HEADER IMMUNE SYSTEM 22-JUL-07 2Z64 TITLE CRYSTAL STRUCTURE OF MOUSE TLR4 AND MOUSE MD-2 COMPLEX CAVEAT 2Z64 NAG A 1441 HAS WRONG CHIRALITY AT ATOM C1 NAG A 1451 HAS CAVEAT 2 2Z64 WRONG CHIRALITY AT ATOM C1 NAG A 1471 HAS WRONG CHIRALITY CAVEAT 3 2Z64 AT ATOM C1 NAG A 1481 HAS WRONG CHIRALITY AT ATOM C1 NAG C CAVEAT 4 2Z64 1511 HAS WRONG CHIRALITY AT ATOM C1 NAG C 1521 HAS WRONG CAVEAT 5 2Z64 CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLL-LIKE RECEPTOR 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TLR4, UNP RESIDUES 27-625; COMPND 5 SYNONYM: CD284 ANTIGEN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: LYMPHOCYTE ANTIGEN 96; COMPND 9 CHAIN: C; COMPND 10 FRAGMENT: MD-2, UNP RESIDUES 21-160; COMPND 11 SYNONYM: MD-2 PROTEIN, ESOP-1; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TLR4; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HI-5; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PVL1393; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 14 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 GENE: MD2; SOURCE 17 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 18 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: HI-5; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PVL1393 KEYWDS TLR4, TOLL-LIKE RECEPTOR, MD-2, LPS, DISEASE MUTATION, GLYCOPROTEIN, KEYWDS 2 IMMUNE RESPONSE, INFLAMMATORY RESPONSE, INNATE IMMUNITY, LEUCINE- KEYWDS 3 RICH REPEAT, MEMBRANE, TRANSMEMBRANE, SECRETED, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.-O.LEE,H.M.KIM,B.S.PARK REVDAT 7 23-OCT-24 2Z64 1 REMARK REVDAT 6 01-NOV-23 2Z64 1 HETSYN REVDAT 5 29-JUL-20 2Z64 1 CAVEAT COMPND REMARK HET REVDAT 5 2 1 HETNAM FORMUL LINK SITE REVDAT 5 3 1 ATOM REVDAT 4 13-JUL-11 2Z64 1 VERSN REVDAT 3 21-JUL-10 2Z64 1 REMARK REVDAT 2 24-FEB-09 2Z64 1 VERSN REVDAT 1 18-SEP-07 2Z64 0 JRNL AUTH H.M.KIM,B.S.PARK,J.-I.KIM,S.E.KIM,J.LEE,S.C.OH,P.ENKHBAYAR, JRNL AUTH 2 N.MATSUSHIMA,H.LEE,O.J.YOO,J.-O.LEE JRNL TITL CRYSTAL STRUCTURE OF THE TLR4-MD-2 COMPLEX WITH BOUND JRNL TITL 2 ENDOTOXIN ANTAGONIST ERITORAN JRNL REF CELL(CAMBRIDGE,MASS.) V. 130 906 2007 JRNL REFN ISSN 0092-8674 JRNL PMID 17803912 JRNL DOI 10.1016/J.CELL.2007.08.002 REMARK 2 REMARK 2 RESOLUTION. 2.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 22180 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) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1183 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) : 2.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 743 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 41.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5867 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 281 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.87000 REMARK 3 B22 (A**2) : -5.87000 REMARK 3 B33 (A**2) : 5.01000 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): 0.464 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.355 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 36.744 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.905 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6307 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8573 ; 1.421 ; 2.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 732 ; 5.814 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 278 ;44.946 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1054 ;18.404 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.556 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1024 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4547 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3025 ; 0.247 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4206 ; 0.325 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 255 ; 0.159 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 35 ; 0.236 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.286 ; 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): 3755 ; 1.602 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5952 ; 2.793 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2807 ; 4.426 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2621 ; 6.952 ; 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 : 2 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 27 A 625 REMARK 3 ORIGIN FOR THE GROUP (A): -16.6135 0.3578 -1.2051 REMARK 3 T TENSOR REMARK 3 T11: -0.0332 T22: -0.1054 REMARK 3 T33: -0.2676 T12: -0.0046 REMARK 3 T13: 0.0096 T23: 0.0588 REMARK 3 L TENSOR REMARK 3 L11: 2.0374 L22: 0.6546 REMARK 3 L33: 0.4853 L12: -0.0046 REMARK 3 L13: -0.0817 L23: 0.0852 REMARK 3 S TENSOR REMARK 3 S11: -0.0221 S12: 0.0219 S13: -0.1763 REMARK 3 S21: -0.0386 S22: 0.0217 S23: -0.0173 REMARK 3 S31: 0.0695 S32: -0.0527 S33: 0.0004 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 21 C 155 REMARK 3 ORIGIN FOR THE GROUP (A): -27.6180 -11.8500 20.0202 REMARK 3 T TENSOR REMARK 3 T11: 0.0505 T22: 0.1247 REMARK 3 T33: -0.1756 T12: 0.0237 REMARK 3 T13: -0.0538 T23: -0.0354 REMARK 3 L TENSOR REMARK 3 L11: 1.9142 L22: 3.2907 REMARK 3 L33: 3.2950 L12: 0.0324 REMARK 3 L13: 0.2521 L23: -2.4279 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: -0.3642 S13: -0.1737 REMARK 3 S21: 0.3350 S22: 0.0289 S23: -0.2046 REMARK 3 S31: 0.2784 S32: 0.2491 S33: -0.0447 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: CYS388 AND CYS389 FORMS AN UNUSUAL REMARK 3 DISULFIDE BRIDGE AND A DISTORTED CIS PEPTIDE BOND REMARK 4 REMARK 4 2Z64 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000027568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23932 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 2Z63 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA-CACODYLATE, 23% PEG 8000, PH REMARK 280 6.5, VAPOR DIFFUSION, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 41.57900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.18200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.94100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.18200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.57900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.94100 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: AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, D, E, 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 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 ND2 ASN A 492 C2 NAG A 1491 2.07 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 CYS A 28 -150.70 -103.38 REMARK 500 ASN A 34 18.07 49.28 REMARK 500 ILE A 35 -57.38 -132.35 REMARK 500 ASP A 41 72.92 44.05 REMARK 500 LYS A 43 16.14 58.78 REMARK 500 PRO A 52 158.80 -42.40 REMARK 500 PRO A 64 81.53 -69.90 REMARK 500 LYS A 66 -71.37 64.58 REMARK 500 ARG A 86 77.87 46.96 REMARK 500 LEU A 100 47.78 -93.64 REMARK 500 PRO A 112 36.56 -68.85 REMARK 500 ILE A 113 49.45 -80.85 REMARK 500 GLN A 114 -47.78 -27.33 REMARK 500 ALA A 132 63.79 -117.48 REMARK 500 PRO A 167 150.54 -46.01 REMARK 500 ALA A 250 138.04 -35.86 REMARK 500 ASP A 264 19.12 -154.61 REMARK 500 ARG A 266 100.76 -38.92 REMARK 500 PRO A 273 -27.79 -37.58 REMARK 500 THR A 290 -164.40 -124.11 REMARK 500 ASP A 297 2.81 -61.57 REMARK 500 ASN A 307 56.38 -104.56 REMARK 500 SER A 317 22.10 -72.48 REMARK 500 GLU A 322 -11.25 -151.69 REMARK 500 LYS A 329 39.90 -87.13 REMARK 500 ASP A 347 36.15 -174.67 REMARK 500 LYS A 360 -63.40 -21.77 REMARK 500 ILE A 363 -178.96 -60.14 REMARK 500 ALA A 382 21.94 -58.28 REMARK 500 LEU A 394 -23.41 -140.81 REMARK 500 SER A 398 -4.51 -57.19 REMARK 500 ASN A 407 -157.80 -111.18 REMARK 500 HIS A 429 15.92 50.60 REMARK 500 GLU A 437 -70.07 -63.99 REMARK 500 PHE A 438 -154.91 -86.58 REMARK 500 ALA A 440 -49.77 -7.55 REMARK 500 LEU A 442 -37.43 -30.63 REMARK 500 ASN A 456 70.85 53.55 REMARK 500 MET A 476 54.38 -157.49 REMARK 500 ASN A 479 -138.31 -91.22 REMARK 500 LYS A 482 133.07 -39.36 REMARK 500 ASP A 483 24.94 43.07 REMARK 500 SER A 487 -161.26 -69.69 REMARK 500 ASN A 488 56.28 -114.71 REMARK 500 THR A 493 46.84 -74.51 REMARK 500 CYS A 504 32.57 -99.55 REMARK 500 GLN A 505 28.34 38.86 REMARK 500 GLU A 507 -33.33 -134.02 REMARK 500 TRP A 511 -76.93 -61.93 REMARK 500 ARG A 519 -8.14 -141.95 REMARK 500 REMARK 500 THIS ENTRY HAS 83 RAMACHANDRAN OUTLIERS. 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 THR A 608 PRO A 609 -148.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ALL POLYSACCHARIDES WERE ORIGINALLY ASSIGNED TO CHAIN N. REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG F 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z62 RELATED DB: PDB REMARK 900 THE TV3 HYBRID OF HUMAN TLR4 AND HAGFISH VLRB.61 REMARK 900 RELATED ID: 2Z63 RELATED DB: PDB REMARK 900 THE TV8 HYBRID OF HUMAN TLR4 AND HAGFISH VLRB.61 REMARK 900 RELATED ID: 2Z65 RELATED DB: PDB REMARK 900 THE HUMAN TLR4 TV3 HYBRID-MD-2-ERITORAN COMPLEX REMARK 900 RELATED ID: 2Z66 RELATED DB: PDB REMARK 900 THE VT3 HYBRID OF HUMAN TLR4 AND HAGFISH VLRB.61 DBREF 2Z64 A 27 625 UNP Q9QUK6 TLR4_MOUSE 27 625 DBREF 2Z64 C 21 155 UNP Q9JHF9 LY96_MOUSE 21 155 SEQRES 1 A 599 PRO CYS ILE GLU VAL VAL PRO ASN ILE THR TYR GLN CYS SEQRES 2 A 599 MET ASP GLN LYS LEU SER LYS VAL PRO ASP ASP ILE PRO SEQRES 3 A 599 SER SER THR LYS ASN ILE ASP LEU SER PHE ASN PRO LEU SEQRES 4 A 599 LYS ILE LEU LYS SER TYR SER PHE SER ASN PHE SER GLU SEQRES 5 A 599 LEU GLN TRP LEU ASP LEU SER ARG CYS GLU ILE GLU THR SEQRES 6 A 599 ILE GLU ASP LYS ALA TRP HIS GLY LEU HIS HIS LEU SER SEQRES 7 A 599 ASN LEU ILE LEU THR GLY ASN PRO ILE GLN SER PHE SER SEQRES 8 A 599 PRO GLY SER PHE SER GLY LEU THR SER LEU GLU ASN LEU SEQRES 9 A 599 VAL ALA VAL GLU THR LYS LEU ALA SER LEU GLU SER PHE SEQRES 10 A 599 PRO ILE GLY GLN LEU ILE THR LEU LYS LYS LEU ASN VAL SEQRES 11 A 599 ALA HIS ASN PHE ILE HIS SER CYS LYS LEU PRO ALA TYR SEQRES 12 A 599 PHE SER ASN LEU THR ASN LEU VAL HIS VAL ASP LEU SER SEQRES 13 A 599 TYR ASN TYR ILE GLN THR ILE THR VAL ASN ASP LEU GLN SEQRES 14 A 599 PHE LEU ARG GLU ASN PRO GLN VAL ASN LEU SER LEU ASP SEQRES 15 A 599 MET SER LEU ASN PRO ILE ASP PHE ILE GLN ASP GLN ALA SEQRES 16 A 599 PHE GLN GLY ILE LYS LEU HIS GLU LEU THR LEU ARG GLY SEQRES 17 A 599 ASN PHE ASN SER SER ASN ILE MET LYS THR CYS LEU GLN SEQRES 18 A 599 ASN LEU ALA GLY LEU HIS VAL HIS ARG LEU ILE LEU GLY SEQRES 19 A 599 GLU PHE LYS ASP GLU ARG ASN LEU GLU ILE PHE GLU PRO SEQRES 20 A 599 SER ILE MET GLU GLY LEU CYS ASP VAL THR ILE ASP GLU SEQRES 21 A 599 PHE ARG LEU THR TYR THR ASN ASP PHE SER ASP ASP ILE SEQRES 22 A 599 VAL LYS PHE HIS CYS LEU ALA ASN VAL SER ALA MET SER SEQRES 23 A 599 LEU ALA GLY VAL SER ILE LYS TYR LEU GLU ASP VAL PRO SEQRES 24 A 599 LYS HIS PHE LYS TRP GLN SER LEU SER ILE ILE ARG CYS SEQRES 25 A 599 GLN LEU LYS GLN PHE PRO THR LEU ASP LEU PRO PHE LEU SEQRES 26 A 599 LYS SER LEU THR LEU THR MET ASN LYS GLY SER ILE SER SEQRES 27 A 599 PHE LYS LYS VAL ALA LEU PRO SER LEU SER TYR LEU ASP SEQRES 28 A 599 LEU SER ARG ASN ALA LEU SER PHE SER GLY CYS CYS SER SEQRES 29 A 599 TYR SER ASP LEU GLY THR ASN SER LEU ARG HIS LEU ASP SEQRES 30 A 599 LEU SER PHE ASN GLY ALA ILE ILE MET SER ALA ASN PHE SEQRES 31 A 599 MET GLY LEU GLU GLU LEU GLN HIS LEU ASP PHE GLN HIS SEQRES 32 A 599 SER THR LEU LYS ARG VAL THR GLU PHE SER ALA PHE LEU SEQRES 33 A 599 SER LEU GLU LYS LEU LEU TYR LEU ASP ILE SER TYR THR SEQRES 34 A 599 ASN THR LYS ILE ASP PHE ASP GLY ILE PHE LEU GLY LEU SEQRES 35 A 599 THR SER LEU ASN THR LEU LYS MET ALA GLY ASN SER PHE SEQRES 36 A 599 LYS ASP ASN THR LEU SER ASN VAL PHE ALA ASN THR THR SEQRES 37 A 599 ASN LEU THR PHE LEU ASP LEU SER LYS CYS GLN LEU GLU SEQRES 38 A 599 GLN ILE SER TRP GLY VAL PHE ASP THR LEU HIS ARG LEU SEQRES 39 A 599 GLN LEU LEU ASN MET SER HIS ASN ASN LEU LEU PHE LEU SEQRES 40 A 599 ASP SER SER HIS TYR ASN GLN LEU TYR SER LEU SER THR SEQRES 41 A 599 LEU ASP CYS SER PHE ASN ARG ILE GLU THR SER LYS GLY SEQRES 42 A 599 ILE LEU GLN HIS PHE PRO LYS SER LEU ALA PHE PHE ASN SEQRES 43 A 599 LEU THR ASN ASN SER VAL ALA CYS ILE CYS GLU HIS GLN SEQRES 44 A 599 LYS PHE LEU GLN TRP VAL LYS GLU GLN LYS GLN PHE LEU SEQRES 45 A 599 VAL ASN VAL GLU GLN MET THR CYS ALA THR PRO VAL GLU SEQRES 46 A 599 MET ASN THR SER LEU VAL LEU ASP PHE ASN ASN SER THR SEQRES 47 A 599 CYS SEQRES 1 C 135 GLN GLN TRP PHE CYS ASN SER SER ASP ALA ILE ILE SER SEQRES 2 C 135 TYR SER TYR CYS ASP HIS LEU LYS PHE PRO ILE SER ILE SEQRES 3 C 135 SER SER GLU PRO CYS ILE ARG LEU ARG GLY THR ASN GLY SEQRES 4 C 135 PHE VAL HIS VAL GLU PHE ILE PRO ARG GLY ASN LEU LYS SEQRES 5 C 135 TYR LEU TYR PHE ASN LEU PHE ILE SER VAL ASN SER ILE SEQRES 6 C 135 GLU LEU PRO LYS ARG LYS GLU VAL LEU CYS HIS GLY HIS SEQRES 7 C 135 ASP ASP ASP TYR SER PHE CYS ARG ALA LEU LYS GLY GLU SEQRES 8 C 135 THR VAL ASN THR SER ILE PRO PHE SER PHE GLU GLY ILE SEQRES 9 C 135 LEU PHE PRO LYS GLY HIS TYR ARG CYS VAL ALA GLU ALA SEQRES 10 C 135 ILE ALA GLY ASP THR GLU GLU LYS LEU PHE CYS LEU ASN SEQRES 11 C 135 PHE THR ILE ILE HIS MODRES 2Z64 ASN A 34 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN A 75 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN A 172 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN A 204 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN A 237 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN A 307 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN A 492 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN A 524 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN A 572 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN C 26 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN C 114 ASN GLYCOSYLATION SITE MODRES 2Z64 ASN C 150 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET FUL F 4 10 HET NAG A1431 14 HET NAG A1441 14 HET NAG A1451 14 HET NAG A1471 14 HET NAG A1481 14 HET NAG A1491 14 HET NAG C1501 14 HET NAG C1511 14 HET NAG C1521 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUL BETA-L-FUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUL BETA-L-FUCOSE; 6-DEOXY-BETA-L-GALACTOPYRANOSE; L- HETSYN 2 FUL FUCOSE; FUCOSE; 6-DEOXY-BETA-L-GALACTOSE FORMUL 3 NAG 17(C8 H15 N O6) FORMUL 4 BMA 3(C6 H12 O6) FORMUL 6 FUL C6 H12 O5 FORMUL 16 HOH *154(H2 O) HELIX 1 1 PRO A 167 ASN A 172 5 6 HELIX 2 2 SER A 238 LEU A 249 1 12 HELIX 3 3 GLU A 272 GLU A 277 5 6 HELIX 4 4 ASP A 298 ALA A 306 5 9 HELIX 5 5 SER A 390 GLY A 395 1 6 HELIX 6 6 SER A 536 TYR A 538 5 3 HELIX 7 7 ILE A 560 PHE A 564 5 5 HELIX 8 8 ILE A 581 GLU A 583 5 3 HELIX 9 9 HIS A 584 GLN A 594 1 11 HELIX 10 10 LYS A 595 LEU A 598 5 4 HELIX 11 11 ASN A 600 MET A 604 5 5 HELIX 12 12 SER A 615 ASP A 619 5 5 HELIX 13 13 TYR C 102 ALA C 107 5 6 SHEET 1 A24 ILE A 29 VAL A 32 0 SHEET 2 A24 THR A 36 GLN A 38 -1 O THR A 36 N VAL A 32 SHEET 3 A24 ASN A 57 ASP A 59 1 O ASN A 57 N TYR A 37 SHEET 4 A24 TRP A 81 ASP A 83 1 O ASP A 83 N ILE A 58 SHEET 5 A24 ASN A 105 ILE A 107 1 O ASN A 105 N LEU A 82 SHEET 6 A24 ASN A 129 VAL A 131 1 O ASN A 129 N LEU A 106 SHEET 7 A24 LYS A 153 ASN A 155 1 O ASN A 155 N LEU A 130 SHEET 8 A24 HIS A 178 ASP A 180 1 O HIS A 178 N LEU A 154 SHEET 9 A24 SER A 206 ASP A 208 1 O ASP A 208 N VAL A 179 SHEET 10 A24 ILE A 225 ARG A 233 1 O GLU A 229 N LEU A 207 SHEET 11 A24 LEU A 252 GLY A 260 1 O ARG A 256 N HIS A 228 SHEET 12 A24 THR A 283 LEU A 289 1 O ARG A 288 N LEU A 259 SHEET 13 A24 ALA A 310 ALA A 314 1 O SER A 312 N LEU A 289 SHEET 14 A24 SER A 332 ILE A 336 1 O SER A 334 N LEU A 313 SHEET 15 A24 SER A 353 THR A 357 1 O THR A 357 N ILE A 335 SHEET 16 A24 TYR A 375 ASP A 377 1 O ASP A 377 N LEU A 354 SHEET 17 A24 HIS A 401 ASP A 403 1 O ASP A 403 N LEU A 376 SHEET 18 A24 HIS A 424 ASP A 426 1 O ASP A 426 N LEU A 402 SHEET 19 A24 TYR A 449 ASP A 451 1 O TYR A 449 N LEU A 425 SHEET 20 A24 THR A 473 LYS A 475 1 O THR A 473 N LEU A 450 SHEET 21 A24 PHE A 498 ASP A 500 1 O PHE A 498 N LEU A 474 SHEET 22 A24 LEU A 522 ASN A 524 1 O ASN A 524 N LEU A 499 SHEET 23 A24 THR A 546 ASP A 548 1 O ASP A 548 N LEU A 523 SHEET 24 A24 PHE A 570 ASN A 572 1 O ASN A 572 N LEU A 547 SHEET 1 B 2 ILE A 67 LEU A 68 0 SHEET 2 B 2 THR A 91 ILE A 92 1 O THR A 91 N LEU A 68 SHEET 1 C 2 THR A 188 ILE A 189 0 SHEET 2 C 2 PHE A 216 ILE A 217 1 O PHE A 216 N ILE A 189 SHEET 1 D 3 PHE A 385 CYS A 388 0 SHEET 2 D 3 ALA A 409 MET A 412 1 O ILE A 411 N PHE A 385 SHEET 3 D 3 THR A 431 LYS A 433 1 O THR A 431 N ILE A 410 SHEET 1 E 2 LYS A 458 ILE A 459 0 SHEET 2 E 2 SER A 480 PHE A 481 1 O SER A 480 N ILE A 459 SHEET 1 F 2 THR A 485 LEU A 486 0 SHEET 2 F 2 GLN A 508 ILE A 509 1 O GLN A 508 N LEU A 486 SHEET 1 G 2 PHE A 532 ASP A 534 0 SHEET 2 G 2 THR A 556 LYS A 558 1 O LYS A 558 N LEU A 533 SHEET 1 H 6 TRP C 23 ASN C 26 0 SHEET 2 H 6 ILE C 31 TYR C 36 -1 O ILE C 32 N CYS C 25 SHEET 3 H 6 LYS C 145 ILE C 154 -1 O ILE C 154 N ILE C 31 SHEET 4 H 6 HIS C 130 ALA C 139 -1 N ALA C 135 O LEU C 149 SHEET 5 H 6 LEU C 74 VAL C 82 -1 N TYR C 75 O ILE C 138 SHEET 6 H 6 ILE C 85 GLU C 86 -1 O ILE C 85 N VAL C 82 SHEET 1 I 6 TRP C 23 ASN C 26 0 SHEET 2 I 6 ILE C 31 TYR C 36 -1 O ILE C 32 N CYS C 25 SHEET 3 I 6 LYS C 145 ILE C 154 -1 O ILE C 154 N ILE C 31 SHEET 4 I 6 HIS C 130 ALA C 139 -1 N ALA C 135 O LEU C 149 SHEET 5 I 6 LEU C 74 VAL C 82 -1 N TYR C 75 O ILE C 138 SHEET 6 I 6 ARG C 90 VAL C 93 -1 O GLU C 92 N PHE C 76 SHEET 1 J 3 SER C 47 GLU C 49 0 SHEET 2 J 3 THR C 57 PHE C 65 -1 O PHE C 60 N GLU C 49 SHEET 3 J 3 VAL C 113 PHE C 121 -1 O VAL C 113 N PHE C 65 SSBOND 1 CYS A 28 CYS A 39 1555 1555 2.05 SSBOND 2 CYS A 280 CYS A 304 1555 1555 2.06 SSBOND 3 CYS A 388 CYS A 389 1555 1555 2.03 SSBOND 4 CYS A 580 CYS A 606 1555 1555 2.04 SSBOND 5 CYS A 582 CYS A 625 1555 1555 2.05 SSBOND 6 CYS C 25 CYS C 51 1555 1555 2.06 SSBOND 7 CYS C 37 CYS C 148 1555 1555 2.06 SSBOND 8 CYS C 95 CYS C 105 1555 1555 2.03 LINK ND2 ASN A 34 C1 NAG A1431 1555 1555 1.45 LINK ND2 ASN A 75 C1 NAG A1441 1555 1555 1.45 LINK ND2 ASN A 172 C1 NAG A1451 1555 1555 1.45 LINK ND2 ASN A 204 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN A 237 C1 NAG A1471 1555 1555 1.45 LINK ND2 ASN A 307 C1 NAG A1481 1555 1555 1.45 LINK ND2 ASN A 492 C1 NAG A1491 1555 1555 1.45 LINK ND2 ASN A 524 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN A 572 C1 NAG B 1 1555 1555 1.46 LINK ND2 ASN C 26 C1 NAG C1501 1555 1555 1.47 LINK ND2 ASN C 114 C1 NAG C1511 1555 1555 1.45 LINK ND2 ASN C 150 C1 NAG C1521 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 2 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 1.45 LINK O6 NAG F 1 C1 FUL F 4 1555 1555 1.45 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.45 CISPEP 1 CYS A 388 CYS A 389 0 -1.85 CISPEP 2 GLU C 49 PRO C 50 0 4.33 CRYST1 83.158 101.882 126.364 90.00 90.00 90.00 P 21 21 21 4 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 0.012025 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009815 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007914 0.00000