HEADER VIRAL PROTEIN 06-JUN-14 4QKM TITLE INFLUENZA A M2 WILD TYPE TM DOMAIN AT LOW PH IN THE LIPIDIC CUBIC TITLE 2 PHASE UNDER ROOM TEMPERATURE DIFFRACTION CONDITIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: INFLUENZA M2 MONOMER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS; SOURCE 4 ORGANISM_TAXID: 385599; SOURCE 5 OTHER_DETAILS: THIS SEQUENCE IS FOUND IN THE INFLUENZA A VIRUS SOURCE 6 (STRAIN A/UDORN/307/1972 H3N2) AND WAS MANUALLY SYNTHESIZED USING SOURCE 7 FMOC CHEMISTRY. N- AND C-TERMINAL MODIFICATIONS ARE PRESENT. KEYWDS TRANSMEMBRANE ALPHA HELIX, PH-ACTIVATED PROTON CHANNEL, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.L.THOMASTON,W.F.DEGRADO REVDAT 4 06-NOV-24 4QKM 1 REMARK REVDAT 3 20-SEP-23 4QKM 1 REMARK SEQADV LINK REVDAT 2 16-DEC-15 4QKM 1 JRNL REVDAT 1 11-NOV-15 4QKM 0 JRNL AUTH J.L.THOMASTON,M.ALFONSO-PRIETO,R.A.WOLDEYES,J.S.FRASER, JRNL AUTH 2 M.L.KLEIN,G.FIORIN,W.F.DEGRADO JRNL TITL HIGH-RESOLUTION STRUCTURES OF THE M2 CHANNEL FROM INFLUENZA JRNL TITL 2 A VIRUS REVEAL DYNAMIC PATHWAYS FOR PROTON STABILIZATION AND JRNL TITL 3 TRANSDUCTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 14260 2015 JRNL REFN ISSN 0027-8424 JRNL PMID 26578770 JRNL DOI 10.1073/PNAS.1518493112 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 5247 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 520 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 18.0019 - 2.2851 0.92 1157 128 0.1421 0.1846 REMARK 3 2 2.2851 - 1.8143 0.97 1175 132 0.1312 0.1429 REMARK 3 3 1.8143 - 1.5851 0.99 1196 129 0.1640 0.1881 REMARK 3 4 1.5851 - 1.4402 0.98 1199 131 0.2043 0.2823 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.85 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 : 0.019 320 REMARK 3 ANGLE : 0.948 433 REMARK 3 CHIRALITY : 0.055 55 REMARK 3 PLANARITY : 0.008 48 REMARK 3 DIHEDRAL : 13.051 126 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 4QKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000086173. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : 5.5 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) : 1.115869 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5254 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 27.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.53100 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: CHAIN A OF 3C9J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M CALCIUM CHLORIDE, 0.9 M MES PH REMARK 280 5.5, 39.6% V/V PEG 400, 0.01M MNCL2, 4H2O ADDITIVE, LCP SANDWICH REMARK 280 PLATES, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 15.04500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 15.04500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.69500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 15.04500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 15.04500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.69500 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 15.04500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 15.04500 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 33.69500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 15.04500 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 15.04500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 33.69500 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 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: 6880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 30.09000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 90.27000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 60.18000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 30.09000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 -30.09000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 60.18000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CA CA A 101 LIES ON A SPECIAL POSITION. REMARK 375 CL CL A 102 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 208 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 211 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 213 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 216 LIES ON A SPECIAL POSITION. REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 22 O REMARK 620 2 SER A 22 O 1.2 REMARK 620 3 HOH A 201 O 77.1 77.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 24 OD2 REMARK 620 2 HOH A 202 O 65.2 REMARK 620 3 HOH A 206 O 80.5 54.4 REMARK 620 4 HOH A 207 O 83.5 85.6 140.0 REMARK 620 5 HOH A 214 O 134.3 80.5 54.5 124.5 REMARK 620 6 HOH A 215 O 91.2 41.5 88.6 55.2 80.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLB A 105 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QK7 RELATED DB: PDB REMARK 900 RELATED ID: 4QKC RELATED DB: PDB REMARK 900 RELATED ID: 4QKL RELATED DB: PDB REMARK 900 RELATED ID: 4QK6 RELATED DB: PDB DBREF 4QKM A 22 46 UNP W8PGZ1 W8PGZ1_9INFA 22 46 SEQADV 4QKM ACE A 21 UNP W8PGZ1 ACETYLATION SEQADV 4QKM NH2 A 47 UNP W8PGZ1 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 HET ACE A 21 6 HET NH2 A 47 3 HET CA A 101 1 HET CL A 102 1 HET CA A 103 1 HET EDO A 104 10 HET OLB A 105 65 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM OLB (2S)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N FORMUL 2 CA 2(CA 2+) FORMUL 3 CL CL 1- FORMUL 5 EDO C2 H6 O2 FORMUL 6 OLB C21 H40 O4 FORMUL 7 HOH *18(H2 O) HELIX 1 1 ASP A 24 LEU A 46 1 23 LINK C ACE A 21 N ASER A 22 1555 1555 1.33 LINK C ACE A 21 N BSER A 22 1555 1555 1.33 LINK C LEU A 46 N NH2 A 47 1555 1555 1.32 LINK O ASER A 22 CA CA A 101 1555 1555 2.47 LINK O BSER A 22 CA CA A 101 1555 1555 2.49 LINK OD2 ASP A 24 CA CA A 103 1555 1555 2.32 LINK CA CA A 101 O HOH A 201 1555 1555 2.50 LINK CA CA A 103 O HOH A 202 1555 1555 2.62 LINK CA CA A 103 O HOH A 206 1555 1555 2.41 LINK CA CA A 103 O HOH A 207 1555 1555 2.40 LINK CA CA A 103 O HOH A 214 1555 1555 2.28 LINK CA CA A 103 O HOH A 215 1555 1555 2.34 SITE 1 AC1 2 SER A 22 HOH A 201 SITE 1 AC2 1 SER A 23 SITE 1 AC3 7 ASP A 24 OLB A 105 HOH A 202 HOH A 206 SITE 2 AC3 7 HOH A 207 HOH A 214 HOH A 215 SITE 1 AC4 3 HIS A 37 TRP A 41 HOH A 212 SITE 1 AC5 11 ASP A 24 PRO A 25 LEU A 26 ILE A 33 SITE 2 AC5 11 LEU A 38 LEU A 40 NH2 A 47 CA A 103 SITE 3 AC5 11 HOH A 206 HOH A 207 HOH A 214 CRYST1 30.090 30.090 67.390 90.00 90.00 90.00 I 4 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 0.033234 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014839 0.00000 HETATM 1 C ACE A 21 14.143 39.671 17.748 1.00 14.85 C ANISOU 1 C ACE A 21 2291 2432 918 -119 -33 416 C HETATM 2 O ACE A 21 13.345 38.780 17.449 1.00 15.47 O ANISOU 2 O ACE A 21 2513 2424 940 -121 -25 329 O HETATM 3 CH3 ACE A 21 15.479 39.357 18.331 1.00 15.10 C ANISOU 3 CH3 ACE A 21 2357 2445 935 -18 -60 523 C HETATM 4 H1 ACE A 21 15.915 40.264 18.750 1.00 18.12 H HETATM 5 H2 ACE A 21 15.366 38.611 19.118 1.00 18.12 H HETATM 6 H3 ACE A 21 16.133 38.966 17.551 1.00 18.12 H