WANG,G.PICARDA,C.A.BENEDICT,M.CROFT, JRNL AUTH 2 D.M.ZAJONC JRNL TITL CRYSTAL STRUCTURE OF MURINE 4-1BB AND ITS INTERACTION WITH JRNL TITL 2 4-1BBL SUPPORT A ROLE FOR GALECTIN-9 IN 4-1BB SIGNALING. JRNL REF J. BIOL. CHEM. V. 293 1317 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29242193 JRNL DOI 10.1074/JBC.M117.814905 REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 16177 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 881 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) : 2.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 747 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3923 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 319 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 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): 0.448 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.284 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.687 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.896 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.864 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4368 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3715 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5934 ; 1.485 ; 2.022 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8683 ; 1.270 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 535 ; 6.172 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;31.699 ;23.818 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 602 ;15.361 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;14.692 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 679 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4780 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 935 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 27 159 B 27 159 10934 0.100 0.050 REMARK 3 2 A 27 159 C 27 159 10960 0.100 0.050 REMARK 3 3 A 27 159 D 27 159 10890 0.100 0.050 REMARK 3 4 B 27 159 C 27 159 10942 0.120 0.050 REMARK 3 5 B 27 159 D 27 159 10928 0.110 0.050 REMARK 3 6 C 27 160 D 27 160 11382 0.080 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5WI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000229064. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR, NON FIXED REMARK 200 EXIT SLIT REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17070 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 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 (%) : 91.8 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 4.5, 30% W/V REMARK 280 POLYETHYLENE GLYCOL (PEG) 8000, AND 0.2 M LITHIUM SULFATE, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295.15K 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 30.88150 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, 3, 4 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, G 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, H 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 LEU A 22 REMARK 465 GLU A 23 REMARK 465 VAL A 24 REMARK 465 GLN A 25 REMARK 465 ASN A 26 REMARK 465 PRO A 163 REMARK 465 ARG A 164 REMARK 465 LEU B 22 REMARK 465 GLU B 23 REMARK 465 VAL B 24 REMARK 465 GLN B 25 REMARK 465 LEU B 161 REMARK 465 VAL B 162 REMARK 465 PRO B 163 REMARK 465 ARG B 164 REMARK 465 LEU C 22 REMARK 465 GLU C 23 REMARK 465 VAL C 24 REMARK 465 GLN C 25 REMARK 465 ASN C 26 REMARK 465 LEU C 161 REMARK 465 VAL C 162 REMARK 465 PRO C 163 REMARK 465 ARG C 164 REMARK 465 LEU D 22 REMARK 465 GLU D 23 REMARK 465 VAL D 24 REMARK 465 GLN D 25 REMARK 465 ASN D 26 REMARK 465 LEU D 161 REMARK 465 VAL D 162 REMARK 465 PRO D 163 REMARK 465 ARG D 164 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 39 CG CD CE NZ REMARK 470 VAL A 43 CG1 CG2 REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 ILE A 55 CG1 CG2 CD1 REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 GLN A 97 CG CD OE1 NE2 REMARK 470 LYS A 113 CG CD CE NZ REMARK 470 GLN A 114 CG CD OE1 NE2 REMARK 470 ARG A 134 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 26 CG OD1 ND2 REMARK 470 ASP B 29 CG OD1 OD2 REMARK 470 ASN B 30 CG OD1 ND2 REMARK 470 GLN B 32 CG CD OE1 NE2 REMARK 470 LYS B 39 CG CD CE NZ REMARK 470 LYS B 45 CG CD CE NZ REMARK 470 ILE B 55 CG1 CG2 CD1 REMARK 470 ILE B 63 CG1 CG2 CD1 REMARK 470 GLU B 89 CG CD OE1 OE2 REMARK 470 GLN B 97 CG CD OE1 NE2 REMARK 470 LYS B 113 CG CD CE NZ REMARK 470 GLN B 114 CG CD OE1 NE2 REMARK 470 GLN C 97 CG CD OE1 NE2 REMARK 470 LYS C 117 CG CD CE NZ REMARK 470 LEU C 141 CG CD1 CD2 REMARK 470 LYS D 39 CG CD CE NZ REMARK 470 LYS D 45 CG CD CE NZ REMARK 470 ILE D 55 CG1 CG2 CD1 REMARK 470 LEU D 111 CG CD1 CD2 REMARK 470 THR D 112 OG1 CG2 REMARK 470 LYS D 113 CG CD CE NZ REMARK 470 GLN D 114 CG CD OE1 NE2 REMARK 470 LEU D 141 CG CD1 CD2 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 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.2 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 GLN D 114 4.64 80.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 5WI8 A 24 160 UNP P20334 TNR9_MOUSE 24 160 DBREF 5WI8 B 24 160 UNP P20334 TNR9_MOUSE 24 160 DBREF 5WI8 C 24 160 UNP P20334 TNR9_MOUSE 24 160 DBREF 5WI8 D 24 160 UNP P20334 TNR9_MOUSE 24 160 SEQADV 5WI8 LEU A 22 UNP P20334 EXPRESSION TAG SEQADV 5WI8 GLU A 23 UNP P20334 EXPRESSION TAG SEQADV 5WI8 LEU A 161 UNP P20334 EXPRESSION TAG SEQADV 5WI8 VAL A 162 UNP P20334 EXPRESSION TAG SEQADV 5WI8 PRO A 163 UNP P20334 EXPRESSION TAG SEQADV 5WI8 ARG A 164 UNP P20334 EXPRESSION TAG SEQADV 5WI8 LEU B 22 UNP P20334 EXPRESSION TAG SEQADV 5WI8 GLU B 23 UNP P20334 EXPRESSION TAG SEQADV 5WI8 LEU B 161 UNP P20334 EXPRESSION TAG SEQADV 5WI8 VAL B 162 UNP P20334 EXPRESSION TAG SEQADV 5WI8 PRO B 163 UNP P20334 EXPRESSION TAG SEQADV 5WI8 ARG B 164 UNP P20334 EXPRESSION TAG SEQADV 5WI8 LEU C 22 UNP P20334 EXPRESSION TAG SEQADV 5WI8 GLU C 23 UNP P20334 EXPRESSION TAG SEQADV 5WI8 LEU C 161 UNP P20334 EXPRESSION TAG SEQADV 5WI8 VAL C 162 UNP P20334 EXPRESSION TAG SEQADV 5WI8 PRO C 163 UNP P20334 EXPRESSION TAG SEQADV 5WI8 ARG C 164 UNP P20334 EXPRESSION TAG SEQADV 5WI8 LEU D 22 UNP P20334 EXPRESSION TAG SEQADV 5WI8 GLU D 23 UNP P20334 EXPRESSION TAG SEQADV 5WI8 LEU D 161 UNP P20334 EXPRESSION TAG SEQADV 5WI8 VAL D 162 UNP P20334 EXPRESSION TAG SEQADV 5WI8 PRO D 163 UNP P20334 EXPRESSION TAG SEQADV 5WI8 ARG D 164 UNP P20334 EXPRESSION TAG SEQRES 1 A 143 LEU GLU VAL GLN ASN SER CYS ASP ASN CYS GLN PRO GLY SEQRES 2 A 143 THR PHE CYS ARG LYS TYR ASN PRO VAL CYS LYS SER CYS SEQRES 3 A 143 PRO PRO SER THR PHE SER SER ILE GLY GLY GLN PRO ASN SEQRES 4 A 143 CYS ASN ILE CYS ARG VAL CYS ALA GLY TYR PHE ARG PHE SEQRES 5 A 143 LYS LYS PHE CYS SER SER THR HIS ASN ALA GLU CYS GLU SEQRES 6 A 143 CYS ILE GLU GLY PHE HIS CYS LEU GLY PRO GLN CYS THR SEQRES 7 A 143 ARG CYS GLU LYS ASP CYS ARG PRO GLY GLN GLU LEU THR SEQRES 8 A 143 LYS GLN GLY CYS LYS THR CYS SER LEU GLY THR PHE ASN SEQRES 9 A 143 ASP GLN ASN GLY THR GLY VAL CYS ARG PRO TRP THR ASN SEQRES 10 A 143 CYS SER LEU ASP GLY ARG SER VAL LEU LYS THR GLY THR SEQRES 11 A 143 THR GLU LYS ASP VAL VAL CYS GLY PRO LEU VAL PRO ARG SEQRES 1 B 143 LEU GLU VAL GLN ASN SER CYS ASP ASN CYS GLN PRO GLY SEQRES 2 B 143 THR PHE CYS ARG LYS TYR ASN PRO VAL CYS LYS SER CYS SEQRES 3 B 143 PRO PRO SER THR PHE SER SER ILE GLY GLY GLN PRO ASN SEQRES 4 B 143 CYS ASN ILE CYS ARG VAL CYS ALA GLY TYR PHE ARG PHE SEQRES 5 B 143 LYS LYS PHE CYS SER SER THR HIS ASN ALA GLU CYS GLU SEQRES 6 B 143 CYS ILE GLU GLY PHE HIS CYS LEU GLY PRO GLN CYS THR SEQRES 7 B 143 ARG CYS GLU LYS ASP CYS ARG PRO GLY GLN GLU LEU THR SEQRES 8 B 143 LYS GLN GLY CYS LYS THR CYS SER LEU GLY THR PHE ASN SEQRES 9 B 143 ASP GLN ASN GLY THR GLY VAL CYS ARG PRO TRP THR ASN SEQRES 10 B 143 CYS SER LEU ASP GLY ARG SER VAL LEU LYS THR GLY THR SEQRES 11 B 143 THR GLU LYS ASP VAL VAL CYS GLY PRO LEU VAL PRO ARG SEQRES 1 C 143 LEU GLU VAL GLN ASN SER CYS ASP ASN CYS GLN PRO GLY SEQRES 2 C 143 THR PHE CYS ARG LYS TYR ASN PRO VAL CYS LYS SER CYS SEQRES 3 C 143 PRO PRO SER THR PHE SER SER ILE GLY GLY GLN PRO ASN SEQRES 4 C 143 CYS ASN ILE CYS ARG VAL CYS ALA GLY TYR PHE ARG PHE SEQRES 5 C 143 LYS LYS PHE CYS SER SER THR HIS ASN ALA GLU CYS GLU SEQRES 6 C 143 CYS ILE GLU GLY PHE HIS CYS LEU GLY PRO GLN CYS THR SEQRES 7 C 143 ARG CYS GLU LYS ASP CYS ARG PRO GLY GLN GLU LEU THR SEQRES 8 C 143 LYS GLN GLY CYS LYS THR CYS SER LEU GLY THR PHE ASN SEQRES 9 C 143 ASP GLN ASN GLY THR GLY VAL CYS ARG PRO TRP THR ASN SEQRES 10 C 143 CYS SER LEU ASP GLY ARG SER VAL LEU LYS THR GLY THR SEQRES 11 C 143 THR GLU LYS ASP VAL VAL CYS GLY PRO LEU VAL PRO ARG SEQRES 1 D 143 LEU GLU VAL GLN ASN SER CYS ASP ASN CYS GLN PRO GLY SEQRES 2 D 143 THR PHE CYS ARG LYS TYR ASN PRO VAL CYS LYS SER CYS SEQRES 3 D 143 PRO PRO SER THR PHE SER SER ILE GLY GLY GLN PRO ASN SEQRES 4 D 143 CYS ASN ILE CYS ARG VAL CYS ALA GLY TYR PHE ARG PHE SEQRES 5 D 143 LYS LYS PHE CYS SER SER THR HIS ASN ALA GLU CYS GLU SEQRES 6 D 143 CYS ILE GLU GLY PHE HIS CYS LEU GLY PRO GLN CYS THR SEQRES 7 D 143 ARG CYS GLU LYS ASP CYS ARG PRO GLY GLN GLU LEU THR SEQRES 8 D 143 LYS GLN GLY CYS LYS THR CYS SER LEU GLY THR PHE ASN SEQRES 9 D 143 ASP GLN ASN GLY THR GLY VAL CYS ARG PRO TRP THR ASN SEQRES 10 D 143 CYS SER LEU ASP GLY ARG SER VAL LEU LYS THR GLY THR SEQRES 11 D 143 THR GLU LYS ASP VAL VAL CYS GLY PRO LEU VAL PRO ARG HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET FUC E 4 10 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET MAN F 4 11 HET FUC F 5 10 HET NAG G 1 14 HET NAG G 2 14 HET BMA G 3 11 HET MAN G 4 11 HET NAG H 1 14 HET NAG H 2 14 HET BMA H 3 11 HET MAN H 4 11 HET FUC H 5 10 HET GOL A 205 6 HET GOL A 206 6 HET GOL A 207 6 HET GOL A 208 6 HET GOL A 209 6 HET EDO A 210 4 HET GOL B 201 6 HET EDO B 202 4 HET EDO B 203 4 HET EDO B 204 4 HET NAG B 210 14 HET GOL B 211 6 HET EDO C 401 4 HET GOL C 406 6 HET EDO D 401 4 HET EDO D 402 4 HET EDO D 403 4 HET GOL D 409 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 NAG 9(C8 H15 N O6) FORMUL 5 BMA 4(C6 H12 O6) FORMUL 5 FUC 3(C6 H12 O5) FORMUL 6 MAN 3(C6 H12 O6) FORMUL 9 GOL 9(C3 H8 O3) FORMUL 14 EDO 8(C2 H6 O2) FORMUL 27 HOH *91(H2 O) HELIX 1 AA1 SER A 27 CYS A 31 5 5 HELIX 2 AA2 SER B 27 CYS B 31 5 5 HELIX 3 AA3 ASN B 138 GLY B 143 5 6 HELIX 4 AA4 SER C 27 CYS C 31 5 5 HELIX 5 AA5 SER D 27 CYS D 31 5 5 SHEET 1 AA1 2 THR A 35 PHE A 36 0 SHEET 2 AA1 2 LYS A 45 SER A 46 -1 O LYS A 45 N PHE A 36 SHEET 1 AA2 2 THR A 51 PHE A 52 0 SHEET 2 AA2 2 ASN A 62 ILE A 63 -1 O ASN A 62 N PHE A 52 SHEET 1 AA3 2 PHE A 71 LYS A 75 0 SHEET 2 AA3 2 GLU A 84 CYS A 87 -1 O GLU A 86 N ARG A 72 SHEET 1 AA4 2 PHE A 91 LEU A 94 0 SHEET 2 AA4 2 ARG A 100 LYS A 103 -1 O ARG A 100 N LEU A 94 SHEET 1 AA5 2 GLN A 109 THR A 112 0 SHEET 2 AA5 2 GLY A 115 THR A 118 -1 O LYS A 117 N GLU A 110 SHEET 1 AA6 2 THR A 123 PHE A 124 0 SHEET 2 AA6 2 ARG A 134 PRO A 135 -1 O ARG A 134 N PHE A 124 SHEET 1 AA7 2 VAL A 146 LYS A 148 0 SHEET 2 AA7 2 VAL A 157 CYS A 158 -1 O VAL A 157 N LEU A 147 SHEET 1 AA8 2 THR B 35 PHE B 36 0 SHEET 2 AA8 2 LYS B 45 SER B 46 -1 O LYS B 45 N PHE B 36 SHEET 1 AA9 2 THR B 51 PHE B 52 0 SHEET 2 AA9 2 ASN B 62 ILE B 63 -1 O ASN B 62 N PHE B 52 SHEET 1 AB1 2 PHE B 71 LYS B 75 0 SHEET 2 AB1 2 GLU B 84 CYS B 87 -1 O GLU B 86 N ARG B 72 SHEET 1 AB2 2 PHE B 91 LEU B 94 0 SHEET 2 AB2 2 ARG B 100 LYS B 103 -1 O ARG B 100 N LEU B 94 SHEET 1 AB3 2 GLN B 109 GLU B 110 0 SHEET 2 AB3 2 LYS B 117 THR B 118 -1 O LYS B 117 N GLU B 110 SHEET 1 AB4 2 THR B 123 PHE B 124 0 SHEET 2 AB4 2 ARG B 134 PRO B 135 -1 O ARG B 134 N PHE B 124 SHEET 1 AB5 2 VAL B 146 LYS B 148 0 SHEET 2 AB5 2 VAL B 157 CYS B 158 -1 O VAL B 157 N LEU B 147 SHEET 1 AB6 2 THR C 35 PHE C 36 0 SHEET 2 AB6 2 LYS C 45 SER C 46 -1 O LYS C 45 N PHE C 36 SHEET 1 AB7 2 THR C 51 PHE C 52 0 SHEET 2 AB7 2 ASN C 62 ILE C 63 -1 O ASN C 62 N PHE C 52 SHEET 1 AB8 2 PHE C 71 LYS C 75 0 SHEET 2 AB8 2 GLU C 84 CYS C 87 -1 O GLU C 86 N ARG C 72 SHEET 1 AB9 2 PHE C 91 LEU C 94 0 SHEET 2 AB9 2 ARG C 100 LYS C 103 -1 O ARG C 100 N LEU C 94 SHEET 1 AC1 2 GLN C 109 THR C 112 0 SHEET 2 AC1 2 GLY C 115 THR C 118 -1 O LYS C 117 N GLU C 110 SHEET 1 AC2 2 THR C 123 PHE C 124 0 SHEET 2 AC2 2 ARG C 134 PRO C 135 -1 O ARG C 134 N PHE C 124 SHEET 1 AC3 2 VAL C 146 LYS C 148 0 SHEET 2 AC3 2 VAL C 157 CYS C 158 -1 O VAL C 157 N LEU C 147 SHEET 1 AC4 2 THR D 35 PHE D 36 0 SHEET 2 AC4 2 LYS D 45 SER D 46 -1 O LYS D 45 N PHE D 36 SHEET 1 AC5 2 THR D 51 PHE D 52 0 SHEET 2 AC5 2 ASN D 62 ILE D 63 -1 O ASN D 62 N PHE D 52 SHEET 1 AC6 2 PHE D 71 LYS D 75 0 SHEET 2 AC6 2 GLU D 84 CYS D 87 -1 O GLU D 86 N ARG D 72 SHEET 1 AC7 2 PHE D 91 LEU D 94 0 SHEET 2 AC7 2 ARG D 100 LYS D 103 -1 O ARG D 100 N LEU D 94 SHEET 1 AC8 2 GLN D 109 THR D 112 0 SHEET 2 AC8 2 GLY D 115 THR D 118 -1 O LYS D 117 N GLU D 110 SHEET 1 AC9 2 THR D 123 PHE D 124 0 SHEET 2 AC9 2 ARG D 134 PRO D 135 -1 O ARG D 134 N PHE D 124 SHEET 1 AD1 2 VAL D 146 LYS D 148 0 SHEET 2 AD1 2 VAL D 157 CYS D 158 -1 O VAL D 157 N LEU D 147 SSBOND 1 CYS A 28 CYS A 37 1555 1555 2.04 SSBOND 2 CYS A 31 CYS A 44 1555 1555 2.04 SSBOND 3 CYS A 47 CYS A 61 1555 1555 2.06 SSBOND 4 CYS A 64 CYS A 77 1555 1555 2.03 SSBOND 5 CYS A 67 CYS A 85 1555 1555 2.06 SSBOND 6 CYS A 87 CYS A 101 1555 1555 2.04 SSBOND 7 CYS A 93 CYS A 98 1555 1555 2.06 SSBOND 8 CYS A 105 CYS A 116 1555 1555 2.05 SSBOND 9 CYS A 119 CYS A 133 1555 1555 2.05 SSBOND 10 CYS A 139 CYS A 158 1555 1555 2.05 SSBOND 11 CYS B 28 CYS B 37 1555 1555 2.04 SSBOND 12 CYS B 31 CYS B 44 1555 1555 2.04 SSBOND 13 CYS B 47 CYS B 61 1555 1555 2.06 SSBOND 14 CYS B 64 CYS B 77 1555 1555 2.05 SSBOND 15 CYS B 67 CYS B 85 1555 1555 2.05 SSBOND 16 CYS B 87 CYS B 101 1555 1555 2.05 SSBOND 17 CYS B 93 CYS B 98 1555 1555 2.06 SSBOND 18 CYS B 105 CYS B 116 1555 1555 2.06 SSBOND 19 CYS B 119 CYS B 133 1555 1555 2.05 SSBOND 20 CYS B 139 CYS B 158 1555 1555 2.05 SSBOND 21 CYS C 28 CYS C 37 1555 1555 2.04 SSBOND 22 CYS C 31 CYS C 44 1555 1555 2.04 SSBOND 23 CYS C 47 CYS C 61 1555 1555 2.05 SSBOND 24 CYS C 64 CYS C 77 1555 1555 2.03 SSBOND 25 CYS C 67 CYS C 85 1555 1555 2.02 SSBOND 26 CYS C 87 CYS C 101 1555 1555 2.04 SSBOND 27 CYS C 93 CYS C 98 1555 1555 2.04 SSBOND 28 CYS C 105 CYS C 116 1555 1555 2.06 SSBOND 29 CYS C 119 CYS C 133 1555 1555 2.04 SSBOND 30 CYS C 139 CYS C 158 1555 1555 2.04 SSBOND 31 CYS D 28 CYS D 37 1555 1555 2.04 SSBOND 32 CYS D 31 CYS D 44 1555 1555 2.05 SSBOND 33 CYS D 47 CYS D 61 1555 1555 2.05 SSBOND 34 CYS D 64 CYS D 77 1555 1555 2.03 SSBOND 35 CYS D 67 CYS D 85 1555 1555 2.04 SSBOND 36 CYS D 87 CYS D 101 1555 1555 2.03 SSBOND 37 CYS D 93 CYS D 98 1555 1555 2.03 SSBOND 38 CYS D 105 CYS D 116 1555 1555 2.06 SSBOND 39 CYS D 119 CYS D 133 1555 1555 2.05 SSBOND 40 CYS D 139 CYS D 158 1555 1555 2.04 LINK ND2 ASN A 138 C1 NAG E 1 1555 1555 1.43 LINK ND2 ASN B 128 C1 NAG B 210 1555 1555 1.46 LINK ND2 ASN B 138 C1 NAG F 1 1555 1555 1.44 LINK ND2 ASN C 138 C1 NAG G 1 1555 1555 1.45 LINK ND2 ASN D 138 C1 NAG H 1 1555 1555 1.46 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 LINK O6 NAG E 1 C1 FUC E 4 1555 1555 1.44 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.43 LINK O6 NAG F 1 C1 FUC F 5 1555 1555 1.44 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.45 LINK O6 BMA F 3 C1 MAN F 4 1555 1555 1.45 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.45 LINK O4 NAG G 2 C1 BMA G 3 1555 1555 1.45 LINK O3 BMA G 3 C1 MAN G 4 1555 1555 1.45 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.45 LINK O6 NAG H 1 C1 FUC H 5 1555 1555 1.46 LINK O4 NAG H 2 C1 BMA H 3 1555 1555 1.45 LINK O6 BMA H 3 C1 MAN H 4 1555 1555 1.45 CISPEP 1 GLY B 115 CYS B 116 0 7.22 CRYST1 65.011 61.763 110.750 90.00 91.53 90.00 P 1 21 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 0.015382 0.000000 0.000411 0.00000 SCALE2 0.000000 0.016191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009033 0.00000