HEADER MEMBRANE PROTEIN 08-NOV-17 6BKL TITLE INFLUENZA A M2 TRANSMEMBRANE DOMAIN BOUND TO RIMANTADINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIX PROTEIN 2; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS; SOURCE 4 ORGANISM_TAXID: 11320 KEYWDS INFLUENZA M2, PROTON CHANNEL, MEMBRANE PROTEIN, RIMANTADINE EXPDTA X-RAY DIFFRACTION AUTHOR J.L.THOMASTON,W.F.DEGRADO REVDAT 4 04-OCT-23 6BKL 1 REMARK REVDAT 3 01-JAN-20 6BKL 1 REMARK REVDAT 2 28-NOV-18 6BKL 1 JRNL REVDAT 1 19-SEP-18 6BKL 0 JRNL AUTH J.L.THOMASTON,N.F.POLIZZI,A.KONSTANTINIDI,J.WANG, JRNL AUTH 2 A.KOLOCOURIS,W.F.DEGRADO JRNL TITL INHIBITORS OF THE M2 PROTON CHANNEL ENGAGE AND DISRUPT JRNL TITL 2 TRANSMEMBRANE NETWORKS OF HYDROGEN-BONDED WATERS. JRNL REF J. AM. CHEM. SOC. V. 140 15219 2018 JRNL REFN ESSN 1520-5126 JRNL PMID 30165017 JRNL DOI 10.1021/JACS.8B06741 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 10543 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1052 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 48.2067 - 3.9894 0.92 1208 133 0.1983 0.2185 REMARK 3 2 3.9894 - 3.1667 0.93 1208 133 0.1883 0.2529 REMARK 3 3 3.1667 - 2.7664 0.94 1206 134 0.1798 0.2311 REMARK 3 4 2.7664 - 2.5135 0.93 1186 133 0.1726 0.2270 REMARK 3 5 2.5135 - 2.3334 0.92 1200 131 0.1838 0.3098 REMARK 3 6 2.3334 - 2.1958 0.91 1163 130 0.1762 0.2385 REMARK 3 7 2.1958 - 2.0858 0.92 1178 132 0.1720 0.2834 REMARK 3 8 2.0858 - 1.9950 0.90 1142 126 0.1975 0.2724 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.120 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 : 0.007 1536 REMARK 3 ANGLE : 0.735 2120 REMARK 3 CHIRALITY : 0.431 302 REMARK 3 PLANARITY : 0.006 226 REMARK 3 DIHEDRAL : 10.977 508 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6BKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1000231032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1158 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10589 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.995 REMARK 200 RESOLUTION RANGE LOW (A) : 48.193 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.34800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 3LBW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 0.1 M SODIUM ACETATE / REMARK 280 ACETIC ACID PH 4.5, 20% W/V PEG 8000, MONOOLEIN, RIMANTADINE, REMARK 280 LIPIDIC CUBIC PHASE, TEMPERATURE 293K 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 23.92000 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, 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 ACE A 21 REMARK 465 SER A 22 REMARK 465 NH2 A 47 REMARK 465 ACE B 21 REMARK 465 SER B 22 REMARK 465 SER B 23 REMARK 465 NH2 B 47 REMARK 465 ACE C 21 REMARK 465 SER C 22 REMARK 465 SER C 23 REMARK 465 NH2 C 47 REMARK 465 ACE D 21 REMARK 465 SER D 22 REMARK 465 SER D 23 REMARK 465 NH2 D 47 REMARK 465 ACE E 21 REMARK 465 SER E 22 REMARK 465 NH2 E 47 REMARK 465 ACE F 21 REMARK 465 SER F 22 REMARK 465 SER F 23 REMARK 465 NH2 F 47 REMARK 465 ACE G 21 REMARK 465 SER G 22 REMARK 465 SER G 23 REMARK 465 NH2 G 47 REMARK 465 ACE H 21 REMARK 465 SER H 22 REMARK 465 SER H 23 REMARK 465 NH2 H 47 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EU7 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RIM D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RIM F 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EU7 G 101 DBREF 6BKL A 22 46 UNP Q20MD5 Q20MD5_I72A8 22 46 DBREF 6BKL B 22 46 UNP Q20MD5 Q20MD5_I72A8 22 46 DBREF 6BKL C 22 46 UNP Q20MD5 Q20MD5_I72A8 22 46 DBREF 6BKL D 22 46 UNP Q20MD5 Q20MD5_I72A8 22 46 DBREF 6BKL E 22 46 UNP Q20MD5 Q20MD5_I72A8 22 46 DBREF 6BKL F 22 46 UNP Q20MD5 Q20MD5_I72A8 22 46 DBREF 6BKL G 22 46 UNP Q20MD5 Q20MD5_I72A8 22 46 DBREF 6BKL H 22 46 UNP Q20MD5 Q20MD5_I72A8 22 46 SEQADV 6BKL ACE A 21 UNP Q20MD5 ACETYLATION SEQADV 6BKL NH2 A 47 UNP Q20MD5 AMIDATION SEQADV 6BKL ACE B 21 UNP Q20MD5 ACETYLATION SEQADV 6BKL NH2 B 47 UNP Q20MD5 AMIDATION SEQADV 6BKL ACE C 21 UNP Q20MD5 ACETYLATION SEQADV 6BKL NH2 C 47 UNP Q20MD5 AMIDATION SEQADV 6BKL ACE D 21 UNP Q20MD5 ACETYLATION SEQADV 6BKL NH2 D 47 UNP Q20MD5 AMIDATION SEQADV 6BKL ACE E 21 UNP Q20MD5 ACETYLATION SEQADV 6BKL NH2 E 47 UNP Q20MD5 AMIDATION SEQADV 6BKL ACE F 21 UNP Q20MD5 ACETYLATION SEQADV 6BKL NH2 F 47 UNP Q20MD5 AMIDATION SEQADV 6BKL ACE G 21 UNP Q20MD5 ACETYLATION SEQADV 6BKL NH2 G 47 UNP Q20MD5 AMIDATION SEQADV 6BKL ACE H 21 UNP Q20MD5 ACETYLATION SEQADV 6BKL NH2 H 47 UNP Q20MD5 AMIDATION SEQRES 1 A 27 ACE SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE SEQRES 2 A 27 GLY ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 3 A 27 NH2 SEQRES 1 B 27 ACE SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE SEQRES 2 B 27 GLY ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 3 B 27 NH2 SEQRES 1 C 27 ACE SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE SEQRES 2 C 27 GLY ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 3 C 27 NH2 SEQRES 1 D 27 ACE SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE SEQRES 2 D 27 GLY ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 3 D 27 NH2 SEQRES 1 E 27 ACE SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE SEQRES 2 E 27 GLY ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 3 E 27 NH2 SEQRES 1 F 27 ACE SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE SEQRES 2 F 27 GLY ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 3 F 27 NH2 SEQRES 1 G 27 ACE SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE SEQRES 2 G 27 GLY ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 3 G 27 NH2 SEQRES 1 H 27 ACE SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE SEQRES 2 H 27 GLY ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 3 H 27 NH2 HET EU7 C 101 13 HET RIM D 101 13 HET RIM F 101 13 HET EU7 G 101 13 HETNAM EU7 (1S)-1-[(3R,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DECAN-1- HETNAM 2 EU7 YL]ETHAN-1-AMINE HETNAM RIM RIMANTADINE HETSYN EU7 S-RIMANTADINE HETSYN RIM 1-(1-ADAMANTYL)ETHANAMINE FORMUL 9 EU7 2(C12 H21 N) FORMUL 10 RIM 2(C12 H21 N) FORMUL 13 HOH *32(H2 O) HELIX 1 AA1 ASP A 24 LEU A 46 1 23 HELIX 2 AA2 PRO B 25 LEU B 46 1 22 HELIX 3 AA3 PRO C 25 LEU C 46 1 22 HELIX 4 AA4 PRO D 25 LEU D 46 1 22 HELIX 5 AA5 ASP E 24 LEU E 46 1 23 HELIX 6 AA6 PRO F 25 LEU F 46 1 22 HELIX 7 AA7 PRO G 25 LEU G 46 1 22 HELIX 8 AA8 PRO H 25 LEU H 46 1 22 SITE 1 AC1 9 SER A 31 SER B 31 ALA C 30 SER C 31 SITE 2 AC1 9 HOH C 201 HOH C 204 SER D 31 RIM D 101 SITE 3 AC1 9 HOH D 203 SITE 1 AC2 9 SER A 31 SER B 31 SER C 31 EU7 C 101 SITE 2 AC2 9 HOH C 201 HOH C 204 ALA D 30 SER D 31 SITE 3 AC2 9 HOH D 203 SITE 1 AC3 10 ALA E 30 SER E 31 SER F 31 HOH F 201 SITE 2 AC3 10 SER G 31 EU7 G 101 HOH G 201 HOH G 203 SITE 3 AC3 10 ALA H 30 SER H 31 SITE 1 AC4 10 SER E 31 SER F 31 RIM F 101 HOH F 201 SITE 2 AC4 10 ALA G 30 SER G 31 GLY G 34 HOH G 201 SITE 3 AC4 10 HOH G 203 SER H 31 CRYST1 36.460 47.840 48.530 90.00 96.76 90.00 P 1 21 1 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.027427 0.000000 0.003251 0.00000 SCALE2 0.000000 0.020903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020750 0.00000