HEADER SIGNALING PROTEIN 16-MAR-15 4YRZ TITLE CRYSTAL STRUCTURE OF LUXP IN COMPLEX WITH L-XYLULOFURANOSE-1,2-BORATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOINDUCER 2-BINDING PERIPLASMIC PROTEIN LUXP; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 21-365; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO HARVEYI; SOURCE 3 ORGANISM_TAXID: 669; SOURCE 4 GENE: LUXP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX4T1 KEYWDS PROTEIN-LIGAND COMPLEX, QUORUM SENSING, PROTEIN BINDING, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.MCDONOUGH,S.SATTIN,P.M.GARDNER,C.LIU,B.G.DAVIS REVDAT 3 10-JAN-24 4YRZ 1 REMARK REVDAT 2 13-SEP-17 4YRZ 1 REMARK SITE ATOM REVDAT 1 23-MAR-16 4YRZ 0 JRNL AUTH S.SATTIN JRNL TITL DISCOVERY OF GLYCOMIMETIC AGONISTS FROM A PROTOCELL JRNL TITL 2 METABOLISM, PROTO-NATURAL PRODUCT LIBRARIES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 26935 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.420 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 49.1961 - 6.1918 1.00 1929 153 0.1678 0.2264 REMARK 3 2 6.1918 - 4.9161 1.00 1839 148 0.1565 0.2065 REMARK 3 3 4.9161 - 4.2950 1.00 1824 147 0.1210 0.1446 REMARK 3 4 4.2950 - 3.9025 1.00 1792 143 0.1395 0.1973 REMARK 3 5 3.9025 - 3.6229 1.00 1801 145 0.1543 0.2105 REMARK 3 6 3.6229 - 3.4094 1.00 1778 142 0.1681 0.2118 REMARK 3 7 3.4094 - 3.2386 1.00 1792 143 0.1948 0.2519 REMARK 3 8 3.2386 - 3.0977 1.00 1781 144 0.2136 0.3029 REMARK 3 9 3.0977 - 2.9785 1.00 1762 141 0.2203 0.2992 REMARK 3 10 2.9785 - 2.8757 1.00 1778 143 0.2188 0.3210 REMARK 3 11 2.8757 - 2.7858 1.00 1767 141 0.2248 0.2931 REMARK 3 12 2.7858 - 2.7062 1.00 1780 143 0.2512 0.3342 REMARK 3 13 2.7062 - 2.6349 0.98 1732 139 0.2633 0.3227 REMARK 3 14 2.6349 - 2.5706 0.91 1582 126 0.2944 0.3178 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 5596 REMARK 3 ANGLE : 1.399 7609 REMARK 3 CHIRALITY : 0.075 825 REMARK 3 PLANARITY : 0.007 988 REMARK 3 DIHEDRAL : 16.498 2041 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 26 THROUGH 53 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.8766 -26.5129 24.4419 REMARK 3 T TENSOR REMARK 3 T11: 0.3267 T22: 0.7196 REMARK 3 T33: 0.5567 T12: 0.0033 REMARK 3 T13: -0.1329 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 5.6590 L22: 7.7148 REMARK 3 L33: 7.1017 L12: 2.2077 REMARK 3 L13: 2.6464 L23: 1.0724 REMARK 3 S TENSOR REMARK 3 S11: 0.1963 S12: -0.0287 S13: -0.5896 REMARK 3 S21: 0.5719 S22: 0.4695 S23: -1.5168 REMARK 3 S31: 0.1285 S32: 1.7359 S33: -0.5442 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 54 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3309 -35.3082 15.8353 REMARK 3 T TENSOR REMARK 3 T11: 0.2662 T22: 0.4623 REMARK 3 T33: 0.5065 T12: 0.0474 REMARK 3 T13: -0.0632 T23: -0.0714 REMARK 3 L TENSOR REMARK 3 L11: 1.2853 L22: 4.8858 REMARK 3 L33: 4.7268 L12: 2.5199 REMARK 3 L13: -0.0233 L23: -0.5054 REMARK 3 S TENSOR REMARK 3 S11: -0.1530 S12: 0.2395 S13: -0.1554 REMARK 3 S21: 0.2075 S22: 0.2249 S23: 0.1995 REMARK 3 S31: 0.0306 S32: -0.1256 S33: -0.0098 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 113 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.6272 -26.6389 29.4137 REMARK 3 T TENSOR REMARK 3 T11: 0.3416 T22: 0.3955 REMARK 3 T33: 0.3071 T12: 0.0419 REMARK 3 T13: -0.0484 T23: 0.0481 REMARK 3 L TENSOR REMARK 3 L11: 3.9931 L22: 4.9342 REMARK 3 L33: 2.2956 L12: 1.2696 REMARK 3 L13: -2.0817 L23: 0.6144 REMARK 3 S TENSOR REMARK 3 S11: -0.0589 S12: -0.0209 S13: 0.0223 REMARK 3 S21: 0.4054 S22: 0.0369 S23: 0.2271 REMARK 3 S31: 0.0404 S32: -0.1632 S33: 0.0297 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 165 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.8623 -13.7405 12.0612 REMARK 3 T TENSOR REMARK 3 T11: 0.2888 T22: 0.5571 REMARK 3 T33: 0.3713 T12: -0.0015 REMARK 3 T13: 0.0090 T23: -0.0219 REMARK 3 L TENSOR REMARK 3 L11: 0.8637 L22: 4.1906 REMARK 3 L33: 1.2052 L12: 0.5023 REMARK 3 L13: -0.1037 L23: -1.2848 REMARK 3 S TENSOR REMARK 3 S11: 0.0281 S12: 0.1241 S13: -0.0996 REMARK 3 S21: -0.0788 S22: -0.0677 S23: -0.1651 REMARK 3 S31: -0.0596 S32: 0.2985 S33: 0.0305 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 26 THROUGH 53 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.0519 -72.1411 8.5982 REMARK 3 T TENSOR REMARK 3 T11: 0.7390 T22: 0.3564 REMARK 3 T33: 0.5459 T12: 0.0868 REMARK 3 T13: -0.0865 T23: -0.1252 REMARK 3 L TENSOR REMARK 3 L11: 7.9759 L22: 4.0758 REMARK 3 L33: 5.9861 L12: 2.1362 REMARK 3 L13: 2.9617 L23: 2.4786 REMARK 3 S TENSOR REMARK 3 S11: 0.7738 S12: 0.6142 S13: -1.5373 REMARK 3 S21: -0.4073 S22: 0.1663 S23: -0.4752 REMARK 3 S31: 1.2442 S32: 0.3406 S33: -0.9455 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 54 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.0588 -53.0787 16.1322 REMARK 3 T TENSOR REMARK 3 T11: 0.3615 T22: 0.3635 REMARK 3 T33: 0.5134 T12: -0.0068 REMARK 3 T13: -0.0767 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 6.2929 L22: 2.5206 REMARK 3 L33: 5.7381 L12: 1.5667 REMARK 3 L13: -0.3312 L23: -0.8864 REMARK 3 S TENSOR REMARK 3 S11: -0.0081 S12: -0.0363 S13: 0.5270 REMARK 3 S21: 0.0302 S22: -0.1620 S23: -0.6069 REMARK 3 S31: -0.0919 S32: 0.2725 S33: 0.1127 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 113 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.4343 -51.8865 2.7992 REMARK 3 T TENSOR REMARK 3 T11: 0.4116 T22: 0.5379 REMARK 3 T33: 0.3456 T12: 0.0008 REMARK 3 T13: -0.0104 T23: 0.1015 REMARK 3 L TENSOR REMARK 3 L11: 3.7066 L22: 4.0293 REMARK 3 L33: 4.3516 L12: -0.7734 REMARK 3 L13: 0.4983 L23: -1.3022 REMARK 3 S TENSOR REMARK 3 S11: 0.1699 S12: 0.5708 S13: 0.4124 REMARK 3 S21: -0.3748 S22: -0.2813 S23: -0.2779 REMARK 3 S31: 0.0567 S32: 0.4160 S33: 0.0018 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 165 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.0724 -59.5647 20.7153 REMARK 3 T TENSOR REMARK 3 T11: 0.4182 T22: 0.3072 REMARK 3 T33: 0.3456 T12: 0.0664 REMARK 3 T13: -0.0586 T23: 0.0160 REMARK 3 L TENSOR REMARK 3 L11: 5.8593 L22: 0.4629 REMARK 3 L33: 1.2070 L12: -0.0767 REMARK 3 L13: -1.2327 L23: 0.1988 REMARK 3 S TENSOR REMARK 3 S11: -0.0525 S12: -0.0142 S13: 0.0863 REMARK 3 S21: 0.0328 S22: 0.0779 S23: -0.1148 REMARK 3 S31: 0.0736 S32: -0.1007 S33: -0.0221 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4YRZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207989. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0719 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DOUBLE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26994 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.570 REMARK 200 RESOLUTION RANGE LOW (A) : 49.187 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.19700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.92900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 4YR7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 8000, 100MM SODIUM CACODYLATE REMARK 280 PH 6.6, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 37.25000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.49000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.51800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.49000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.25000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.51800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: A 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 APPLY THE FOLLOWING TO CHAINS: 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 21 REMARK 465 SER A 22 REMARK 465 MET A 23 REMARK 465 VAL A 24 REMARK 465 LEU A 25 REMARK 465 ASN A 365 REMARK 465 GLY B 21 REMARK 465 SER B 22 REMARK 465 MET B 23 REMARK 465 VAL B 24 REMARK 465 LEU B 25 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 ASN A 26 CG OD1 ND2 REMARK 470 LYS A 61 CE NZ REMARK 470 GLN A 64 CG CD OE1 NE2 REMARK 470 ARG A 108 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 125 CD CE NZ REMARK 470 LYS A 301 NZ REMARK 470 LYS A 357 NZ REMARK 470 ASN B 26 CG OD1 ND2 REMARK 470 LYS B 61 CD CE NZ REMARK 470 GLN B 64 CG CD OE1 NE2 REMARK 470 LYS B 68 CE NZ REMARK 470 GLN B 76 CG CD OE1 NE2 REMARK 470 ARG B 108 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 110 CG OD1 ND2 REMARK 470 LYS B 125 CD CE NZ REMARK 470 LYS B 127 CD CE NZ REMARK 470 ASP B 168 CG OD1 OD2 REMARK 470 LYS B 169 CG CD CE NZ REMARK 470 GLU B 282 CG CD OE1 OE2 REMARK 470 ASN B 365 CG OD1 ND2 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 OE2 GLU A 282 O HOH A 501 2.03 REMARK 500 OG1 THR B 63 O ARG B 65 2.04 REMARK 500 OG1 THR B 161 O HOH B 501 2.06 REMARK 500 OE1 GLN A 32 NH2 ARG A 42 2.06 REMARK 500 OE1 GLU A 145 O HOH A 502 2.12 REMARK 500 OE1 GLN A 300 O HOH A 503 2.12 REMARK 500 NH1 ARG B 351 O HOH B 502 2.13 REMARK 500 OD2 ASP A 339 O HOH A 504 2.14 REMARK 500 O ARG B 139 O HOH B 503 2.14 REMARK 500 OE1 GLU B 353 O HOH B 504 2.16 REMARK 500 O HOH B 505 O HOH B 506 2.18 REMARK 500 O THR A 137 NH1 ARG A 141 2.19 REMARK 500 NH1 ARG B 141 OE2 GLU B 166 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 590 O HOH B 580 1565 2.12 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 PRO A 58 173.17 -50.50 REMARK 500 HIS A 140 40.17 -144.65 REMARK 500 PHE A 206 -160.69 -75.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A2B A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A2B B 401 DBREF 4YRZ A 21 365 UNP P54300 LUXP_VIBHA 21 365 DBREF 4YRZ B 21 365 UNP P54300 LUXP_VIBHA 21 365 SEQADV 4YRZ GLY A 21 UNP P54300 ALA 21 CONFLICT SEQADV 4YRZ SER A 22 UNP P54300 THR 22 CONFLICT SEQADV 4YRZ MET A 23 UNP P54300 GLN 23 CONFLICT SEQADV 4YRZ GLY B 21 UNP P54300 ALA 21 CONFLICT SEQADV 4YRZ SER B 22 UNP P54300 THR 22 CONFLICT SEQADV 4YRZ MET B 23 UNP P54300 GLN 23 CONFLICT SEQRES 1 A 345 GLY SER MET VAL LEU ASN GLY TYR TRP GLY TYR GLN GLU SEQRES 2 A 345 PHE LEU ASP GLU PHE PRO GLU GLN ARG ASN LEU THR ASN SEQRES 3 A 345 ALA LEU SER GLU ALA VAL ARG ALA GLN PRO VAL PRO LEU SEQRES 4 A 345 SER LYS PRO THR GLN ARG PRO ILE LYS ILE SER VAL VAL SEQRES 5 A 345 TYR PRO GLY GLN GLN VAL SER ASP TYR TRP VAL ARG ASN SEQRES 6 A 345 ILE ALA SER PHE GLU LYS ARG LEU TYR LYS LEU ASN ILE SEQRES 7 A 345 ASN TYR GLN LEU ASN GLN VAL PHE THR ARG PRO ASN ALA SEQRES 8 A 345 ASP ILE LYS GLN GLN SER LEU SER LEU MET GLU ALA LEU SEQRES 9 A 345 LYS SER LYS SER ASP TYR LEU ILE PHE THR LEU ASP THR SEQRES 10 A 345 THR ARG HIS ARG LYS PHE VAL GLU HIS VAL LEU ASP SER SEQRES 11 A 345 THR ASN THR LYS LEU ILE LEU GLN ASN ILE THR THR PRO SEQRES 12 A 345 VAL ARG GLU TRP ASP LYS HIS GLN PRO PHE LEU TYR VAL SEQRES 13 A 345 GLY PHE ASP HIS ALA GLU GLY SER ARG GLU LEU ALA THR SEQRES 14 A 345 GLU PHE GLY LYS PHE PHE PRO LYS HIS THR TYR TYR SER SEQRES 15 A 345 VAL LEU TYR PHE SER GLU GLY TYR ILE SER ASP VAL ARG SEQRES 16 A 345 GLY ASP THR PHE ILE HIS GLN VAL ASN ARG ASP ASN ASN SEQRES 17 A 345 PHE GLU LEU GLN SER ALA TYR TYR THR LYS ALA THR LYS SEQRES 18 A 345 GLN SER GLY TYR ASP ALA ALA LYS ALA SER LEU ALA LYS SEQRES 19 A 345 HIS PRO ASP VAL ASP PHE ILE TYR ALA CYS SER THR ASP SEQRES 20 A 345 VAL ALA LEU GLY ALA VAL ASP ALA LEU ALA GLU LEU GLY SEQRES 21 A 345 ARG GLU ASP ILE MET ILE ASN GLY TRP GLY GLY GLY SER SEQRES 22 A 345 ALA GLU LEU ASP ALA ILE GLN LYS GLY ASP LEU ASP ILE SEQRES 23 A 345 THR VAL MET ARG MET ASN ASP ASP THR GLY ILE ALA MET SEQRES 24 A 345 ALA GLU ALA ILE LYS TRP ASP LEU GLU ASP LYS PRO VAL SEQRES 25 A 345 PRO THR VAL TYR SER GLY ASP PHE GLU ILE VAL THR LYS SEQRES 26 A 345 ALA ASP SER PRO GLU ARG ILE GLU ALA LEU LYS LYS ARG SEQRES 27 A 345 ALA PHE ARG TYR SER ASP ASN SEQRES 1 B 345 GLY SER MET VAL LEU ASN GLY TYR TRP GLY TYR GLN GLU SEQRES 2 B 345 PHE LEU ASP GLU PHE PRO GLU GLN ARG ASN LEU THR ASN SEQRES 3 B 345 ALA LEU SER GLU ALA VAL ARG ALA GLN PRO VAL PRO LEU SEQRES 4 B 345 SER LYS PRO THR GLN ARG PRO ILE LYS ILE SER VAL VAL SEQRES 5 B 345 TYR PRO GLY GLN GLN VAL SER ASP TYR TRP VAL ARG ASN SEQRES 6 B 345 ILE ALA SER PHE GLU LYS ARG LEU TYR LYS LEU ASN ILE SEQRES 7 B 345 ASN TYR GLN LEU ASN GLN VAL PHE THR ARG PRO ASN ALA SEQRES 8 B 345 ASP ILE LYS GLN GLN SER LEU SER LEU MET GLU ALA LEU SEQRES 9 B 345 LYS SER LYS SER ASP TYR LEU ILE PHE THR LEU ASP THR SEQRES 10 B 345 THR ARG HIS ARG LYS PHE VAL GLU HIS VAL LEU ASP SER SEQRES 11 B 345 THR ASN THR LYS LEU ILE LEU GLN ASN ILE THR THR PRO SEQRES 12 B 345 VAL ARG GLU TRP ASP LYS HIS GLN PRO PHE LEU TYR VAL SEQRES 13 B 345 GLY PHE ASP HIS ALA GLU GLY SER ARG GLU LEU ALA THR SEQRES 14 B 345 GLU PHE GLY LYS PHE PHE PRO LYS HIS THR TYR TYR SER SEQRES 15 B 345 VAL LEU TYR PHE SER GLU GLY TYR ILE SER ASP VAL ARG SEQRES 16 B 345 GLY ASP THR PHE ILE HIS GLN VAL ASN ARG ASP ASN ASN SEQRES 17 B 345 PHE GLU LEU GLN SER ALA TYR TYR THR LYS ALA THR LYS SEQRES 18 B 345 GLN SER GLY TYR ASP ALA ALA LYS ALA SER LEU ALA LYS SEQRES 19 B 345 HIS PRO ASP VAL ASP PHE ILE TYR ALA CYS SER THR ASP SEQRES 20 B 345 VAL ALA LEU GLY ALA VAL ASP ALA LEU ALA GLU LEU GLY SEQRES 21 B 345 ARG GLU ASP ILE MET ILE ASN GLY TRP GLY GLY GLY SER SEQRES 22 B 345 ALA GLU LEU ASP ALA ILE GLN LYS GLY ASP LEU ASP ILE SEQRES 23 B 345 THR VAL MET ARG MET ASN ASP ASP THR GLY ILE ALA MET SEQRES 24 B 345 ALA GLU ALA ILE LYS TRP ASP LEU GLU ASP LYS PRO VAL SEQRES 25 B 345 PRO THR VAL TYR SER GLY ASP PHE GLU ILE VAL THR LYS SEQRES 26 B 345 ALA ASP SER PRO GLU ARG ILE GLU ALA LEU LYS LYS ARG SEQRES 27 B 345 ALA PHE ARG TYR SER ASP ASN HET A2B A 401 13 HET A2B B 401 13 HETNAM A2B L-XYLULOFURANOSE-1,2-BORATE FORMUL 3 A2B 2(C5 H10 B O7 1-) FORMUL 5 HOH *187(H2 O) HELIX 1 AA1 GLY A 30 PHE A 38 1 9 HELIX 2 AA2 PHE A 38 ALA A 54 1 17 HELIX 3 AA3 ASP A 80 LEU A 96 1 17 HELIX 4 AA4 ASP A 112 SER A 126 1 15 HELIX 5 AA5 HIS A 140 THR A 151 1 12 HELIX 6 AA6 VAL A 164 LYS A 169 5 6 HELIX 7 AA7 ASP A 179 PHE A 195 1 17 HELIX 8 AA8 GLY A 209 ASN A 228 1 20 HELIX 9 AA9 THR A 240 HIS A 255 1 16 HELIX 10 AB1 SER A 265 GLY A 280 1 16 HELIX 11 AB2 GLY A 292 GLY A 302 1 11 HELIX 12 AB3 ASN A 312 GLU A 328 1 17 HELIX 13 AB4 SER A 348 PHE A 360 1 13 HELIX 14 AB5 GLY B 30 PHE B 38 1 9 HELIX 15 AB6 PHE B 38 ALA B 54 1 17 HELIX 16 AB7 ASP B 80 LEU B 96 1 17 HELIX 17 AB8 ASP B 112 LEU B 124 1 13 HELIX 18 AB9 LYS B 125 LYS B 127 5 3 HELIX 19 AC1 HIS B 140 ASP B 149 1 10 HELIX 20 AC2 VAL B 164 ASP B 168 5 5 HELIX 21 AC3 ASP B 179 PHE B 195 1 17 HELIX 22 AC4 GLY B 209 ASN B 228 1 20 HELIX 23 AC5 THR B 240 HIS B 255 1 16 HELIX 24 AC6 SER B 265 LEU B 279 1 15 HELIX 25 AC7 GLY B 292 GLY B 302 1 11 HELIX 26 AC8 ASP B 313 GLU B 328 1 16 HELIX 27 AC9 SER B 348 PHE B 360 1 13 SHEET 1 AA1 6 TYR A 100 THR A 107 0 SHEET 2 AA1 6 ILE A 67 PRO A 74 1 N ILE A 69 O GLN A 101 SHEET 3 AA1 6 TYR A 130 PHE A 133 1 O ILE A 132 N SER A 70 SHEET 4 AA1 6 LYS A 154 GLN A 158 1 O GLN A 158 N PHE A 133 SHEET 5 AA1 6 LEU A 174 GLY A 177 1 O VAL A 176 N LEU A 157 SHEET 6 AA1 6 VAL A 335 SER A 337 1 O TYR A 336 N GLY A 177 SHEET 1 AA2 4 GLU A 230 TYR A 235 0 SHEET 2 AA2 4 TYR A 200 LEU A 204 1 N TYR A 201 O GLN A 232 SHEET 3 AA2 4 PHE A 260 ALA A 263 1 O TYR A 262 N LEU A 204 SHEET 4 AA2 4 MET A 285 ILE A 286 1 O MET A 285 N ILE A 261 SHEET 1 AA3 2 ILE A 306 ARG A 310 0 SHEET 2 AA3 2 PHE A 340 THR A 344 -1 O VAL A 343 N THR A 307 SHEET 1 AA4 6 TYR B 100 THR B 107 0 SHEET 2 AA4 6 ILE B 67 PRO B 74 1 N ILE B 69 O ASN B 103 SHEET 3 AA4 6 TYR B 130 PHE B 133 1 O ILE B 132 N SER B 70 SHEET 4 AA4 6 LYS B 154 GLN B 158 1 O GLN B 158 N PHE B 133 SHEET 5 AA4 6 LEU B 174 GLY B 177 1 O LEU B 174 N LEU B 157 SHEET 6 AA4 6 VAL B 335 SER B 337 1 O TYR B 336 N TYR B 175 SHEET 1 AA5 4 GLU B 230 TYR B 235 0 SHEET 2 AA5 4 TYR B 200 LEU B 204 1 N TYR B 201 O GLN B 232 SHEET 3 AA5 4 PHE B 260 ALA B 263 1 O TYR B 262 N SER B 202 SHEET 4 AA5 4 MET B 285 ILE B 286 1 O MET B 285 N ILE B 261 SHEET 1 AA6 2 ILE B 306 ARG B 310 0 SHEET 2 AA6 2 PHE B 340 THR B 344 -1 O GLU B 341 N MET B 309 CISPEP 1 PRO A 109 ASN A 110 0 -11.04 SITE 1 AC1 10 GLN A 77 SER A 79 TYR A 81 TRP A 82 SITE 2 AC1 10 ASN A 159 ARG A 215 SER A 265 THR A 266 SITE 3 AC1 10 TRP A 289 ARG A 310 SITE 1 AC2 11 GLN B 77 SER B 79 TYR B 81 TRP B 82 SITE 2 AC2 11 ASN B 159 ARG B 215 SER B 265 THR B 266 SITE 3 AC2 11 TRP B 289 ARG B 310 HOH B 557 CRYST1 74.500 85.036 130.980 90.00 90.00 90.00 P 21 21 21 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 0.013423 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011760 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007635 0.00000