HEADER VIRAL PROTEIN 06-JUN-14 4QKL TITLE INFLUENZA A M2 WILD TYPE TM DOMAIN AT HIGH PH IN THE LIPIDIC CUBIC TITLE 2 PHASE UNDER ROOM TEMPERATURE DIFFRACTION CONDITIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: INFLUENZA M2 MONOMER, TM DOMAIN (22-46); 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 3 20-SEP-23 4QKL 1 REMARK SEQADV LINK REVDAT 2 16-DEC-15 4QKL 1 JRNL REVDAT 1 11-NOV-15 4QKL 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. 1.71 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 3115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.370 REMARK 3 FREE R VALUE TEST SET COUNT : 323 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 20.9319 - 2.1547 0.95 1368 162 0.1627 0.1947 REMARK 3 2 2.1547 - 1.7105 0.99 1424 161 0.1745 0.2065 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.65 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 : 0.005 267 REMARK 3 ANGLE : 0.606 363 REMARK 3 CHIRALITY : 0.033 52 REMARK 3 PLANARITY : 0.004 42 REMARK 3 DIHEDRAL : 10.953 94 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 4QKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000086172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : 8.0 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 : 3128 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 27.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.15800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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 (%): 54.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M CALCIUM CHLORIDE, 0.9 M TRIS HCL REMARK 280 PH 8.0, 39.6% V/V PEG 400, 3% W/V XYLITOL 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 14.80000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 14.80000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.07000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 14.80000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 14.80000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.07000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 14.80000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 14.80000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 34.07000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 14.80000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 14.80000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 34.07000 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: 6360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -221.0 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 29.60000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 88.80000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 59.20000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 29.60000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 -29.60000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 59.20000 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 CL CL A 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 219 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 222 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 224 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 225 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 226 LIES ON A SPECIAL POSITION. 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 O HOH A 204 O HOH A 208 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 22 O REMARK 620 2 HOH A 201 O 80.8 REMARK 620 N 1 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 204 O 75.0 REMARK 620 3 HOH A 205 O 98.5 80.3 REMARK 620 4 HOH A 208 O 122.3 54.4 98.3 REMARK 620 5 HOH A 210 O 73.4 120.2 153.2 107.7 REMARK 620 6 HOH A 215 O 72.1 134.4 74.4 165.2 78.8 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 CL A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QK6 RELATED DB: PDB REMARK 900 RELATED ID: 4QK7 RELATED DB: PDB REMARK 900 RELATED ID: 4QKC RELATED DB: PDB REMARK 900 RELATED ID: 4QKM RELATED DB: PDB DBREF 4QKL A 22 46 UNP W8PGZ1 W8PGZ1_9INFA 22 46 SEQADV 4QKL ACE A 21 UNP W8PGZ1 ACETYLATION SEQADV 4QKL 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 CL A 101 1 HET CA A 102 1 HET CA A 103 1 HET EDO A 104 10 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM CL CHLORIDE ION HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N FORMUL 2 CL CL 1- FORMUL 3 CA 2(CA 2+) FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *26(H2 O) HELIX 1 1 ASP A 24 LEU A 46 1 23 LINK C ACE A 21 N SER A 22 1555 1555 1.33 LINK C LEU A 46 N NH2 A 47 1555 1555 1.33 LINK O SER A 22 CA CA A 102 1555 1555 2.37 LINK OD2 ASP A 24 CA CA A 103 1555 1555 2.35 LINK CA CA A 102 O HOH A 201 1555 1555 2.38 LINK CA CA A 103 O HOH A 204 1555 1555 2.42 LINK CA CA A 103 O HOH A 205 1555 1555 2.38 LINK CA CA A 103 O HOH A 208 1555 1555 2.36 LINK CA CA A 103 O HOH A 210 1555 1555 2.40 LINK CA CA A 103 O HOH A 215 1555 1555 2.42 SITE 1 AC1 1 SER A 23 SITE 1 AC2 2 SER A 22 HOH A 201 SITE 1 AC3 7 ASP A 24 HOH A 204 HOH A 205 HOH A 207 SITE 2 AC3 7 HOH A 208 HOH A 210 HOH A 215 SITE 1 AC4 2 HIS A 37 TRP A 41 CRYST1 29.600 29.600 68.140 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 0.033784 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033784 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014676 0.00000 HETATM 1 C ACE A 21 13.904 38.919 18.701 1.00 17.24 C HETATM 2 O ACE A 21 13.186 38.005 18.298 1.00 15.04 O HETATM 3 CH3 ACE A 21 15.234 38.666 19.351 1.00 18.39 C HETATM 4 H1 ACE A 21 16.016 39.176 18.789 1.00 22.07 H HETATM 5 H2 ACE A 21 15.216 39.044 20.373 1.00 22.07 H HETATM 6 H3 ACE A 21 15.435 37.595 19.363 1.00 22.07 H